This document summarizes rice mutants and genes related to organ development, morphogenesis, and physiological traits. Over 1,698 rice genes have been identified based on mutant phenotypes and are classified into categories such as vegetative organs, reproductive organs, seed traits, and physiological traits. Many genes have been cloned that are involved in the development of organs like leaves, culms, and roots. Mutants in gibberellin and brassinosteroid biosynthesis and signaling pathways affect traits like plant height. The collection of rice mutants and identification of underlying genes provides insights into gene functions and rice development.
This document provides information on mutation breeding including definitions, types of mutations, mutagens, procedures for mutation breeding, applications, advantages, and limitations. It defines mutation as a sudden heritable change in a characteristic of an organism. It describes spontaneous and induced mutations and lists common mutagens like radiation and chemicals. The key steps in mutation breeding procedures are selection of crop variety, treatment with mutagen, handling of subsequent generations, and selection of desirable mutants. Applications include improving disease resistance and quantitative traits. However, limitations include the low frequency of beneficial mutations and difficulties associated with undesirable side effects and pleiotropic effects.
This document describes the development of 160 novel simple sequence repeat (SSR) markers in bitter gourd (Momordica charantia L.) through enriched genomic libraries. Genomic DNA from bitter gourd was used to construct libraries enriched for 10 different repeat motifs. Of the 3,072 clones screened, 93.7% contained microsatellite repeats. Unique primer pairs were designed and validated for 151 loci. Genetic diversity analysis of 51 loci among 54 accessions found 20% were polymorphic. The markers distinguished 15 Indian varieties and 78.4% were transferable across six Momordica species. The new SSR markers will be useful for genetic studies in bitter gourd.
Molecular marker to identify gynoecious lines in bitter gourdSwati Saxena
This document discusses the identification of molecular markers associated with the gynoecious trait in bitter gourd. Twenty-four gynoecious plants were screened using 200 RAPD and 28 ISSR markers. One ISSR primer amplified a 1000 base pair fragment present in all gynoecious plants but absent in two monoecious varieties. This fragment was repeatably amplified and could serve as a diagnostic marker for gynoecy, allowing identification of the trait at an early stage for hybrid seed production.
Genetic diversity in pea germplasm using RAPD MarkersShujaul Mulk Khan
Selection of the genotypes using plasmid assisted technology provides an efficient and useful tool for elaborating genetic relationships among genotypes. In present study, 48 Pea (Pisum sativum var sativum L.) genotypes obtained from different sources were analyzed through 20 RAPD, DNA markers for assessment of intraspecific DNA variations. Results revealed that significant variations were present in minor bands. Major bands also showed significant diversity. Considerable variations were also recorded in density of some common bands. Maximum and minimum genetic diversity i.e., 80% and 20% was found among 08 and 23 comparisons, respectively from banding profile. These variations can be
used further for enhancing variability, a prerequisite for crop breeding. Phylogenetic clustering (through dendrogram analysis) of genotypes revealed that genetic diversity is independent of origin of genotypes. Forty eight genotypes of pea clustered in three main groups A, B and C comprising 23, 5 and 20 genotypes, respectively. Group A1 and C1 included the most distantly related genotypes and hence can be recommended for breeding to obtain genetically diverse segregating populations.
16. varietal characterization of tomato cultivars based on rapd markersVishwanath Koti
This study characterized 24 tomato cultivars using RAPD markers. Eleven primers produced 100 bands, of which 89.39% were polymorphic. Each cultivar had unique DNA sequences not found in others. The primers OPC-02, OPC-19, OPD-19, OPD-18 and OPC-08 generated the most unique bands, producing 13 unique bands among 10 cultivars. The combination of OPB-10 with either OPC-19 or OPB-08 was sufficient to identify all 24 tomato cultivars.
This document analyzed the genetic diversity of 50 Asian bitter gourd genotypes using morphological traits and molecular markers. Key findings:
1. Significant variation was found for yield and other traits based on morphological analysis, indicating genetic diversity. The highest yielding genotype was Sel-2.
2. Molecular analysis using RAPD and ISSR markers found high levels of polymorphism, with ISSR showing more polymorphic bands.
3. Cluster analyses based on morphological, RAPD, ISSR, and combined data grouped genotypes into clusters largely correlating with geographical origin and domestication status. The analyses demonstrate large genetic variability in the collection.
This document describes a DNA marker-based technology developed to identify citrus rootstocks at the seedling stage. Traditionally, Rough lemon and Rangpur lime are preferred rootstocks but are difficult to distinguish from Galgal at an early stage. Galgal is an undesirable rootstock due to susceptibility to diseases. The new technology uses microsatellite markers and PCR to differentiate Rough lemon, Rangpur lime, and Galgal based on presence or absence of DNA fragments. It provides a non-destructive method to ensure nurseries are supplying quality rootstock varieties. The technique has been transferred to agricultural organizations to benefit citrus farmers.
Mutation breeding and its application in our life.it contains the information about mutation,mution types,mutation breeding,mutation breeding process,its mutagen and the view of mutation breeding in BANGLADESH ......
it also have amazing examples of mutation breeding.....
This document provides information on mutation breeding including definitions, types of mutations, mutagens, procedures for mutation breeding, applications, advantages, and limitations. It defines mutation as a sudden heritable change in a characteristic of an organism. It describes spontaneous and induced mutations and lists common mutagens like radiation and chemicals. The key steps in mutation breeding procedures are selection of crop variety, treatment with mutagen, handling of subsequent generations, and selection of desirable mutants. Applications include improving disease resistance and quantitative traits. However, limitations include the low frequency of beneficial mutations and difficulties associated with undesirable side effects and pleiotropic effects.
This document describes the development of 160 novel simple sequence repeat (SSR) markers in bitter gourd (Momordica charantia L.) through enriched genomic libraries. Genomic DNA from bitter gourd was used to construct libraries enriched for 10 different repeat motifs. Of the 3,072 clones screened, 93.7% contained microsatellite repeats. Unique primer pairs were designed and validated for 151 loci. Genetic diversity analysis of 51 loci among 54 accessions found 20% were polymorphic. The markers distinguished 15 Indian varieties and 78.4% were transferable across six Momordica species. The new SSR markers will be useful for genetic studies in bitter gourd.
Molecular marker to identify gynoecious lines in bitter gourdSwati Saxena
This document discusses the identification of molecular markers associated with the gynoecious trait in bitter gourd. Twenty-four gynoecious plants were screened using 200 RAPD and 28 ISSR markers. One ISSR primer amplified a 1000 base pair fragment present in all gynoecious plants but absent in two monoecious varieties. This fragment was repeatably amplified and could serve as a diagnostic marker for gynoecy, allowing identification of the trait at an early stage for hybrid seed production.
Genetic diversity in pea germplasm using RAPD MarkersShujaul Mulk Khan
Selection of the genotypes using plasmid assisted technology provides an efficient and useful tool for elaborating genetic relationships among genotypes. In present study, 48 Pea (Pisum sativum var sativum L.) genotypes obtained from different sources were analyzed through 20 RAPD, DNA markers for assessment of intraspecific DNA variations. Results revealed that significant variations were present in minor bands. Major bands also showed significant diversity. Considerable variations were also recorded in density of some common bands. Maximum and minimum genetic diversity i.e., 80% and 20% was found among 08 and 23 comparisons, respectively from banding profile. These variations can be
used further for enhancing variability, a prerequisite for crop breeding. Phylogenetic clustering (through dendrogram analysis) of genotypes revealed that genetic diversity is independent of origin of genotypes. Forty eight genotypes of pea clustered in three main groups A, B and C comprising 23, 5 and 20 genotypes, respectively. Group A1 and C1 included the most distantly related genotypes and hence can be recommended for breeding to obtain genetically diverse segregating populations.
16. varietal characterization of tomato cultivars based on rapd markersVishwanath Koti
This study characterized 24 tomato cultivars using RAPD markers. Eleven primers produced 100 bands, of which 89.39% were polymorphic. Each cultivar had unique DNA sequences not found in others. The primers OPC-02, OPC-19, OPD-19, OPD-18 and OPC-08 generated the most unique bands, producing 13 unique bands among 10 cultivars. The combination of OPB-10 with either OPC-19 or OPB-08 was sufficient to identify all 24 tomato cultivars.
This document analyzed the genetic diversity of 50 Asian bitter gourd genotypes using morphological traits and molecular markers. Key findings:
1. Significant variation was found for yield and other traits based on morphological analysis, indicating genetic diversity. The highest yielding genotype was Sel-2.
2. Molecular analysis using RAPD and ISSR markers found high levels of polymorphism, with ISSR showing more polymorphic bands.
3. Cluster analyses based on morphological, RAPD, ISSR, and combined data grouped genotypes into clusters largely correlating with geographical origin and domestication status. The analyses demonstrate large genetic variability in the collection.
This document describes a DNA marker-based technology developed to identify citrus rootstocks at the seedling stage. Traditionally, Rough lemon and Rangpur lime are preferred rootstocks but are difficult to distinguish from Galgal at an early stage. Galgal is an undesirable rootstock due to susceptibility to diseases. The new technology uses microsatellite markers and PCR to differentiate Rough lemon, Rangpur lime, and Galgal based on presence or absence of DNA fragments. It provides a non-destructive method to ensure nurseries are supplying quality rootstock varieties. The technique has been transferred to agricultural organizations to benefit citrus farmers.
Mutation breeding and its application in our life.it contains the information about mutation,mution types,mutation breeding,mutation breeding process,its mutagen and the view of mutation breeding in BANGLADESH ......
it also have amazing examples of mutation breeding.....
Reverse Breeding: a tool to create homozygous plants from the heterozygous po...Sanjay Kumar
This document provides an overview of reverse breeding, a novel plant breeding technique to directly produce homozygous parental lines from any heterozygous plant. It discusses how reverse breeding uses RNA interference to suppress meiotic recombination and produce doubled haploids from gametes, generating homozygous parental lines. The document summarizes a case study applying this to Arabidopsis thaliana and discusses applications like reconstructing hybrids, breeding at the chromosome level, and implications for food safety. Limitations and future research directions are also outlined.
21. Mutation Breeding in crop improvement Naveen Kumar
Mutation breeding in crop improvement can utilize both spontaneous and induced mutations. Induced mutations are caused by physical mutagens like radiation (x-rays, gamma rays, UV light) or chemical mutagens. Mutation rates can vary between genes and induced mutations occur more frequently than spontaneous mutations. Mutation breeding is useful for crop improvement by generating genetic variation for selection of desirable traits.
Marker free transgenics: concept and approachesShilpa Malaghan
This document discusses approaches for producing marker-free transgenic plants. It describes three main strategies: 1) Co-transformation of the gene of interest and selectable marker genes, followed by segregation of the genes in subsequent generations. 2) Using site-specific recombination systems like Cre/lox and FLP/FRT to excise the selectable marker gene. 3) Using transposon-based systems to remove the marker gene. It provides examples of each method and discusses their advantages and disadvantages. The goal is to eliminate the use of selectable marker genes to address issues like food safety, gene stacking, and horizontal gene transfer.
To handle complex Traits like Yield, different stress we must do modification in DNA molecular breeding techniques help us to do such changes in DNA to archive the Goals.
The document discusses mutation breeding, including defining key terms like mutation, breeding, mutagens, mutagenesis, and mutants. It explains the process of mutation breeding using chemical mutagens like EMS and DMS or radiation to generate mutants. Examples are given of radiation breeding in atomic gardens and the discovery of this technique in the 1920s. Successful mutation examples are listed for oranges in California and rice in China. The overall goal is for students to understand mutation breeding techniques and important contributors to the field.
22. utilization of ssr markers for seed purity testing in popular rice hybridsVishwanath Koti
This document describes a study that used simple sequence repeat (SSR) markers to identify two popular rice hybrids (KRH-2 and DRRH-2) and their parental lines. Thirty-five SSR markers were tested, and six were found to be polymorphic across the hybrids and parents, allowing unique fingerprints for each. Five markers (RM 206, RM 276, RM 204, RM 234 and RM 228) differentiated the two hybrids. Analysis of parental lines found residual heterozygosity at two loci, highlighting the importance of SSR markers for maintaining genetic purity. A 20x20 grow-out matrix trial validated the SSR markers for detecting contaminants in commercial seed lots of the two hybrids.
Mutagenesis techniques like EMS and radiation are used to generate mutations in plant genomes for genomics research. TILLING is a reverse genetics technique that combines chemical mutagenesis with PCR and enzymatic digestion to detect point mutations in genes of interest. It allows researchers to discover mutations without transgenic techniques. The TILLING process involves mutagenizing a plant population, growing the plants, extracting DNA, pooling DNA samples, amplifying and enzymatically digesting genes of interest, and using fragment analysis to identify point mutations. TILLING has been applied to study many plant species and genes to further understand plant genetics.
Dioscorea rotundata is a staple food crop for millions of people in the tropical and subtropical regions. In vitro germplasm conservation is a very useful tool in yam improvement strategies but very little is known about the genetic integrity and stability of in-vitro conserved yam plants. In this study, 42 accessions from in vitro and field populations were genotyped using 11 microsatellite markers and 23 morphological descriptors to assess variability within and between accessions. Out of the 23 morphological variables used, 13 were identified as most discriminate and were used to cluster the accessions into 4 clusters using the unweighted pair group arithmetic mean average (UPGMA). Accession maintained in field as well as in in-vitro showed high genetic similarity (R2 = 0.91, p-value: 1e-04). Out of the 42 accessions analyzed, nine accessions maintained in the field and in-vitro displayed different genetic profiles. This study provided basic information on the possible somaclonal variation of yam accessions maintained through in-vitro. Further study with advanced tools such as next-generation sequencing is required to elucidate the nature of the observed variation within clones.
This document discusses the application of genomics in improving crop plants. It explains that genomics tools like tissue culture, genetic engineering, molecular diagnostics and molecular markers have revolutionized crop breeding programs. Specifically, it describes how tissue culture allows for rapid propagation of disease-free plants at scale. It also outlines how genetic engineering has been used to develop transgenic crops with improved traits like herbicide tolerance, pathogen resistance, stress tolerance, fruit quality and pest resistance. Molecular diagnostics using probes and monoclonal antibodies enable early disease detection. Molecular markers aid in selecting desirable traits at early stages.
