This document discusses applying genomic selection to a rice breeding program using a synthetic population and recurrent selection. Key points:
- Genomic selection was tested on 343 rice families from a synthetic population with 10 cycles of recombination to estimate its feasibility. Various regression models were evaluated.
- Accuracy of genomic selection was found to depend on trait architecture, heritability, and marker selection. Flowering date saw improved accuracy when markers were selected based on linkage disequilibrium.
- The results indicate genomic selection is feasible for this rice breeding program, though further data across sites and years is still needed to develop stronger prediction models. Genomic selection could help increase selection intensity and reduce time in the recurrent selection scheme.
A new era of genomics for plant science research has opened due the complete genome sequencing projects of Arabidopsis thaliana and rice. The sequence information available in public database has highlighted the need to develop genome scale reverse genetic strategies for functional analysis (Till et al., 2003). As most of the phenotypes are obscure, the forward genetics can hardly meet the demand of a high throughput and large-scale survey of gene functions. Targeting Induced Local Lesions in Genome TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identity point mutations in regions of interest (McCallum et al., 2000). This strategy works with a mismatch-specific endonuclease to detect induced or natural DNA polymorphisms in genes of interest. A newly developed general reverse genetic strategy helps to locate an allelic series of induced point mutations in genes of interest. It allows the rapid and inexpensive detection of induced point mutations in populations of physically or chemically mutagenized individuals. To create an induced population with the use of physical/chemical mutagens is the first prerequisite for TILLING approach. Most of the plant species are compatible with this technique due to their self-fertilized nature and the seeds produced by these plants can be stored for long periods of time (Borevitz et al., 2003). The seeds are treated with mutagens and raised to harvest M1 plants, which are consequently, self-fertilized to raise the M2 population. DNA extracted from M2 plants is used in mutational screening (Colbert et al., 2001). To avoid mixing of the same mutation only one M2 plant from each M1 is used for DNA extraction (Till et al., 2007). The M3 seeds produce by selfing the M2 progeny can be well preserved for long term storage. Ethyl methane sulfonate (EMS) has been extensively used as a chemical mutagen in TILLING studies in plants to generate mutant populations, although other mutagens can be effective. EMS produces transitional mutations (G/C, A/T) by alkylating G residues which pairs with T instead of the conservative base pairing with C (Nagy et al., 2003). It is a constructive approach for users to attempt a range of chemical mutagens to assess the lethality and sterility on germinal tissue before creating large mutant populations.
Current Status of TILLING and EcoTILLING:
TILLING and EcoTILLING technique have been adapted in diverse species including rice, maize, Lotus, poplar, Arabidopsis, wheat, barley, potato, tomato, sunflower, common bean, Field Mustard, clover, melon, pea, peanut, sorghum, rapeseed, soybean, melon, poplar, sugarcane, brassica and other for the purpose of gene detection, functional genomics, polymorphism assessment, plant breeding as described in case study part.
Ecotilling:
EcoTILLING is similar to TILLING, except that its objective is to identify natural genetic variation as opposed to induced mutations.
Many species are not amenable to chemical mutagenesis; therefore, EcoTILLING can aid in the discovery of natural variants and their putative gene function
This approach allows one to rapidly screen through many samples with a gene of interest to identify naturally occurring SNPs and / or small INs/DELS
iTILLING:
A new approach to the TILLING method that reduces costs and the time necessary to carry out mutation screening was developed for Arabidopsis and it is called iTILLING, individualized TILLING
The document discusses MAGIC (Multi-parent Advanced Generation Inter-Cross) populations, which are created by intercrossing multiple parent lines