Association of Diaporthe longicolla with Black Zone Lines on Mature Soybean P...Ahmed Shawky
1) Zone lines were observed on the lower stems of mature soybean plants in multiple Midwestern states. Diaporthe longicolla was consistently isolated from these zone lines.
2) Molecular analysis confirmed the identity of 10 representative isolates as D. longicolla. Phylogenetic analysis placed these isolates in a well-supported clade with known D. longicolla cultures.
3) Greenhouse pathogenicity tests reisolated D. longicolla from zone lines on inoculated soybean plants, fulfilling Koch's postulates and demonstrating that D. longicolla is associated with and causes the black zone lines observed on mature soybean stems.
Inter Simple Sequence Repeats (ISSR) markers were utilized to identify the levels of heritable varieties and patterns of the populace structure among the five populaces of Pteris biaurita, a natural fern in India. A comprehensive examination was directed in three replicates at 2013-14 seasons in the Western Ghats, South India. Five wild P. biaurita, accessions (maiden hair) were assessed for genotyping studies. Results demonstrated a pivotal discrepancy among genotypes for they were characterized in view of this uniqueness in four groups by the genetic cluster examination. In this trial, ISSR primers amplified 63 polymorphic groups. In view of the genetic identity data, genotypes were figured and differed from 0.5714 to 0.6984. The percentage of polymorphism indicated predominant genotype that may be utilized for the conservation of species. ISSR appeared to be an obliging marker for prediction of genotype inside a closed group of inter specific populace in the investigation territory
This document discusses organellar heterosis and complementation. It defines organellar genomes as the genomes present in chloroplasts and mitochondria. It describes some key features of organellar DNA, including that it replicates semi-conservatively and is inherited separately from nuclear genes. The document discusses how organellar heterosis can originate from mitochondrial and chloroplast genes and DNA, leading to enhanced structures and functions in hybrids. It provides several examples of organellar heterosis being observed in plants like maize and wheat. The role of intergenomic interaction and complementation between nuclear and organellar genes in generating heterosis is also covered. Finally, the document discusses how transgenic techniques can be used to engineer male sterility for use in hybrid seed
Marker free transgenic crops can be generated using several strategies to avoid issues with marker genes. Selectable marker genes allow selection of transformed cells but their products may be undesirable in food. Strategies include co-transformation using two plasmids without linking marker and trait genes, replacing selectable markers with screenable markers, and excising the selectable marker from the genome after selection using site-specific recombination, transposition, or homologous recombination. Case studies demonstrate applying these strategies successfully in tobacco and mustard to generate marker free transgenic plants.
Paternal radiation exposure led to increased expression of miR-29a and miR-29b in the male germline. This upregulation of miR-29 caused decreased expression of the de novo methyltransferase DNMT3a and profound hypomethylation of LINE1 and SINE B2 transposable elements in the germline. Hypomethylation of these transposable elements was also found in the thymus tissue of offspring conceived from exposed fathers and was associated with decreased expression of the LSH chromatin remodeling protein. Furthermore, miR-468 expression was significantly upregulated in the offspring thymus and directly targeted LSH, contributing to its decreased expression and hypomethylation of transposable
Marker Assisted Gene Pyramiding for Disease Resistance in RiceIndrapratap1
Why marker assisted gene pyramiding?
For traits that are simply inherited, but that are difficult or expensive to measure phenotypically, and/or that do not have a consistent phenotypic expression under specific selection conditions, marker-based selection is more effective than phenotypic selection.
Traits which are traditionally regarded as quantitative and not targeted by gene pyramiding program can be improved using gene pyramiding if major genes affecting the traits are identified.
Genes with very similar phenotypic effects, which are impossible or difficult to combine in single genotype using phenotypic selection, can be pyramided through marker assisted selection.
Markers provides a more effective option to control linkage drag and make the use of genes contained in unadapted resources easier.
Pyramiding is possible through conventional breeding but is extremely difficult or impossible at early generations..
DNA markers may facilitate selection because DNA marker assays are non destructive and markers for multiple specific genes/QTLs can be tested using a single DNA sample without phenotyping.
CONCLUSION:
• Molecular marker offer great scope for improving the efficiency of conventional plant breeding.
• Gene pyramiding may not be the most suitable strategy when many QTL with small effects control the trait and other methods such as marker-assisted recurrent selection should be considered.
• With MAS based gene pyramiding, it is now possible for breeder to conduct many rounds of selections in a year.
• Gene pyramiding with marker technology can integrate into existing plant breeding program all over the world to allow researchers to access, transfer and combine genes at a rate and with precision not previously possible.
• This will help breeders get around problems related to larger breeding populations, replications in diverse environments, and speed up the development of advance lines.
For further queries please contact at isag2010@gmail.com
This document describes a method for rapidly detecting whether plant mutants are homozygous or heterozygous using CEL-I endonuclease. CEL-I endonuclease is a mismatch-specific endonuclease that can cleave DNA at sites of mismatches between DNA strands. The method involves isolating genomic DNA from mutant plants, amplifying a region by PCR, and treating the PCR products with CEL-I endonuclease. Digestion products are then analyzed by gel electrophoresis. For homozygous mutants, no cleavage will occur as there are no mismatches. For heterozygous mutants, cleavage will occur at mismatch sites, producing distinctive banding patterns that allow identification of heterozygotes. This method provides a low
Ossiannilsson mmvc15 the battle for innovation towards opening up educationEbba Ossiannilsson
The document discusses the "battle for innovation towards opening up education." It notes that there are conflicting visions between open education and traditional education, significant advantages to be gained, and a battle over the prevailing narrative. Stakeholders in this battle include educators, students, technology companies, and policymakers. The document argues that strategic decisions need to be made at the macro-level regarding open education given changes in globalization, demographics, and technology. It also asserts that expansion, personalization, networking and automation can enhance education.
Quality is one of the key factors for open educational resources (OER) to gain mainstream acceptance and become part of an open educational practice (OEP) within higher education. Students and teachers need to be able to see the resource’s trustworthiness, target groups, areas of use, context, accessibility etc. What quality criteria can be placed on OER and how do we establish credibility?
In this webinar you will meet the following experts in this area:
Professor Gráinne Conole (University of Leicester, UK) is a well-known expert in the field of open education and is involved in many international initiatives and organisations. She will describe current work with OER quality issues. She will also give examples of a number of relevant projects.
Dr. Ebba Ossiannilsson (University of Lund, Sweden) has recently published a doctoral thesis on quality and benchmarking of e-learning in higher education (http://jultika.oulu.fi/Record/isbn978-952-62-0041-5). She will focus on how benchmarking can be used as a method for quality assurance in an open educational culture. She will also briefly present the main international quality methods in this field.
Reverse Breeding: a tool to create homozygous plants from the heterozygous po...Sanjay Kumar
This document provides an overview of reverse breeding, a novel plant breeding technique to directly produce homozygous parental lines from any heterozygous plant. It discusses how reverse breeding uses RNA interference to suppress meiotic recombination and produce doubled haploids from gametes, generating homozygous parental lines. The document summarizes a case study applying this to Arabidopsis thaliana and discusses applications like reconstructing hybrids, breeding at the chromosome level, and implications for food safety. Limitations and future research directions are also outlined.
21. Mutation Breeding in crop improvement Naveen Kumar
Mutation breeding in crop improvement can utilize both spontaneous and induced mutations. Induced mutations are caused by physical mutagens like radiation (x-rays, gamma rays, UV light) or chemical mutagens. Mutation rates can vary between genes and induced mutations occur more frequently than spontaneous mutations. Mutation breeding is useful for crop improvement by generating genetic variation for selection of desirable traits.
Marker free transgenics: concept and approachesShilpa Malaghan
This document discusses approaches for producing marker-free transgenic plants. It describes three main strategies: 1) Co-transformation of the gene of interest and selectable marker genes, followed by segregation of the genes in subsequent generations. 2) Using site-specific recombination systems like Cre/lox and FLP/FRT to excise the selectable marker gene. 3) Using transposon-based systems to remove the marker gene. It provides examples of each method and discusses their advantages and disadvantages. The goal is to eliminate the use of selectable marker genes to address issues like food safety, gene stacking, and horizontal gene transfer.
To handle complex Traits like Yield, different stress we must do modification in DNA molecular breeding techniques help us to do such changes in DNA to archive the Goals.
The document discusses mutation breeding, including defining key terms like mutation, breeding, mutagens, mutagenesis, and mutants. It explains the process of mutation breeding using chemical mutagens like EMS and DMS or radiation to generate mutants. Examples are given of radiation breeding in atomic gardens and the discovery of this technique in the 1920s. Successful mutation examples are listed for oranges in California and rice in China. The overall goal is for students to understand mutation breeding techniques and important contributors to the field.
22. utilization of ssr markers for seed purity testing in popular rice hybridsVishwanath Koti
This document describes a study that used simple sequence repeat (SSR) markers to identify two popular rice hybrids (KRH-2 and DRRH-2) and their parental lines. Thirty-five SSR markers were tested, and six were found to be polymorphic across the hybrids and parents, allowing unique fingerprints for each. Five markers (RM 206, RM 276, RM 204, RM 234 and RM 228) differentiated the two hybrids. Analysis of parental lines found residual heterozygosity at two loci, highlighting the importance of SSR markers for maintaining genetic purity. A 20x20 grow-out matrix trial validated the SSR markers for detecting contaminants in commercial seed lots of the two hybrids.
Mutagenesis techniques like EMS and radiation are used to generate mutations in plant genomes for genomics research. TILLING is a reverse genetics technique that combines chemical mutagenesis with PCR and enzymatic digestion to detect point mutations in genes of interest. It allows researchers to discover mutations without transgenic techniques. The TILLING process involves mutagenizing a plant population, growing the plants, extracting DNA, pooling DNA samples, amplifying and enzymatically digesting genes of interest, and using fragment analysis to identify point mutations. TILLING has been applied to study many plant species and genes to further understand plant genetics.
Dioscorea rotundata is a staple food crop for millions of people in the tropical and subtropical regions. In vitro germplasm conservation is a very useful tool in yam improvement strategies but very little is known about the genetic integrity and stability of in-vitro conserved yam plants. In this study, 42 accessions from in vitro and field populations were genotyped using 11 microsatellite markers and 23 morphological descriptors to assess variability within and between accessions. Out of the 23 morphological variables used, 13 were identified as most discriminate and were used to cluster the accessions into 4 clusters using the unweighted pair group arithmetic mean average (UPGMA). Accession maintained in field as well as in in-vitro showed high genetic similarity (R2 = 0.91, p-value: 1e-04). Out of the 42 accessions analyzed, nine accessions maintained in the field and in-vitro displayed different genetic profiles. This study provided basic information on the possible somaclonal variation of yam accessions maintained through in-vitro. Further study with advanced tools such as next-generation sequencing is required to elucidate the nature of the observed variation within clones.
This document discusses the application of genomics in improving crop plants. It explains that genomics tools like tissue culture, genetic engineering, molecular diagnostics and molecular markers have revolutionized crop breeding programs. Specifically, it describes how tissue culture allows for rapid propagation of disease-free plants at scale. It also outlines how genetic engineering has been used to develop transgenic crops with improved traits like herbicide tolerance, pathogen resistance, stress tolerance, fruit quality and pest resistance. Molecular diagnostics using probes and monoclonal antibodies enable early disease detection. Molecular markers aid in selecting desirable traits at early stages.
Association of Diaporthe longicolla with Black Zone Lines on Mature Soybean P...Ahmed Shawky
1) Zone lines were observed on the lower stems of mature soybean plants in multiple Midwestern states. Diaporthe longicolla was consistently isolated from these zone lines.
2) Molecular analysis confirmed the identity of 10 representative isolates as D. longicolla. Phylogenetic analysis placed these isolates in a well-supported clade with known D. longicolla cultures.
3) Greenhouse pathogenicity tests reisolated D. longicolla from zone lines on inoculated soybean plants, fulfilling Koch's postulates and demonstrating that D. longicolla is associated with and causes the black zone lines observed on mature soybean stems.
Inter Simple Sequence Repeats (ISSR) markers were utilized to identify the levels of heritable varieties and patterns of the populace structure among the five populaces of Pteris biaurita, a natural fern in India. A comprehensive examination was directed in three replicates at 2013-14 seasons in the Western Ghats, South India. Five wild P. biaurita, accessions (maiden hair) were assessed for genotyping studies. Results demonstrated a pivotal discrepancy among genotypes for they were characterized in view of this uniqueness in four groups by the genetic cluster examination. In this trial, ISSR primers amplified 63 polymorphic groups. In view of the genetic identity data, genotypes were figured and differed from 0.5714 to 0.6984. The percentage of polymorphism indicated predominant genotype that may be utilized for the conservation of species. ISSR appeared to be an obliging marker for prediction of genotype inside a closed group of inter specific populace in the investigation territory
This document discusses organellar heterosis and complementation. It defines organellar genomes as the genomes present in chloroplasts and mitochondria. It describes some key features of organellar DNA, including that it replicates semi-conservatively and is inherited separately from nuclear genes. The document discusses how organellar heterosis can originate from mitochondrial and chloroplast genes and DNA, leading to enhanced structures and functions in hybrids. It provides several examples of organellar heterosis being observed in plants like maize and wheat. The role of intergenomic interaction and complementation between nuclear and organellar genes in generating heterosis is also covered. Finally, the document discusses how transgenic techniques can be used to engineer male sterility for use in hybrid seed
Marker free transgenic crops can be generated using several strategies to avoid issues with marker genes. Selectable marker genes allow selection of transformed cells but their products may be undesirable in food. Strategies include co-transformation using two plasmids without linking marker and trait genes, replacing selectable markers with screenable markers, and excising the selectable marker from the genome after selection using site-specific recombination, transposition, or homologous recombination. Case studies demonstrate applying these strategies successfully in tobacco and mustard to generate marker free transgenic plants.
Paternal radiation exposure led to increased expression of miR-29a and miR-29b in the male germline. This upregulation of miR-29 caused decreased expression of the de novo methyltransferase DNMT3a and profound hypomethylation of LINE1 and SINE B2 transposable elements in the germline. Hypomethylation of these transposable elements was also found in the thymus tissue of offspring conceived from exposed fathers and was associated with decreased expression of the LSH chromatin remodeling protein. Furthermore, miR-468 expression was significantly upregulated in the offspring thymus and directly targeted LSH, contributing to its decreased expression and hypomethylation of transposable
Marker Assisted Gene Pyramiding for Disease Resistance in RiceIndrapratap1
Why marker assisted gene pyramiding?
For traits that are simply inherited, but that are difficult or expensive to measure phenotypically, and/or that do not have a consistent phenotypic expression under specific selection conditions, marker-based selection is more effective than phenotypic selection.
Traits which are traditionally regarded as quantitative and not targeted by gene pyramiding program can be improved using gene pyramiding if major genes affecting the traits are identified.
Genes with very similar phenotypic effects, which are impossible or difficult to combine in single genotype using phenotypic selection, can be pyramided through marker assisted selection.
Markers provides a more effective option to control linkage drag and make the use of genes contained in unadapted resources easier.
Pyramiding is possible through conventional breeding but is extremely difficult or impossible at early generations..
DNA markers may facilitate selection because DNA marker assays are non destructive and markers for multiple specific genes/QTLs can be tested using a single DNA sample without phenotyping.
CONCLUSION:
• Molecular marker offer great scope for improving the efficiency of conventional plant breeding.
• Gene pyramiding may not be the most suitable strategy when many QTL with small effects control the trait and other methods such as marker-assisted recurrent selection should be considered.
• With MAS based gene pyramiding, it is now possible for breeder to conduct many rounds of selections in a year.
• Gene pyramiding with marker technology can integrate into existing plant breeding program all over the world to allow researchers to access, transfer and combine genes at a rate and with precision not previously possible.
• This will help breeders get around problems related to larger breeding populations, replications in diverse environments, and speed up the development of advance lines.
For further queries please contact at isag2010@gmail.com
This document describes a method for rapidly detecting whether plant mutants are homozygous or heterozygous using CEL-I endonuclease. CEL-I endonuclease is a mismatch-specific endonuclease that can cleave DNA at sites of mismatches between DNA strands. The method involves isolating genomic DNA from mutant plants, amplifying a region by PCR, and treating the PCR products with CEL-I endonuclease. Digestion products are then analyzed by gel electrophoresis. For homozygous mutants, no cleavage will occur as there are no mismatches. For heterozygous mutants, cleavage will occur at mismatch sites, producing distinctive banding patterns that allow identification of heterozygotes. This method provides a low
Ossiannilsson mmvc15 the battle for innovation towards opening up educationEbba Ossiannilsson
The document discusses the "battle for innovation towards opening up education." It notes that there are conflicting visions between open education and traditional education, significant advantages to be gained, and a battle over the prevailing narrative. Stakeholders in this battle include educators, students, technology companies, and policymakers. The document argues that strategic decisions need to be made at the macro-level regarding open education given changes in globalization, demographics, and technology. It also asserts that expansion, personalization, networking and automation can enhance education.
Quality is one of the key factors for open educational resources (OER) to gain mainstream acceptance and become part of an open educational practice (OEP) within higher education. Students and teachers need to be able to see the resource’s trustworthiness, target groups, areas of use, context, accessibility etc. What quality criteria can be placed on OER and how do we establish credibility?
In this webinar you will meet the following experts in this area:
Professor Gráinne Conole (University of Leicester, UK) is a well-known expert in the field of open education and is involved in many international initiatives and organisations. She will describe current work with OER quality issues. She will also give examples of a number of relevant projects.
Dr. Ebba Ossiannilsson (University of Lund, Sweden) has recently published a doctoral thesis on quality and benchmarking of e-learning in higher education (http://jultika.oulu.fi/Record/isbn978-952-62-0041-5). She will focus on how benchmarking can be used as a method for quality assurance in an open educational culture. She will also briefly present the main international quality methods in this field.
Keynote delivered at the occasion of the WDP event "Trends in logistics 2020. Opportunities or threats?" ("Logistieke trends 2020. Kans of bedreiging?") on October 16th, 2013 during the "Transport & Logistics 2013" fair in Antwerp (Belgium). The presentation was intended to tease the audience to assess future challenges. It built upon a series of examples of today's changing world in view of challenging futures.
This document discusses user research methods like personas, scenarios, use cases, and hierarchical task analysis that are used to understand users and define requirements. It provides examples of a persona profile, scenario, use case, and hierarchical task analysis. The goal is to design for specific individuals with specific needs by understanding users through research and defining requirements based on the data collected.
Crowdfunding In The Kitchen - Seattle Chefs Collaborative National Sustainabl...Gregory Heller
Crowd-funding in the kitchen: non-traditional financing and funding for your food-related project
Small business owners have found it difficult to access tradition financing from banks over the past few years. An increasing number of them, including chefs and value added producers, have turned toward crowd funding to put together the capital necessary to start or expand their businesses. From food trucks to fine dining, a variety of different models have been successfully employed. What’s worked? What’s flopped? We’ll discuss with our colleagues who have gotten help from the crowd to fund their projects. Whether by Kickstarter or pre-sale of discounted goods or gift cards, crowd funding builds on the familiar concept of Community Supported Agriculture (CSA) and takes it to the next level. Moderated by Gregory Heller, Seattle Chefs Collaborative. Presenters include Tim Crosby and Arno Hesse, both of Slow Money, chef Thierry Rautureau of Luc and Rover’s restaurants, and Jared Stoneberger of the Lark Cookbook Project.
This document discusses open educational resources (OER) including definitions, practices, and quality considerations. It defines OER as teaching, learning and research materials that are in the public domain or introduced with an open license allowing free use, reuse, adaptation and distribution. Issues addressed include finding and sharing resources, open licensing models, the UNESCO Paris Declaration on OER, and ensuring quality through self-assessment, ratings, and review. Pedagogical and technical aspects of using and producing OER are also covered.
The document discusses innovative learning approaches and open education. It summarizes Ebba Ossiannilsson's presentation on these topics, which touched on moving from traditional "sage on the stage" education to connectivist models where students guide their own learning. It also discusses the transformation of education through open educational resources, massive open online courses, and other digital innovations that provide more flexible learning opportunities. Key drivers of this transformation include technology, internationalization, collaboration, and changing attitudes about educational quality and possibilities.
ConceptDraw MINDMAP 7 is a new software that transforms how people create presentations. It allows users to easily create mind maps to organize ideas and information in a visual manner. The software helps presenters convey their message in a clear and engaging way through its mind mapping features.
Social Media Adoption: U.S., Individual Level, Teens & Young AdultsDr. V Vorvoreanu
The document discusses trends in social media adoption among teens and young adults in the United States. It finds that 93% of teens and young adults use the internet, with social networks being their primary online activity. Usage of social networks has risen significantly between 2006 and 2010, with 73% of wired American teens now using social networks. The most commonly used social networks are Facebook, MySpace, and Twitter. Daily usage of social networks is high, with 45% of teens and young adults reporting using social networks daily.
The document discusses open educational resources (OER) and their benefits. It notes that OER emphasize learning communities and engagement, support developing problem-solving skills, and create opportunities for personalized learning by allowing students to create and share content. OER also promote digital skills, improve content quality through collaboration and feedback, and support lifelong learning through greater accessibility of resources.
PRIME is an online CRM system developed over 5 years to facilitate collaboration between financial advisers, accountants, and solicitors. It provides 3 customized interfaces for different user types. PRIME streamlines the referral process, automatically handles communication and documentation between parties, and generates management reports to ensure compliance while building the client database. It establishes a turn-key solution that manages relationships and meets all regulatory requirements for introducers and advisers.
The document discusses quality in online and open education. It identifies three significant areas related to quality in online learning: self-assessment, internal quality assurance processes, and rating systems. It also discusses quality assurance occurring through community review and comments on open educational resources. Finally, it proposes several lenses for evaluating quality, including accuracy, reputation, technical standards, accessibility, and fitness for purpose.
Este documento breve presenta cuatro títulos de canciones o secciones de un álbum musical: "El Album Del MORO!!!", "El Negro.", "El rumano de handert.", y "Yo y La Grassa...". La cuarta sección se titula "EL PARAÍSO DE MARIHUANA".
This document discusses the use of various "omics" technologies in crop breeding, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics. It provides examples of each type of omics analysis in crop plants like potato and wheat. Integrating multi-omics datasets can provide a powerful tool for crop improvement by identifying genes and networks controlling important traits. However, future work is still needed to reduce costs and develop bioinformatic tools to fully leverage omics technologies in breeding programs.
Genomics and its application in crop improvementKhemlata20
meaning ,definition of genome ,genomics ,tools of genomics ,what is genome sequencing ,methods of genome sequencingand genome mapping ,advantage of genomics over traditional breeding program, examples of some crops whose genome has been sequenced, important points about genomics, work in the field of genomics ,applications of genomics .classification of genomics .different Omics in genomics like Proteomics ,Transcriptomics ,Metabolomics ,Need of genome sequencing
Inter Simple Sequence Repeats (ISSR) markers were utilized to identify the levels of heritable varieties and patterns of the populace structure among the five populaces of Pteris biaurita, a natural fern in India. A comprehensive examination was directed in three replicates at 2013-14 seasons in the Western Ghats, South India. Five wild P. biaurita, accessions (maiden hair) were assessed for genotyping studies. Results demonstrated a pivotal discrepancy among genotypes for they were characterized in view of this uniqueness in four groups by the genetic cluster examination. In this trial, ISSR primers amplified 63 polymorphic groups. In view of the genetic identity data, genotypes were figured and differed from 0.5714 to 0.6984. The percentage of polymorphism indicated predominant genotype that may be utilized for the conservation of species. ISSR appeared to be an obliging marker for prediction of genotype inside a closed group of inter specific populace in the investigation territory.
The document summarizes various rice breeding methods including conventional breeding methods like introduction, pureline selection, recombination breeding, and mutation breeding as well as molecular methods like MAS and transgenics. It then provides details on breeding rice for traits like drought tolerance where QTLs like qDTY1.1 and qDTY12.1 have been identified, submergence tolerance using the Sub1 locus, salinity tolerance using the Saltol QTL, and herbicide tolerance through mutagenesis. Varieties developed for these abiotic stresses through marker-assisted backcrossing are also mentioned.
Rice stress related gene expression analysisRonHazarika
The document summarizes research on stress response proteins in rice (Oryza sativa). It identifies 17 proteins commonly up-regulated and 3 commonly down-regulated in response to drought, heat, and salinity stress. It analyzes the protein with the highest interaction for each group and identifies 10 similar proteins in each family. It examines the proteins' physicochemical properties, 3D structures, and functions in plant defense. The study finds the proteins structurally similar but functionally diverse, concluding they help rice cope with stress through complex regulatory interactions.
Post genomic tools for genetic enhancement of germplasmVishu1234567
This document discusses how post-genomic tools like transcriptomics, proteomics, and metabolomics can be used for genetic enhancement of germplasm. It provides an introduction to each omics technique, examples of technologies used, and applications in understanding biological processes and identifying genes/proteins involved in traits. The conclusion states that omics expression analysis of germplasm will help characterize genome function and restore traits from wild varieties, aiding development of more sustainable crop varieties.
Plant Taxonomy with the passage of time deserves holistic approach in the domain of biology.Now, it becomes a synthetic science due to application of other branches of knowledge like Chemistry, Molecular biology etc.This slide is intended to UG & PG students of Botany.
The document discusses allele mining, which aims to identify allelic variations in genetic resources collections that are relevant for traits of interest. It describes how allele mining works to unlock hidden genetic variation by identifying single nucleotide polymorphisms and new haplotypes. The document then provides details on a case study of allele mining focused on three genes - calmodulin, LEA3, and SalT - important for abiotic stress tolerance in rice and related species. Primers were developed to amplify regions of these three genes from 64 accessions representing rice and other grasses.
This document discusses mutation breeding, including its history, types of mutations, how mutations occur, and procedures for mutation breeding. Some key points include:
- Mutation breeding uses artificial mutagens like radiation or chemicals to induce genetic variation for plant breeding. It has been used successfully to develop varieties with improved traits.
- There are two types of mutations - spontaneous and induced. Induced mutations are artificially created while spontaneous mutations occur naturally.
- When DNA is replicated, mistakes can occur leading to mutations. Different types of mutations include substitutions, insertions, deletions, and frameshifts.
- Procedures for mutation breeding involve selecting plant material, applying mutagens, handling mutated populations for several generations of selection and
Genetic engineering can be used to induce male sterility in plants by expressing genes that disrupt pollen development. Researchers have successfully transformed tobacco and oilseed rape plants with the barnase gene, which encodes an RNAse enzyme that destroys tapetal cells, preventing pollen formation. Restoration of fertility was achieved by co-expressing the barstar gene, which inhibits barnase. Similarly, expressing the argE gene in rice under a pollen-specific promoter induces male sterility when activated by an inducer, allowing hybrid seed production. Genetic engineering offers possibilities for more efficient hybrid seed systems in crops where traditional methods have not generated usable male sterility.
This document discusses diversity in linseed (flax) crops in Ethiopia. It finds high genetic diversity among Ethiopian linseed landraces in morphological traits, oil content and quality, and molecular markers. Traits like seed size, color, and oil content show variation. Molecular analysis clusters linseed species and some Ethiopian accessions by altitude and geographical region. The research aims to exploit this diversity through breeding to develop more sustainable and higher value linseed varieties meeting agricultural, economic and cultural needs. Work on linseed could help develop the crop for multiple uses like food, fiber, feed, and industry, benefiting smallholders and exports.
Talk on Phylogenomics for MBL Molecular Evolution Course 2004Jonathan Eisen
This document discusses phylogenomics and how analyzing genome sequences through an evolutionary lens can provide insights into how species evolve. It covers several topics: introducing phylogenomics and how evolutionary analysis is key to interpreting genomes; examples of phylogenomic studies of species evolution, uncultured organisms, and functional predictions; and the importance of increasing phylogenetic diversity in genome sequencing to better understand evolution. The document advocates for taking an evolutionary perspective in comparative genomic studies.
Allele mining in orphan underutilized cropsCCS HAU, HISAR
This document discusses allele mining as a research field aimed at identifying allelic variation in genetic resources collections that can be used for crop improvement. It defines key terms like alleles, orphan crops, and describes two major approaches for allele mining - TILLING and sequencing-based methods. Case studies on allele mining in cassava and sorghum are presented, outlining methodology used and results obtained, including the identification of superior alleles. The prospects of allele mining in molecular plant breeding are discussed, and the need for standardizing bioinformatics tools and developing advanced strategies to efficiently identify novel alleles from genetic resources.
Prevention of Lysosomal Storage Diseases and Derivation of Mutant StemCell Li...Palaelo
Preimplantation genetic diagnosis was used to avoid the transmission of four lysosomal storage disorders (TSD, GD, FD, HS) in couples at risk. 329 eggs from 56 cycles underwent PGD and analysis, resulting in 20 families avoiding transmission. Two human embryonic stem cell lines were derived from embryos diagnosed with Hunter syndrome and Gaucher disease. The cell lines expressed stem cell markers and had a normal karyotype. PGD is an effective technique for avoiding genetic transmission of lysosomal storage disorders and generating disease-specific stem cell lines.
Evaluation of genetic diversity of soybean introductions and north american a...hiensh02
This document evaluates the genetic diversity of 87 soybean plant introductions and 18 major ancestors of North American soybean germplasm using RAPD and SSR markers. Genetic distances among the 105 genotypes ranged from 0.08 to 0.76. Clustering analysis grouped the genotypes into 11 clusters of varying stability. Several groups of plant introductions were distinct from the major ancestors and may provide new genetic variation for soybean breeding programs seeking to broaden the genetic base.
Access to large-scale omics datasets i.e. genomics, transcriptomics, proteomics, metabolomics, phenomics, etc. has revolutionized biology and led to the emergence of systems approaches to advance our understanding of biological processes. With decreasing time and cost to generate these datasets, omics data integration has created both exciting opportunities and immense challenges for biologists, computational biologists, biostatisticians and biomathematicians. Genomics, transcriptomics, proteomics, and metabolomics together they help to bring out the best of characters in plants.
Marker assisted selection of male sterility in rice --vipin Vipin Kannan
This document provides information on various methods of inducing male sterility in plants, especially rice, for the purpose of hybrid seed production. It discusses chemical, genetic, and transgenic approaches. Specifically, it describes cytoplasmic male sterility (CMS), nuclear male sterility (NMS), and cytoplasmic-genetic male sterility (CGMS). It also discusses the use of marker-assisted selection (MAS) to more efficiently select for male sterility genes and introgress them into adapted varieties through techniques like marker-assisted backcrossing (MAB). Overall, the document outlines methods for inducing and tracking male sterility that can facilitate efficient hybrid rice breeding programs.
The document introduces the budding yeast Saccharomyces cerevisiae as a model organism for genetics studies, describing its life cycle between haploid and diploid forms and advantages like its small genome and rapid growth. Methods for conducting genetic screens in yeast are discussed, including how early work isolating cell cycle genes used temperature-sensitive mutants and screening for cell cycle arrest. Meiosis and sporulation in yeast allows studying meiotic divisions and genetic analysis by ensuring mutations are present in only one gene.
The document introduces the budding yeast Saccharomyces cerevisiae as a model organism for genetics studies, describing its life cycle between haploid and diploid forms and advantages like its small genome and rapid growth. Methods for conducting genetic screens in yeast are discussed, including how early work isolating cell cycle genes used temperature-sensitive mutants and screening for cell cycle arrest. Meiosis and sporulation in yeast allows studying meiotic divisions and genetic analysis by ensuring mutations are present in only one gene.
A number of developments have been made in the molecular biology of oat (Avena spp.) in recent years. Many of these were recently described at the Fourth International Oat Conference, held on 18 to 23 October, in Adelaide, South Australia. These advances include a report of oat transformation and regeneration, the characterisation of J3-glucanase genes in oat, the further development of a molecular genetic map in oats, and the characterisation of genes encoding novel oat grain proteins. A technique for assessing pedigrees in the oat and other cereal crops has been reported using a modified electrophoretic technique.
Similar to 2005 rice mutants and genes related to organ development, morphogenesis and (20)
2010 food security measurement in cultural pluralismAgrin Life
This document discusses the concept of food security and argues that current approaches to measuring food security, especially among culturally diverse groups, are incomplete and can lead to misguided policies. It proposes that food security encompasses not just availability and access to food, but also utilization of food and asset creation, which must be understood within specific cultural contexts. Relying solely on coping strategies or food access fails to capture the social and cultural factors influencing food practices and outcomes among different communities. A more holistic definition of food security is needed to inform effective social and nutrition policies.
2010 focus on the short- and long-term effects of ghrelin on energyAgrin Life
Ghrelin is a peptide hormone that regulates energy homeostasis by stimulating appetite and food intake. It is secreted by the stomach and its levels rise before meals and in response to fasting. Ghrelin activates neurons in the hypothalamus that stimulate appetite and feeding behavior. It also acts on reward centers in the brain to influence food motivation. Long-term, ghrelin promotes weight gain by increasing food intake and fat storage while reducing energy expenditure. Polymorphisms in the ghrelin and ghrelin receptor genes have been linked to obesity and eating disorders. Ghrelin antagonists may help treat obesity by reducing appetite and food intake.
2010 expression of a truncated form of yeast ribosomal protein l3Agrin Life
Transgenic wheat plants were generated that express a truncated form of yeast ribosomal protein L3 (L3D) to determine if it improves resistance to Fusarium head blight (FHB). In greenhouse tests, two transgenic lines expressing high levels of L3D showed reductions in disease severity and kernel deoxynivalenol (DON) levels compared to non-transgenic plants after Fusarium graminearum infection. In a field test, a transgenic line with high L3D expression from the maize Ubi1 promoter had significant reductions in visually scabby kernels and kernel DON levels, demonstrating that expression of a modified form of the ribosomal protein targeted by DON can improve FHB resistance in wheat
2010 inhibition of suicidal erythrocyte death by vitamin cAgrin Life
1) The study investigated whether vitamin C can inhibit suicidal death of erythrocytes, similar to how it inhibits apoptosis in nucleated cells.
2) Experiments showed that energy depletion, oxidative stress, and cell shrinkage triggered suicidal erythrocyte death, as evidenced by increased cytosolic calcium levels, decreased cell volume, and increased phosphatidylserine exposure on the cell surface.
3) Vitamin C did not affect erythrocytes under normal conditions but significantly attenuated the suicidal erythrocyte death triggered by energy depletion, oxidative stress, and cell shrinkage by reducing cytosolic calcium levels and phosphatidylserine exposure.
The document discusses various routes for administering insulin, including intrapulmonary and intranasal delivery. Intrapulmonary delivery has advantages like a large surface area for absorption and avoidance of first-pass metabolism. Many studies optimized factors like particle size and delivery devices to enhance pulmonary absorption. Intranasal delivery has a smaller surface area but different absorption characteristics. In 2006, the FDA approved Exubera, an intrapulmonary insulin delivery product, but it was later withdrawn from the market due to expense and potential side effects. Research continues on intrapulmonary and intranasal insulin delivery methods.
2010 engineering tocopherol biosynthetic pathway in arabidopsis leavesAgrin Life
This study genetically engineered the tocopherol biosynthetic pathway in Arabidopsis thaliana by overexpressing five genes (HPPD, VTE2, VTE3, VTE1, and VTE4) involved in tocopherol production, both individually and in combinations. The results showed that elevated expression of these biosynthetic genes affected total tocopherol content and composition. Additionally, engineering the tocopherol pathway also impacted endogenous ascorbate and glutathione pools in the leaves. Further analysis found that genes in the Halliwell-Asada antioxidant cycle were upregulated. These findings provide insight into the relationship between lipid-soluble vitamin E and water-soluble antioxidants vitamin C and
2010 effect of pistachio diet on lipid parameters, endothelial functionAgrin Life
This study investigated the effects of consuming a pistachio-enriched Mediterranean diet on cardiovascular risk factors in 32 healthy young men. Compared to a standard Mediterranean diet, the pistachio diet for 4 weeks significantly decreased blood glucose, LDL cholesterol, total cholesterol, and triglycerides. It also significantly improved endothelial function and decreased markers of inflammation and oxidative stress. The findings suggest that pistachios may have beneficial effects beyond lipid lowering and cardiovascular health.
This document reviews the effects of exenatide, a glucagon-like peptide-1 receptor agonist, on weight loss. It summarizes findings from clinical trials that reported consistent weight loss associated with exenatide treatment compared to placebo. Exenatide is thought to cause weight loss by decreasing energy intake through effects on satiety and by possibly increasing energy expenditure, though evidence for each mechanism is inconsistent. Further research is needed to better understand the mechanisms through which exenatide induces weight loss.
2010 dietary intakes of essential nutrients among arab andAgrin Life
This study investigated dietary intakes and anthropometric measurements between Arab and Berber ethnic groups on the island of Jerba, Tunisia. The researchers found:
1) Berber women had a significantly higher prevalence of obesity than Arab women.
2) Berber women had a significantly shorter height than Arab women.
3) Intakes of calcium, zinc, iron and folate were below recommended levels in both men and women of both ethnic groups.
4) Vitamin E intake was significantly higher in Berbers than Arabs.
2010 carbohydrate for weight and metabolic control- where do we standAgrin Life
This document reviews the evidence on carbohydrate intake for weight and metabolic control. It discusses how recommendations have generally advocated high carbohydrate intake but the prevalence of obesity and diabetes has still increased. Recent evidence suggests diets lower in carbohydrates and higher in unsaturated fats or protein may facilitate weight loss and improve health markers independent of weight loss. The document concludes that future studies are still needed to determine if diets with a more balanced macronutrient composition than currently recommended could better support weight and metabolic health.
2007 plant stress physiology- opportunities and challenges for the food industryAgrin Life
This document discusses how plant stress responses can be advantageous or disadvantageous for the food industry. It provides an overview of how environmental stresses and industrial processing can induce stress responses in plants. The document aims to analyze how understanding these stress responses could help food engineers optimize industrial food processing and avoid potential negative effects.
2008 molecular mechanism of enzymatic allene oxide cyclization in plantsAgrin Life
This document summarizes the molecular mechanism of enzymatic allene oxide cyclization in plants. It discusses allene oxide cyclase (AOC), an enzyme that catalyzes the cyclization of 12,13-epoxy-9(Z),11,15(Z)-octadecatrienoic acid (12,13-EOT) to produce the oxylipin 12-oxo-phytodienoic acid (OPDA) in the jasmonic acid biosynthesis pathway. The review focuses on the crystal structure of AOC2 from Arabidopsis thaliana and putative binding sites for its unstable substrate 12,13-EOT. It also discusses possible intermolecular rearrangements during the cyclization reaction
2007 overexpression of an r1 r2r3 myb gene, osmyb3r-2,Agrin Life
Overexpression of the rice gene OsMYB3R-2, which encodes an R1R2R3 MYB transcription factor, increases tolerance to freezing, drought, and salt stress in transgenic Arabidopsis plants. OsMYB3R-2 expression is induced by cold, drought, and salt stress. Transgenic Arabidopsis plants overexpressing OsMYB3R-2 showed increased tolerance to these stresses compared to wild-type plants. The overexpression also led to higher expression of several cold-related genes. This suggests that OsMYB3R-2 acts as a master switch that increases stress tolerance.
2007 differential expression of the tfiiia regulatoryAgrin Life
This document summarizes a study comparing the responses of two Medicago truncatula genotypes (108-R and Jemalong A17) to salt stress. The study found that Jemalong A17 was more tolerant to salt stress, with less reduction in root growth and nodulation under salt conditions. A gene expression analysis using a stress-related macroarray identified several genes that were more highly expressed in Jemalong A17, even without stress, potentially contributing to its greater tolerance. Two transcription factors (TFs), MtZpt2-1 and MtZpt2-2, that regulate a stress-related gene were found to be more highly expressed in roots of Jemalong A17. Overexpression of these
2006 a novel lipoxygenase in pea roots. its functionAgrin Life
This document summarizes research on a novel lipoxygenase enzyme found in pea roots called LOXN2. Key findings include:
1) LOXN2 was cloned from pea and shown to encode a 93.7 kD protein with two deletions compared to other plant lipoxygenases.
2) When expressed in yeast, LOXN2 exhibited lipoxygenase enzyme activity, preferentially oxygenating linoleic acid to produce both 9- and 13- hydroperoxy octadecadienoic acids in a 3:1 ratio.
3) LOXN2 transcription was found to be downregulated in pea roots infected with the cyst nematode Heterodera goet
2006 a novel lipoxygenase in pea roots. its functionAgrin Life
This document summarizes research on a novel lipoxygenase enzyme found in pea roots called LOXN2. Key findings include:
1) LOXN2 was cloned from pea and shown to encode a 93.7 kD protein with two deletions compared to other plant lipoxygenases.
2) When expressed in yeast, LOXN2 exhibited lipoxygenase enzyme activity, preferentially oxygenating linoleic acid to produce both 9- and 13- hydroperoxy octadecadienoic acids in a 3:1 ratio.
3) LOXN2 transcription was found to be downregulated in pea roots infected with the cyst nematode Heterodera goet
2006 overexpressing a nam, ataf, and cuc (nac)Agrin Life
1) Overexpressing the SNAC1 transcription factor gene enhances drought resistance and salt tolerance in rice. Transgenic rice lines that overexpressed SNAC1 showed significantly higher seed setting (22-34%) than control lines under severe drought stress conditions.
2) SNAC1 is predominantly induced by drought in guard cells. The transgenic rice lines that overexpressed SNAC1 closed their stomata more effectively in response to drought and maintained leaf turgor pressure at lower water potentials.
3) DNA microarray analysis revealed that many stress-related genes were up-regulated in the SNAC1-overexpressing rice, suggesting that SNAC1 improves stress tolerance by activating other stress response genes.
2006 genetic basis of drought resistance at reproductive stage in riceAgrin Life
This study analyzed the genetic basis of drought tolerance and drought avoidance in rice at the reproductive stage using a recombinant inbred line population. Drought stress was applied individually to rice plants grown in pipes to separate drought tolerance from other factors. A total of 21 traits related to yield, fitness, and root morphology were measured under control and drought conditions. Quantitative trait locus mapping identified multiple loci associated with the different traits, suggesting a complex genetic basis for both drought tolerance and avoidance. There was little overlap between loci for above-ground traits and root traits, indicating that drought tolerance and avoidance have distinct genetic mechanisms.
How to Setup Warehouse & Location in Odoo 17 InventoryCeline George
In this slide, we'll explore how to set up warehouses and locations in Odoo 17 Inventory. This will help us manage our stock effectively, track inventory levels, and streamline warehouse operations.
Beyond Degrees - Empowering the Workforce in the Context of Skills-First.pptxEduSkills OECD
Iván Bornacelly, Policy Analyst at the OECD Centre for Skills, OECD, presents at the webinar 'Tackling job market gaps with a skills-first approach' on 12 June 2024
How to Make a Field Mandatory in Odoo 17Celine George
In Odoo, making a field required can be done through both Python code and XML views. When you set the required attribute to True in Python code, it makes the field required across all views where it's used. Conversely, when you set the required attribute in XML views, it makes the field required only in the context of that particular view.
Temple of Asclepius in Thrace. Excavation resultsKrassimira Luka
The temple and the sanctuary around were dedicated to Asklepios Zmidrenus. This name has been known since 1875 when an inscription dedicated to him was discovered in Rome. The inscription is dated in 227 AD and was left by soldiers originating from the city of Philippopolis (modern Plovdiv).
2. Rice mutants and trait genes 49
Table 1 Classification and number of mutant/variant genes
Class of genes No. of genes Class of genes No. of genes
Vegetative organ 276 Seed 236
SAM 30 Morphological traits 55
Leaf 53 • Embryo 28
Culm 141 • Endosperm 3
Root 52 • Grain shape 24
Reproductive organ 464 Physiological traits 181
Heading date 115 • Dormancy 30
Inflorescence 111 • Longevity 3
Spikelet 46 • Storage substances 80
Pollination, fertilization, fertility 238 • Shattering 28
• Fertility restoration 16 • Taste 40
• Segregation distortion 15 Tolerance, resistance 288
• Hybrid sterility, 58 Disease resistance 134
• Hybrid weakness 22 Insect resistance 72
• Male sterility 107 Stress tolerance 82
• Female sterility 3 Characters as QTLs 297
• Meiosis 12 Grain quality 47
• Other sterilities 5 Yield and productivity 134
Heterochrony 4 Plant growth activity 72
Coloration 133 Germination 11
Anthocyanin 40 Root activity 11
Chlorophyll 77 Seed sterility 22
Others 16 Total 1698
tion according to phenotype is underway; see Appendix 1 (1) Genes specifically expressed in the SAM
for Tos17 tagging mutants and Appendix 1 (2) for the MNU- In the vegetative development of rice, the SAM maintains
induced mutants. itself and simultaneously generates lateral organs such as
In this review, rice trait genes important for the under- leaves and tillers. Several different families of homeobox genes
standing of rice are documented. Detailed data including chro- have been cloned and analysed in plants. One of them is a
mosomal locations, trait ontology (TO)/plant ontology (PO) KNOX class 1 homeobox gene family which is a pivotal regula-
and gene ontology (GO) IDs and reference for all 1,698 trait tor of SAM formation and maintenance in plants. In rice there
genes are available in the Oryzabase [see Appendix 1 (3)]. are six KNOX class 1 genes, OSH1, OSH3, OSH6, OSH15,
Such information could be useful for comparative studies of OSH43 and OSH71, in its genome (Sentoku et al. 1999). Five
organ development, and for structural variation of genes among of these genes are expressed in the SAM. Their constitutive
species and genera. expression results in inhibition of regeneration from the callus
by maintaining the cells in an undifferentiated state or results in
Mutants and Genes in Vegetative Organ Development abnormal morphology of regenerated shoots mainly on the
leaves (Sentoku et al. 2000, Ito et al. 2001). Among these
In vegetative development, leaves are generated succes- genes, only the mutant of OSH15 has been analyzed (Sato et al.
sively from flanks of the shoot apical meristem (SAM) with an 1999). The osh15 mutant shows reduced plant height and is
alternate phyllotaxy. Culm, crown roots and lateral roots are allelic to the dwarf mutant, d6. Thus, OSH15 is involved in the
also formed in this developmental phase. A large number of control of normal plant height in addition to SAM formation
mutants defective in development of various organs have been and maintenance. Another gene family that plays a role in
reported in rice, and in several cases causal genes have been SAM is the NAC gene family that shares an evolutionarily con-
cloned. Mutants and genes associated with vegetative organ served NAC domain. Expression analysis suggests diverse
development are categorized into four groups: (i) genes specifi- functions for each member of this family (Kikuchi et al. 2000).
cally expressed in the SAM; (ii) leaf mutants; (ii) culm
mutants; and (iv) root mutants. Leaf mutants
In leaf development, various types of mutants have been
identified and can be categorized into two large groups; a leaf
3. 50 Rice mutants and trait genes
morphology group and a leaf color group. The leaf morphol- 2001). Mutants lacking each of these gene activities show spe-
ogy group contains seven types of mutants: rolled leaves, drip- cific patterns in reducing internode length. These gibberellin
ping-wet leaves, narrow leaves, drooping leaves, blade–sheath synthesis genes form small gene families in the rice genome,
boundary defect leaves, glabrous leaves and hairy leaves; and and the members of each gene family show different expres-
QTLs controlling leaf angle, leaf length and leaf width. sion patterns.
Mutants of three loci have been categorized in the droop- In addition to gibberellin synthesis genes, several gib-
ing leaf subgroup. Among them, DROOPING LEAF (DL) has berellin signaling genes have been cloned and a signaling
been thoroughly analyzed (Nagasawa et al. 2003, Yamaguchi et mechanism has been studied. These genes are, D1, GA-INSEN-
al. 2004). DL is expressed in the central region of the develop- SITIVE DWARF2 (GID2) and SLENDER RICE1 (SLR1). Loss-
ing young leaf and its loss-of-function mutation results in a of-function mutants of D1 and GID2 show a dwarf phenotype,
defective midrib formation and drooping leaves. DL encodes a whereas a loss-of function mutant of SLR1 resembles the phe-
putative transcription factor of the YABBY family. DL is a notype of an exogenous application of gibberellins on plants
pleiotropic gene and also specifies carpel identity during flower (Ashikari et al. 1999, Fujisawa et al. 1999, Ikeda et al. 2001).
development (see Organ Identity section). Detailed analyses of D1 and GID2 encode positive regulators for gibberellin signal-
other mutants remain to be carried out. ing, whilst SLR1 encodes a negative regulator. GID2 is
Seven lamina joint angle QTLs, two leaf length QTLs, involved in the degradation of SLR1 (Sasaki et al. 2003). GID2
five leaf width QTLs and one leaf length mutant have been encodes an F-box protein in a component of ubiquitin ligase E3
identified. In a coleoptile photomorphogenesis1 (cpm1) mutant, named SCFGID2.
coleoptiles elongate more than wild-type coleoptiles under red D1 encodes an α-subunit of the trimeric G protein, which
light or in the darkness (Biswas et al. 2003). is localized in the plasma membrane as a complex with the β-
There are three mutants affecting leaf blade–sheath and the γ-subunits (Ashikari et al. 1999, Fujisawa et al. 1999,
boundary, auricleless (aul), liguleless (lg) and collarless (col). Kato et al. 2004). The d1 mutant is insensitive to low concen-
The auricleless (aul) mutant lacks auricles and the ligule is trations of gibberellins, but still shows a response to high con-
rudimentary, whereas liguleless (lg) lacks ligule, auricle and centrations of gibberellins (Ueguchi-Tanaka et al. 2000).
leaf collar (Maekawa 1988). The collarless mutant lacks collar Two genes have been cloned which encode proteins cata-
(Sanchez and Khush 1998). Another two classes of mutants, lyzing brassinosteroid synthesis. In d2 mutants, the second
two glabrous leaf and two hairy leaf mutants were also found in internode from the top has been shown to be shortened,
the leaf mutants. The other leaf mutant group has abnormali- whereas elongation of the other internodes is rarely affected
ties in leaf color including lesion mimic spotted phenotype. (Hong et al. 2003). The d2 mutant also shows an erect leaf phe-
notype. D2 encodes brassinosteroid C-3 oxidase (also called
Culm mutants CYP90D2, a member of cytochrome P450), which catalyzes a
Culm mutants can be categorized into eight groups; C-3 oxidation step of brassinosteroid synthesis. In the rice
dwarfism/elongation, floating, tiller formation, tiller angle, brit- genome, one homolog of D2 has been found, which is
tleness, thickness, twisted and others. The dwarfism/elonga- expressed mainly in the root.
tion group includes mutants impaired in gibberellin synthesis, BRASSINOSTEROID-DEPENDENT1/BRASSINOSTEROID-
gibberellin signaling, brassinosteroid synthesis and brassinos- DEFICIENT DWARF1 (BRD1) encodes a brassinosteroid C-6
teroid signaling. oxidase (OsDWARF), which catalyzes the C-6 oxidation step
of brassinosteroid synthesis (Hong et al. 2002, Mori et al.
DWARFISM/ELONGATION 2002). The brd1 mutant shows almost no internode elongation,
Since plant height in rice is an agronomically important a reduced ratio of leaf sheath to leaf blade, and a short root.
trait for breeding high-yielding cultivars, numerous dwarf and The brd1 mutant also shows constitutive photomorphogenesis
semi-dwarf mutants have been collected. Some of them have in the dark.
been shown to be gibberellin- or brassinosteroid-related In the brassinosteroid signaling pathway in rice, only one
mutants. gene has been cloned. D61 encodes a receptor-like protein
D35, SD1 and D18 genes encode gibberellin biosynthesis kinase with extensive sequence identity to the Arabidopsis
enzymes which catalyze specific steps. D35 encodes ent-kau- brassinosteroid receptor BRI1 (Yamamuro et al. 2000). This
rene oxidase which catalyzes the early three steps of gibberel- suggests that D61 is the receptor for brassinosteroid in rice.
lin synthesis (ent-kaurene→ent-kaurenol→ent-kaurenal→ent- The d61 mutant shows less sensitivity to exogenously applied
kaurenoic acid) (Itoh et al. 2004). SD1, the ‘green revolution’ brassinosteroid. More endogenous brassinosteroids accumulate
gene, encodes GA20 oxidase which catalyzes three steps in the d61 mutant than the wild-type plant. The relative ratio of
(GA53→GA44→GA19→GA20) (Sasaki et al. 2002). D18 leaf blade to sheath length is also smaller compared with the
encodes GA3 β-hydroxylase that catalyzes the step from GA20 wild type. The results of these phenotypic analyses are consist-
to GA1, which is an active form of gibberellin (Itoh et al. ent with the idea that D61 is the brassinosteroid receptor.
4. Rice mutants and trait genes 51
FLOATING
Another group of mutants are related to floating characters
or deep water tolerance. These genes exist in the floating rice
strains, and are involved in reactions mainly for extreme elon-
gation of the internodes. These genes are analyzed as QTLs and
are described in the Stress tolerance section.
TILLER FORMATION
Seven mutants with a reduced number of tillers have been
identified. Among them, MONOCULM1 (MOC1) has been
shown to be involved in tiller bud initiation (Li et al. 2003a).
The moc1 mutant shows no tillering owing to a defect in tiller
bud formation during the vegetative phase, and produces no
rachis branches in the inflorescence. MOC1 encodes a tran- Fig. 1 Histological characterization of seminal roots of the crl1, crl2,
scription factor of the plant-specific GRAS family. Expression rrl1 and rrl2 mutants in rice. (A–C) Transverse sections of the nodes
of MOC1 starts in the presumptive region of the axillary bud of wild type (A), crl1 (B) and crl2 (C). In crl1, no crown root primor-
formation, and continues until maturation of the tiller buds. dia is initiated (B), and in crl2 development of crown roots is impaired
(C). (D–G) Longitudinal sections of seminal roots of the wild type (D
and F), rrl1 (E) and rrl2 (G). In rrl1, the cortical cell length is signifi-
BRITTLE cantly reduced (E), and in rrl2 the root apical meristem is small and
Six mutants with brittle culm have been identified. Brittle the root cell length is reduced (G). Photographs are kind gifts from H.
mutants are easily broken by bending. Among them, BRITTLE Kitano and Y. Inukai (Nagoya University).
CULM1 (BC1) has been studied most extensively (Li et al.
2003b). The bc1 mutant has less cellulose and more lignin than
the wild-type plant. Monosaccharide composition is also Mutants and Genes in Reproductive Organ Development
affected in the bc1 mutant. Thus, BC1 controls the mechanical
strength of plants through the cell wall composition. BC1 Heading date
encodes a COBRA-like protein and is expressed mainly in Rice is a model plant for analysis of flowering of short-
developing sclerenchyma cells and in vascular bundles. day plants, and also for comparative studies of flowering with
long-day plants such as Arabidopsis. A large number of QTLs
TILLER ANGLE AND THICKNESS have been identified from a cross between wild and cultivated
Seven genes identified as mutations or QTLs are catego- rice strains and between japonica and indica strains. In one
rized in the tiller angle group. However, detailed morphological combination, detailed analyses of every QTL have been car-
and molecular analyses of these genes have not yet been ried out using near isogenic lines (NILs) (Yano et al. 2001).
reported. Big uppermost culm (Buc) is categorized in the thick- Heading date1 (Hd1) encodes a zinc-finger transcription factor
ness group. closely related to the Arabidopsis flowering gene product
CONSTANS (CO), and Hd3a encodes a protein closely related
Root mutants to Arabidopsis FLOWERING LOCUS T (FT) (Yano et al.
In contrast to the understanding of shoot development, 2000, Kojima et al. 2002). Under short-day conditions, Hd1
analysis of root development lags behind, even though a activates expression of Hd3a and induces flowering. Under
number of mutants have been isolated which affect various long-day conditions, Hd1 suppresses the expression of Heading
aspects of root development. These include mutants for root date 3a (Hd3a) and inhibits transition to a reproductive phase.
number, root branching, root length, root thickness, root This pattern of regulation contrasts with that of Arabidopsis in
weight, root pulling force and rhizome formation. The crl1 which under long-day conditions CO (Hd1) induces flowering
(crown rootless1) mutant forms radicle and lateral roots through expression of FT (Hd3a) (Hayama et al. 2003).
normally, but is impaired in the initiation of crown root primor- Early heading date1 (Ehd1) encodes a B-type response
dia (Fig. 1A, B) (Inukai et al. 2001a). Thus, CRL1 specifically regulator of a two-component signaling system and confers
regulates initiation of crown root primordia. CROWN early flowering, especially under short-day conditions (Doi et
ROOTLESS2 (CRL2) regulates various aspects of rice develop- al. 2004). The effect of Ehd1 is observed in the hd1 mutant
ment including initiation and subsequent growth of crown root background, but in the ehd1 mutant background Hd1 functions
primordia (Fig. 1C, D, Inukai et al. 2001a). The reduced root normally as a floral inducer under short-day conditions and
length1 (rrl1) and reduced root length2 (rrl2) mutations cause also as a floral repressor under long-day conditions. Under
short roots (Inukai et al. 2001b). In the rrl1 mutant, only the short-day conditions, expression of Hd3a is higher in the Ehd1
cortical cell length is significantly reduced, whilst in the rrl2 background than in the ehd1 background. This indicates that
mutant, the root apical meristem is also small (Fig. 1E, G). Ehd1 and Hd1 function independently and that the two path-
5. 52 Rice mutants and trait genes
Fig. 3 Flower mutants of rice. (A) Wild-type flower. (B) fon1-2
flower. (C) spw1 flower. (D) dl flower. Photographs are kind gifts from
H. Hirano and Y. Nagato (University of Tokyo).
In the panicle phytomer1 (pap1) mutant, the numbers of
Fig. 2 Inflorescence images of lax and fzp mutants of rice. (A) Wild-
type inflorescence. (B) Inflorescence images of lax mutants. (C) Inflo-
primary branches are increased. In addition, internode length
rescence of fzp mutant. (D) Terminal spikelet of wild-type branch. (E) and number of rachis are reduced, and rudimentary and empty
Apical region of fzp branches. Photographs are kind gifts from J. Kyo- glumes are elongated (Takahashi et al. 1998).
zuka (University of Tokyo).
LATERAL MERISTEM IDENTITY
This group of mutants fails to specify the identity of the
ways are integrated into a flowering pathway with Hd3a. lateral branch meristem as the spikelet or flower meristem.
Heading date 6 (Hd6) delays flowering under long-day condi- This group includes FRIZZY PANICLE (FZP). In fzp mutants,
tions but not short-day conditions. Although Hd6 has been primary rachis branch meristems develop normally, but spike-
shown to encode an α-(catalytic) subunit of protein kinase CK2 lets are replaced by branch meristems (Fig. 2C–E, Komatsu et
(Takahashi et al. 2001), interaction with other flowering genes al. 2003b). As a result, branch meristems are continuously gen-
and alleles remains to be studied. erated in the inflorescence of the fzp mutant. FZP encodes a
In addition to these excellent examples of QTL analysis, transcriptional activator with the ERF domain, and is expressed
other QTL analyses have revealed many trait genes from a in a region where the rudimentary glume primordia develop.
variety of strains. Several QTLs are introduced in this mini-
review; however, QTLs showing growth activities in vegeta- FLOWER ORGANIZATION
tive and reproductive organs are not incorporated. They are This group of mutants has defects in flower organization.
agronomically important traits, such as grain quality, yield and A mutant flower of this group has an abnormal number or
productivity, plant growth activity, germination, root activity arrangement of whorls. Although some mutants are known,
and seed sterility, and are listed in the rice genes and mutants of such as extra glume-1 (eg1) and extra glume-2 (eg2), their
Oryzabase [see Appendix 1 (3)]. detailed analyses remain to be carried out.
Inflorescence ORGAN NUMBER
Inflorescence and flower mutants can be categorized into This group of mutants has defects in controlling the
seven groups according to the developmental step at which number of organs developed in each whorl. In these mutants,
mutant phenotypes are observed, such as lateral branching, lat- only the number of floral organs is affected, whereas flower
eral meristem identity, flower organization, organ number, organization and organ identity are normal. floral organ
organ identity, organ development and others. number1 (fon1) and fon2 are mutants in this group. In these
mutants, the number of floral organs such as carpel, stamen and
LATERAL BRANCHING lodicule is increased, whereas the number of glumes such as
This group of mutants has defects in the formation and lemma and palea is not affected (Fig. 3B, Nagasawa et al.
elongation of lateral branches. The mutants of this group form 1996). fon1 and fon2 control organ numbers by regulating mer-
fewer numbers of rachis branches and spikelets or compact istem size or number of meristem cells. The FON1 gene
panicle(s). In this group, LAX PANICLE (LAX) has been stud- encodes a receptor-like protein kinase with a high homology to
ied most extensively. In lax mutants, spikelets are formed only Arabidopsis CLAVATA1 (CLV1) (Suzaki et al. 2004).
on the apices of rachis branches, and no lateral spikelets are
formed (Fig. 2A, B, Komatsu et al. 2001, Komatsu et al. ORGAN IDENTITY
2003a). LAX is necessary for initiation of lateral meristem for- This group of mutants has defects in specification of the
mation. LAX encodes a putative transcription factor with a identity of organs. In rice, several genes involved in organ
plant-specific basic helix–loop–helix (bHLH) domain and is identification have been identified. Among them, SUPER-
expressed at the boundary between the lateral meristem and WOMAN (SPW) specifies lodicules and stamens. In spw mutant
apical meristem. flowers, lodicules and stamens are homeotically transformed
6. Rice mutants and trait genes 53
into palea-like organs and carpels, respectively (Fig. 3C, CMS lines require combination with the fertility restorer lines
Nagasawa et al. 2003). The SPW gene has been shown to be to maintain a hybrid system, whereas alteration of environmen-
identical to OsMADS16, a rice MADS-box gene. SPW is tal conditions, such as day length and temperature shift, can
expressed in the lodicules and stamens. These analyses indi- restore fertility in PMS and TGMS (Liu et al. 2001, Wang et al.
cate that SPW is a class B gene and the ABC model is applica- 2003).
ble, at least in part, to rice. In Oryza sativa, only a single CMS system has been thor-
DROOPING LEAF (DL), which plays a role in leaf devel- oughly studied using cybrids with the cytoplasm of cv. Chinsu-
opment (see Leaf mutants section), also specifies carpel iden- rah Boro II (Boro, indica rice) and the nuclear genome of cv.
tity (Nagasawa et al. 2003, Yamaguchi et al. 2004). In the dl Taichung 65 (T65, japonica rice), called ms-bo type or BT type
mutant, the carpel has been homeotically transformed into the CMS (Shinjo 1975, Shinjo 1984). A mitochondrial atp6 and a
stamens (Fig. 3D). In flower development, expression of DL unique sequence orf79 downstream of atp6 are known to relate
starts in the presumptive region where carpel primordium is to CMS (Kadowaki et al. 1990, Iwabuchi et al. 1993, Akagi et
initiated, and continues in the carpel primordium. Thus, DL al. 1994). The Rf-1 gene has been reported to encode a protein
specifies the identity of only a single whorl. In this respect, the with a mitochondrial transit peptide and pentatricopeptide
ABC model is modified in rice. repeat (PPR) (Kazama and Toriyama 2003, Komori et al.
Another gene involved in specification of organ identity is 2004). On the other hand, neither PMS nor TGMS genes have
LEAFY HULL STERILE1 (LHS1) (Jeon et al. 2000). In the lhs1 been isolated as yet. Ku et al. (2003) reported that pro-
mutant flower, lemma and palea show a leaf-like appearance. grammed cell death of premature tapetum is associated with
Lodicules also become leafy. The number of stamens is TGMS in rice.
reduced. In some flowers, a new abnormal flower is formed in Several other genic mutations exhibiting pollen sterility or
the whorl of the stamens, indicating that specification of floral abnormal anther development have also been reported (mostly
meristem identity is incomplete. LHS1 is identical to designated ms). Recently, the aid1 mutant showing a defect in
OsMADS1, a close member of Arabidopsis AP1. LHS pro- anther dehiscence was identified using an Ac/Ds transposon
motes determination of the floral meristem identity and specifi- tagging system (Zhu et al. 2004). The AID1 gene encodes a
cation of the lemma, palea and lodicules. Other genes have novel protein with a single MYB DNA-binding domain.
been cloned which have resulted in homeotic transformation of
floral organs when they are ectopically expressed or their anti- Hybrid sterility and reproductive barrier
sense is expressed (Kang et al. 1998, Kyozuka and Shimamoto Although there are several genic models for hybrid steril-
2002). ity, only two models are applied to interspecific rice hybrids.
One is the ‘single locus sporo-gametophytic interaction’ model,
ORGAN DEVELOPMENT AND OTHERS and the other is the ‘duplicate loci gametic lethal’ model (Oka
Mutants of the organ development group have defects in 1974, Sano et al. 1979).
development of each organ and show abnormal development of Gamete eliminator genes play key functions in preferen-
awn, lemma and palea after specification of their organ iden- tial inheritance of one of the alleles in the heterozygous F1
tity. Twenty genes or QTLs involved in awn development are plants, and support the former model. The Mendelian segrega-
known, whilst six genes are known for each of lemma and tion of marker genes linked with the gamete eliminator is dis-
palea. In malformed lemma1 (mls1) and mls2, morphological torted in progenitors. Many gamete eliminator loci, designated
abnormalities in the lemma and low pollen fertility are as S in most cases, have been identified in various cross-combi-
observed, and in mls3, lemma and palea are malformed (Taka- nations among the Oryza species. In the cross-combination
mure and Kinoshita 1992). Mutants involved in gametophyte between O. sativa and O. glaberrima, at least seven S loci have
development are described below. been identified using NILs of a T65 background (Sano 1983,
Sano 1990, Doi et al. 1998, Doi et al. 1999, Taguchi et al.
Sexual Reproduction Processes 1999). The loci S1, S3, S19 and S20 act to abort pollen carry-
ing the T65 haplotype, and the loci S2 and S21 act to abort
In this section, we describe the genes and mutations asso- pollen carrying the glaberrima haplotype (Fig. 4A–D). Hetero-
ciated with gamete or seed sterility. zygous plants in the S18 locus probably exhibit a defect in male
sporocyte development. In addition to the gamete eliminator
Male sterility and fertility restoration alleles, Ikehashi and Araki (1986) have reported the existence
Male sterility, for which a large number of mutants are of a neutral S allele (S5n) in javanicas, called wide-compatibil-
found, is classified into four major groups: male sterility ity varieties (WCVs). The WCVs enable generation of fertile
caused by cytoplasmic male sterility (CMS), photoperiod-sen- F1 plants when crossed with japonica and indica, whilst
sitive genic male sterility (PMS), thermosensitive genic male japonica–indica hybrids exhibit high sterility and are primarily
sterility (TGMS) and other genic male sterilities. CMS, PMS attributed to the S5 locus. Thus the WCVs have actually con-
and TGMS can be used for practical hybrid production. The tributed to overcoming hybrid sterility (Wan et al. 1993). In
7. 54 Rice mutants and trait genes
Fig. 4 Hybrid sterility found in the genus Oryza. (A–D) Pollen from
cross-combination between O. sativa L. and O. glaberrima Steud.
stained with I2-KI solution. (A) O. sativa L. cv. T65. (B) O. glaber-
rima Steud. (IRGC1104038). (C) An F1 hybrid. (D) A near isogenic
line heterozygous for the S21 locus. (E and F) Paraffin sections of the
matured embryo sac in the F1 plants between cv. Asominori (japonica)
and cv. IR24 (indica). (E) Asominori (wild type). (F) A collapsed
embryo sac in the double recessive plants for the hsa1and hsa2 loci.
(G) Hybrid weakness segregated in the F2 population between O.
sativa L. and O. glumaepatula Steud. From left to right, O. sativa
(T65), a vigorous progeny, two progenies exhibiting hybrid weakness Fig. 5 Phenotypes of pair1 and msp1 mutants of rice. (A) Twelve
(indicated by arrows), and O. glumaepatula (IRGC1105688). Photo- bivalents at diakinesis in the wild type. (B) Twenty-four univalents in
graphs are kind gifts from K. Doi (Kyushu University) and T. Kubo the pair1 mutant. (C) Normal anaphase I in the wild type. Magenta and
(Cancer Institute). green represent chromosomes and tubulin fibers, respectively. (D)
Chromosome non-disjunction at anaphase I of the pair1 mutant. (E) A
addition to S genes, many loci or genes distorting Mendelian normal megaspore mother cell (MMC, arrowhead) formed in an ovule
segregation of flanking marker genes in interspecific hybrids of the wild type. (F) Plural MMCs (arrowheads) in a single ovule of
the msp1 mutant. (G and H) In situ hybridization of the MSP1 mRNA
have been identified, many of which are designated ga. against a longitudinal section of the wild-type anther (G) and ovule
Recently, Harushima et al. (2002) reported that many map posi- (H). (G) PMC, pollen mother cell; Ta, tapetum; Ml, middle layer; En,
tions for numerous segregation distorter loci of japonica and endothecium; Ep, epidermis. The tapetum layer is intensely stained,
indica strains differed with cross-combinations, suggesting but the PMCs are not. (H) The nucellar cells are stained, but the MMC
rapid evolution of reproductive barrier genes. (arrow) is not.
Only a few pairs of loci involved in complementary F2
hybrid sterility support another genic model. Recently, Kubo chromosome 8. The double recessive plant causes female ste-
and Yoshimura (1999) reported a pair of complementary loci rility (Fig. 4E, F), whilst the single recessive homozygotes of
for F2 hybrid sterility, hsa1 on chromosome 12 and hsa2 on each locus exhibit moderate sterility.
8. Rice mutants and trait genes 55
Hybrid weakness regulator of gibberellin-dependent α-amylase (Gubler et al.
Hybrid weakness or hybrid breakdown is not directly 1995). Even though OsGAMYB is also highly expressed in the
related to sexual reproduction, but is worth noting in this sec- aleurone layer of rice seeds, one of its essential functions might
tion because they are one of the components of the reproduc- be in pollen development (Kaneko et al. 2004).
tive barriers. All hw loci reported so far (Hwa, hwb, Hwc, hwd
and hwe) complementarily affect viability of F1 or F2 plants Large-scale monitoring of specific gene expression in reproduc-
(Oka 1957, Amemiya and Akamine 1963, Chu and Oka 1972, tive organs
Fukuoka et al. 1998, Kubo and Yoshimura 2002). The plants Using cDNA microarray analyses and in situ hybridiza-
affected by the complementary gene sets generally show a tion techniques, Endo et al. (2004) revealed 259 non-redun-
small number of tillers, short culms and panicles, chlorosis or dant cDNA clones specifically or predominantly expressed in
necrosis of leaves, absence of seed sets, root growth inhibition, rice anthers, and classified into four groups. Lan et al. (2004)
and so on (Fig. 4G). reported the 253 ESTs exhibiting differential expression dur-
ing pollination and fertilization.
MEIOSIS
In the majority of eukaryotes, chromosome synapsis is Genes and Mutants Identified as Seed Characters
mediated by an evolutionarily conserved, tripartite, protein
structure called the synaptonemal complex (SC) (Wettstein et Embryo and endosperm mutants are divided into catego-
al. 1984, Zickler and Kleckner 1999). Synaptic mutants are ries of embryo, endosperm and grain shape for the morphologi-
classified into two categories, asynaptic and desynaptic cal characters, and dormancy, longevity, storage substances,
mutants (Li et al. 1945). The former class is characterized by shattering and taste for the physiological characters.
partial or complete inhibition of the synapsis of homologous
chromosomes, whereas the latter shows precocious separation Embryo
of bivalents following chromosome pairing. In O. sativa, many A large number of mutations affecting various aspects of
asynaptic (as) and desynaptic (ds) mutants have been isolated seed development have been reported in rice. Rice seeds con-
so far (Katayama 1963, Kitada and Omura 1983). sist of two distinct parts, an embryo and an endosperm. Over
Recently, Nonomura et al. (Nonomura et al. 2004a, Non- 200 embryo mutants reported to date (Nagato et al. 1989,
omura et al. 2004b) identified the rice meiotic genes PAIR1 and Kitano et al. 1993, Hong et al. 1995a) are categorized into five
PAIR2 from sterile mutant lines tagged with Tos17 (Hirochika groups: embryoless, deletion of embryonic organs, altered
et al. 1996). The loss-of-function mutations of two PAIR genes embryo size, modified organ position and aberrant morphology.
result in asynapsis and chromosome non-disjunction in male
and female meiocytes (Fig. 5A–D). The PAIR1 gene encodes a EMBRYOLESS AND ORGAN DELETION
novel nuclear protein (Nonomura et al. 2004a). PAIR2 encodes The embryoless1 (eml1) mutant develops seeds that lack
a protein homologous to the yeast HOP1 and Arabidopsis an embryo (Fig. 6A) (Hong et al. 1995a, Hong et al. 1995b).
ASY1 (Nonomura, K., Eiguchi, M., Nakano, M., Suzuki, T. and The eml1 embryo degenerates at the early stage (∼3 d after pol-
Kurata, N. unpublished data). lination), but endosperm development seems normal. Notably,
manifestation of an embryoless phenotype depends on the
OTHER STERILITIES growing temperature.
There are only a few other genes or mutations that are The globular embryo (gle) mutants develop embryos with
involved in sexual reproduction but not classified in the above a globular shape and completely lack embryonic organs (Fig.
categories. In the msp1 mutant flowers, the number of male and 6B). At least four loci (gle1–gle4) cause this phenotype. Analy-
female sporocytes increases abnormally (Fig. 5F) (Nonomura sis of a gle4 embryo using molecular markers indicates that
et al. 2003). The MSP1 gene encodes a putative leucine-rich GLE4 plays a role in radial pattern formation during rice
repeat (LRR) receptor-like protein kinase, and is expressed in embryogenesis, but not in formation of embryonic organs
the nurse cells surrounding the male and female sporocytes (Kamiya et al. 2003). The club-shaped embryo (cle) mutants
(Fig. 5G, H). Lee et al. (2004) identified the OsCP1 gene from fail to form both a shoot and a radicle, as does the gle muta-
T-DNA-tagged mutant lines. The oscp1 mutant showed a sig- tions (Fig. 6C). Unlike the gle embryos, palisade-shaped cells
nificant defect in pollen development, in addition to dwarfism. characteristic of the scutellar epithelium are formed in the
OsCP1 expression is observed mainly in anther locules but not whole epidermis of cle. Since the palisade-shaped cells of cle
in vegetative tissues. OsCP1 encodes the papain family express an α-amylase gene, it is considered that the most cle
cysteine protease. embryo comprises the scutellum (Hong et al. 1995a).
Kaneko et al. (2004) identified a MYB domain gene The organless (orl) mutants also lack both a shoot and a
OsGAMYB, from the Tos17-tagged lines. The osgamyb mutant radicle (Fig. 6D). Unlike cle1, the orl1 embryo differentiates
exhibits defects especially in anther and pistil development, but palisade-shaped cells in the epidermis-facing endosperm, sug-
not in vegetative tissues. GAMYB is a positive transcriptional gesting that embryonic polarity is not affected in orl1. Consist-
9. 56 Rice mutants and trait genes
Fig. 6 Phenotypes of rice embryo mutants from median longitudinal sections. (A) eml1 seed showing no embryo. (B) gle1 embryo without
organs. (C) cle1 embryo without organs. (D) orl1 without organs. (E) shl1 embryo lacking a shoot but with a normal radicle. (F) sho1 embryo
with an aberrant shoot lacking a coleoptile but with a normal radicle. (G) Wild-type embryo (left), ge embryo with enlarged scutellum (center)
and re1 embryo in which every organ is reduced (right). (H) apd1 embryo with apically displaced shoot and radicle. (I) enl large embryo lacking
endosperm. S, shoot; Sc, scutellum; R, radicle. Photographs are kind gifts from Y. Nagato (University of Tokyo).
ently, tissue specificity of OSH1 gene expression is maintained chron, resulting in deformed shoot architecture (Itoh et al.
in orl1 (Sato et al. 1996). 2000).
Four shootless (shl) mutants, shl1, shl2, shl3 and shl4,
have been reported to be indispensable in shoot formation dur- EMBRYO SIZE
ing embryogenesis (Satoh et al. 1999). Of these, shl1, shl2 and Two types of mutations causing either a reduction or
shl4 exhibit indistinguishable phenotypes; complete loss of enlargement of embryo size have been reported (Hong et al.
shoots, coleoptile and epiblast and normal radicle formation 1996). The giant embryo (ge) mutants have a 1.2–1.5 times
(Fig. 6E). In another mutant, shl3, in addition to deletion of the longer embryo and reduced endosperm (Fig. 6G). The scutel-
shoot, the radicle is exogenously produced and cells in the lum is enlarged but the sizes of the shoot and radicle are not
remaining tissues are highly vacuolated. SHL1, SHL2 and affected (Hong et al. 1996). Three reduced embryo (re)
SHL4 function upstream of OSH1 (Satoh et al. 1999). At least mutants, re1, re2 and re3, exhibit a reduction in embryo size.
two loci, RAL1 and RAL2, are required for radicle formation. The re embryo is less than half the length of the wild-type
The ral embryo seems to be truncated in the apical–basal direc- embryo, and shows a reduction in all embryonic organs includ-
tion but develops a shoot. After germination, the ral plant pro- ing the apical meristems and the enlarged endosperm (Fig. 6G)
duces normal crown roots. Thus, it is supposed that the ral (Hong et al. 1996). Anatomical and double mutant analyses
phenotype bears root-producing ability, but is caused by dele- using ge, re and other mutants suggest that the primary func-
tion of the basal embryonic region where the radicle develops. tion of GE and RE resides in endosperm development, not in
In addition, ral1 affects vascular pattern formation (Scarpella et embryogenesis (Hong et al. 1996).
al. 2003).
ORGAN POSITION
ORGAN MORPHOGENESIS The APD1 locus is related to organ position. In the apical
Two shoot organization (sho) mutants, sho1 and sho2, displacement (apd) mutant embryo, the shoot is formed at the
show severe defects in embryonic organ development. In sho apex of the embryo and the radicle at the center of the embryo
embryos, the first to the third leaves are malformed, but the (Fig. 6H). This phenotype is due mostly to an enlargement of
radicle develops normally (Fig. 6F). The sho1 plant produces the basal region of the embryo and underdevelopment of the
malformed leaves with a random phyllotaxy and a short plasto- scutellum (Hong et al. 1995a).
10. Rice mutants and trait genes 57
Endosperm Seed dormancy
Because the cereal endosperm is an important staple diet Since seed dormancy is a complex and quantitative char-
in many countries, studies on genes acting in the endosperm acter influenced by both genetic and environmental factors, the
are important issues for both basic research and plant breeding. regulatory mechanism of dormancy is not well understood.
Although a large number of genes that are associated with stor- OsVP1 is a rice ortholog of VP1 in maize and ABI3 in Arabi-
age substances in the endosperm, such as protein and starch, dopsis (Hattori et al. 1994). Molecular analysis and in situ
have been identified, analysis of genes regulating endosperm expression patterns indicate the involvement of OsVP1 in seed
development is limited. Only one mutant affecting endosperm maturation processes including dormancy, as in maize and Ara-
development has been reported. The endospermless (enl) bidopsis (Hattori et al. 1995, Miyoshi et al. 2002). The rice
mutant fails to form an endosperm (Fig. 6I) (Kageyama et al. vivipary (riv) mutants, riv1 and riv2, exhibit precocious germi-
1991). After fertilization, the enl1 endosperm starts to develop nation before harvesting and reduced sensitivity to abscisic
but degenerates at an early stage (∼3 d after pollination), result- acid (Miyoshi et al. 2000).
ing in the production of a very large embryo (Kageyama et al. QTL analysis has detected dormancy-related genes. By
1991, Miyoshi et al. 2000). The mutations associated with using RILs (recombinant inbred lines) between cultivated and
embryo size, ge and re, are also supposed to affect endosperm wild rice strains, 17 QTLs have been detected (Cai and
growth (Hong et al. 1996). Morishima 2000). In addition, five QTLs have been detected
using BILs (backcross inbred lines) derived from a backcross
SEED MATURATION of Nipponbare/Kasalath/Nipponbare (Miura et al. 2002).
To date, a large number of rice genes related to seed matu-
ration processes, mainly starch and storage protein synthesis
Heterochrony
and their accumulation, have been identified.
The heterochronic genes control the temporal regulation
Rice seeds accumulate various kinds of substances as
of development and greatly affect plant architecture. Two hete-
nutrients to support seedling growth. Starch, which consists of
rochronic genes have been identified and characterized in rice.
amylose and amylopectin, is the major source of nutrition for
One is PLASTOCHRON1 (PLA1) (Itoh et al. 1998). In the pla1
seedling growth. The Waxy (Wx) gene encodes a granule-bound
mutant, primary rachis branches in the panicle are converted
starch synthase involved in amylose synthesis (Nelson and Pan
into vegetative shoots (Fig. 7B). Because vegetative to repro-
1995). Two naturally occurring Wx alleles, Wxa and Wxb, are
ductive phase transition occurs normally, the vegetative phase
known (Sano 1984, Sano et al. 1986). Rice cultivars (mainly is elongated and both vegetative and reproductive programs are
japonica cultivars) with a Wxb allele produce lower amounts of expressed simultaneously in the pla1 mutant. Thus, PLA1 is a
Wx protein than those (mainly indica cultivars) carrying Wxa heterochronic gene controlling proper termination of the vege-
(Sano et al. 1986). Wxb carries a substitution mutation at the 5′ tative phase. The pla1 mutant also shows short plastochron, an
spliced site of the first intron, and causes a low content of amy- enlarged SAM, small leaves, bending of the lamina joint and
lose (Cai et al. 1998, Isshiki et al. 1998). The dull (du) muta- dwarfism (Fig. 7A). PLA1 encodes a member of CYP78A, a
tions also affect amylose content. In du-1 and du-2, the amount subfamily of the large cytochrome P450 family, and is
of spliced Wxb mature transcript, but not Wxa transcript, is expressed in young leaves and bracts (Fig. 7C, D, Miyoshi et
reduced (Isshiki et al. 2000). al. 2004).
Cereal seed proteins have been classified into four types, The mori1 mutant reiterates the wild-type second leaf
water-soluble albumin, salt-soluble globulin, alcohol-soluble stage and fails to induce adult phase (Asai et al. 2002). MORI1
prolamin and acidic or basic solution-soluble glutelins. Among is a heterochronic gene playing an important role in juvenile to
them, glutelin has been studied intensively because it is the adult phase transition.
most abundant storage protein occupying 60–80% of the total
endosperm protein. Glutelin precursors are encoded by a multi- Tolerance and Resistance
gene family that consists of the GluA and GluB subfamilies
(Takaiwa et al. 1991). Mutations showing a reduction or lack of Rice has evolved many kinds of resistance or tolerance
a particular subunit or precursor polypeptide have been identi- genes against biotic and abiotic stresses. Almost all of the
fied. Three loss-of-function mutants, gulutelin1 (glu1), glu2 resistance or tolerance genes have been found as variant alleles
and glu3, have defects in subunits 1a, 2a and 3a, respectively. in a variety of cultivated and wild strains.
A dominant mutation of Low glutelin content1 (Lgc1) causes a
reduction in glutelin content. Unlike the above glu mutations, Disease resistance
the Lgc1 mutation has been found to influence the amount of A large number of resistant genes or alleles specific to
most glutelin subunits (Iida et al. 1997). It is revealed that Lgc1 individual races of fungi and bacteria have been identified.
suppresses accumulation of glutelin gene family transcripts via Two serious and well-studied rice diseases are rice blast, a fun-
RNA silencing (Kusaba et al. 2003). gal disease caused by Magnaporthe grisea, and bacterial bright
11. 58 Rice mutants and trait genes
avilurence gene that is interactive with Pi-ta has also been iso-
lated (Orback et al. 2000). In addition, an intensive gene-for-
gene analysis has been carried out of the multiple steps of the
infectious process of Magnaporthe in rice (Sesuma and
Osbourn 2004), and a variety of cDNAs induced during the
defense steps in the rice blast-resistant mutant have also been
identified (Han et al. 2004).
Recently, an approach has been used to identify mutants
which confer breakdown of Xa21-mediated resistance from
thousands of mutant strains (Wang et al. 2004). Xa21 is a wide
spectrum resistance gene for multiple varieties of X. oryzae.
Therefore, findings of the breakdown mutants for Xa21 resist-
ance would clarify genes composed of the Xa21 multispectrum
defense pathway.
A hundred disease-resistant or defense-response gene-like
sequences have been mapped into several clusters on the rice
chromosomes, and some of them coincide with QTLs or major
resistance genes (Wang et al. 2001). The NBS family has
around 400 members in the rice genome (Monosi et al. 2004),
and the receptor-like kinase (RLK) family has about 1,200
members (Shiu et al. 2004).
Lesion mimic mutants
The lesion mimic mutants show symptom-like spots on
leaves and sometimes on the panicles. Over 11 mutants have
been identified and are classified as spotted leaves (spl) or cell
death and resistance (cdr) (Fig. 8A). Most of them are thought
to have defects in genes with roles in the disease defense path-
ways against attack from fungi, bacteria or viruses, althought a
Fig. 7 Expression and mutant phenotype of PLA1. (A) Seedlings of few spl mutants do not show resistance. Some mutant genes
the pla1 mutant and the wild type. Due to the shortened plastochron,
which produce lesions mimicking symptoms are well charac-
the pla1 mutant produces more leaves than the wild type. (B) Panicles
of the pla1 mutant and the wild type. Primary rachis branches of pla1 terized (Takahashi et al. 1999, Yamanouchi et al. 2002). Two
are converted into vegetative shoots. (C and D) In situ hybridization of genes cloned from spl mutants are the heat stress transcription
PLA1 mRNA in wild-type leaves. (C) Expression of PLA1 at the base factor (HSF) gene (Kawasaki et al. 1999), and a U-box/Arma-
of young leaves. (D) Expression of PLA1 in bracts. dillo repeat protein gene involved in the ubiqitination pathway
(Zeng et al. 2004).
caused by Xanthomonas oryzae. Most resistance genes identi- Insect resistance
fied for bacterial and fungal pathogens have nucleotide-bind- More than 200 species of insects are associated with rice
ing sites/LRRs (NBS-LRR) and/or serine/threonine receptor plants as pests. Among them, the brown planthopper (BPH;
kinase domains. In total, >20 resistance genes to Xanthomonus Nilaparvata lugens Stål), whitebacked planthopper (WBPH;
are identified, and three genes are cloned; Xanthomonus resist- Sogatella furcifera Horvath), green leafhopper (GLH; Nepho-
ance gene 1 (Xa1), Xa21 and Xa26, encoding LRR receptor tettix virescens Distant), green rice leafhopper (GRH; Nepho-
kinase proteins (Yoshimura et al. 1998, Wang et al. 1998, Sun tettix cincticeps Uhler) and Asian rice gall midge (ARGM;
et al. 2004). Among >60 blast resistance genes/alleles includ- Orseolia oryzae Wood-Mason) are the worst pests for which
ing QTLs, two genes are cloned: Pyricularia oryzae (Mag- the major host resistance genes have been well studied. Most of
naporthe grisea) resistance gene ta (Pi-ta) encoding NBS-LLR the >70 resistance genes reported so far have been identified
and a gene found in a resistant strain Zhai Ye Qing8 (ZYQ8) using RILs, NILs or detected as QTLs.
encoding a protein carrying a low homology to the serine/thre- More than 13 resistance genes against BPH and six genes
onine kinase domain and a calmodulin-binding domain (Wang against WBPH have been identified, and several BPH resist-
et al. 1999, Zheng et al. 2004). ance genes have been tagged on a molecular linkage map. An
A single base change in Pi-ta confers a difference between example of antibiosis is shown in Fig. 8B–D. Rice ovicidal
resistance and susceptibility (Bryan et al. 2000). Avirulence response to WBPH is characterized by the formation of watery
genes in the infectious blast fugi are also characterized. An lesions and production of an ovicidal substance, benzyl ben-
12. Rice mutants and trait genes 59
RILs or NILs is the most convenient way to detect multiple
loci for tolerance and sensitivity (Nguyen et al. 2004). Instead
of identification of stress tolerance genes using genetic meth-
ods, another molecular approach to identify and isolate such
tolerance-related genes is employed (de los Reyes et al. 2003,
Dubouzet et al. 2003). Dubouzet et al. (2003) isolated five
stress responsible rice genes of the DREB/CBF transcription
factor by homolog hunting of Arabidopsis genes. The cloned
genes are expressed under cold or dehydration and high-salt
stress and then activate a number of target genes. Attempts to
generate stress-tolerant transgenic rice with stress tolerance-
related genes have also been made (Garg et al. 2002, Mukho-
Fig. 8 (A) Leaf phenotypes of spl2, spl4 and spl9 mutants. (B) A padhyay et al. 2004). Recently, a more sophisticated genomic
watery lesion attacked by WBPH. (C) Resistance response of a approach has become available involving combinational analy-
japonica cultivar Asominori with dead eggs. (D) Susceptible response sis of expression profiling using microarray analysis with seg-
of an indica cultivar IR24 with live eggs. Photographs are kind gifts
regated progeny from a cross of tolerant and sensitive parent
from A. Yoshimura and H. Yasui (Kyushu University).
strains (Cooper et al. 2003, Hazen et al. 2004).
Stress tolerance is tightly related to the developmental
zoate, which causes high egg mortality of WBPH (Seino et al. stages and specific organs. For instance, metal ion and salinity
1996, Suzuki et al. 1996). A gene with ovicidal activity to tolerance is expressed mainly in the root during the process of
WBPH, Ovc, and four ovicidal QTLs, qOVA-1–3, qOVA-4, ion absorption through water uptake. Cold tolerance is espe-
qOVA-5–1 and qOVA-5–2, have been identified (Yamasaki et cially needed during the germinating and flowering stages. It
al. 2003). Ovc was the first gene to be identified that kills might be possible to identify tolerant mutants/genes in the
insect eggs in plants. mutant/variant groups of these organs. Submergence tolerance
Another type of antibiosis is found in resistant varieties may be specifically important in rice, a character enabling sur-
against GLH and GRH. The resistant plants cause delayed vival during deep water stress. A group of wild rice strains and
growth and eventual death of infesting insects. The resistance landraces show submergence tolerance, which results in rapid
may be concerned with sucking inhibition after their infesta- internode elongation. This specific character must also be regu-
tion. So far, six loci for resistance to GRH, Grh1–Grh6, are lated by a genetic program for culum development. A recent
known. NILs carrying single resistance genes show weak review and a QTL analysis for submergence sensitivity have
resistance (Grh1and Grh2) and susceptibility (Grh4). On the shown various aspects of this reaction (Jackson and Ram 2003,
other hand, NILs carrying two resistance genes, Grh2 and Toojinda et al. 2003).
Grh4, express strong resistance to GRH and GLH. The interac-
tion of Grh2 and Grh4 expresses a strong resistance against Coloration
two leafhopper species in rice.
Gm2 is a dominant gene conferring resistance to biotype 1 Coloration is one of the most important characters of
of ARGM (Diptera: Cecidomyiidae), the major dipteran pest. plants, especially in relation to the chlorophyll biosynthesis
Tissue necrosis, represented by a typical hypersensitive reac- pathway. Tissue-specific coloration with anthocyanin is an
tion accompanied by maggot mortality, is observed within 4 d interesting phenomenon, which is partly integrated in the organ
after infestation of avirulent biotype 1 of the ARGM (Bentur developmental program. A large number of mutants and vari-
and Kalode 1996). Two other resistance genes, Gm6 and Gm7 ants have been identified in these categories.
(both may be identical), are tightly linked to Gm2 (Katiyar et
al. 2001, Sardesai et al. 2002). Anthocyanin and other colorations
Wild rice species are excellent genetic resources for resist- More than 40 mutants and/or variants have been found to
ance genes and can also be used to integrate their resistance possess purple coloration genes/alleles by modifying anthocy-
loci into cultivated rice (Brar and Khush 1997). Some loci have anin biosynthesis in rice. The divergent pattern of anthocyanin
been confirmed as being transferred successfully into culti- coloration in specific organs, e.g. coleoptile, leaf axil, leaf
vated rice via homologous chromosome recombination. None sheath, leaf blade, leaf margin, midrib, leaf apex, internode,
of the rice resistance genes to insects have yet been cloned. nodal ring, pericarp and stigma, is detected in the mutants/vari-
ants. It has been reported that these specific patterns in expres-
Stress tolerance sion of anthocyanin are attributed to dysfunction of the key
Sensitivities to various stresses such as drought, cold (low regulator of anthocyanin biosynthesis R genes/alleles in rice. R
temperature), salt/osmotic stress, herbicides and metals vary genes encode bHLH protein transcription factors and regulate
from strain to strain. QTL analysis using an F2 population, pigmentation in specific organs. One of the rice R loci, purple
13. 60 Rice mutants and trait genes
leaf (PI), has a complex allele PI(w) composed of at least two Mutant and Variant Genes in Future Functional Genom-
genes of the bHLH proteins (Sakamoto et al. 2001). The com- ics of Rice
plex nature of multiple alleles of the R loci may be involved in
a variety of organ/tissue-specific regulations of anthocyanin As shown in this mini-review, many trait genes revealed
biosynthesis. Sixteen mutants for coloration with substances by mutant and QTL analyses have been accumulated. In the
other than anthocyanin have been reported: Brown furrows of next decade, full genome sequence information should help to
hull (Bf), gold furrows of hull (gf1and2), gold hull and inter- promote the rapid growth in isolation and characterization of
node (gh1-3), redpericarp and seed coat (Rd), and so on. These these trait genes. The collection and positioning of many pieces
mutants also show organ-specific coloration. of genes in the developmental and physiological pathways will
decipher the many gene networks and thus determine the mor-
Chlorophyll phological and developmental regulations for those gene net-
Chlorophyll synthesis is very important to all plants in works. Morphological mutants play an indispensable role in the
relation to photosynthesis. Chlorophyll and its encasing study of rice development and of QTLs with regards to plant
organelle, the chloroplast, are both synthesized from chloro- growth reactions. However, individual gene characterization is
plast- and nucleus-encoded genes. Studies on chlorophyll and not enough to achieve such kinds of studies, but systematic
chloroplast biosynthesis pathways have been extensively com- work using genomic and bioinformatic approaches is required.
piled for many plants. In rice, >70 chlorophyll mutants exhibit- Generation of a search system for knock-out mutants for all
ing albino, chlorina, stripe, virescent, yellow-green and zebra rice genes, microarray analysis for mutant and variant strains,
leaves have been recorded. Albino has no chlorophyll, com- gene/genome comparative studies with Arabidopsis, wild rice
and other cereal species, and an ideal analytical system for
pletely lacks any green color and dies soon after germination.
handling large quantities of data using bioinformatic tools will
Chlorina mutants have light green leaves and a low ability for
together promote functional genomic studies in the very near
photosynthesis, thus growing weakly and depending on the
future.
gene locus or allele. The stripe phenotype appears as a white
sectored leaf in the longitudinal direction, and is different in
Appendix 1
size and number of white stripes among the loci. On the con-
trary, zebra has a white or yellow transverse banding phenotype
(1) http://tos.nias.affrc.go.jp/~miyao/pub/tos17/
in the green leaves. This phenotype is highly variegated in (2) http://www.shigen.nig.ac.jp/rice/oryzabase/nbrpStrains/kyushu-
band size, frequency and color at every stage of plant growth. Grc.jsp
Virescent mutants also show conditional chlorosis in the leaf to (3) http://www.shigen.nig.ac.jp/rice/oryzabase/genes/geneClasses.jsp
different degrees depending on the temperature, strength and
wavelength of light. One of the virescent mutant inhibits the Acknowledgments
translation of plastid transcripts during chloroplast differentia-
tion (Sugimoto et al. 2004). These analyses indicate there are We are grateful to Dr. Y. Nagato (The Univeristy of Tokyo) for
his valuable discussions and helpful comments, and also for kindly
several components used in chlorophyll synthesis and the pho-
providing photographs. We would also like to thank Drs. A.
tosynthesis pathways. Most classes of chlorophyll mutants are Yoshimura, H. Yasui, K. Doi (Kyushu University), T. Kubo (Cancer
composed of >10 independent loci, suggesting that each bio- Institute, Tokyo), J. Kyozuka, H. Hirano (The University of Tokyo),
synthesis pathway is constructed with at least 10 proteins that and Y. Inukai, H. Kitano, M. Matsuoka (Nagoya University) for their
are necessary to complete chlorophyll/chloroplast biogenesis. useful advice and kindly providing photographs. Finally, we would
like to thank Dr. S. Iyama (National Institute of Genetics) for his huge
One chrolina mutant has been revealed to encode OsCHLH, a
effort in selecting and gathering information for rice genes and
key enzyme in the chlorophyll branch biosynthesis pathway mutants for Oryzabase.
(Jung et al. 2003).
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(Received October 30, 2004; Accepted November 10, 2004)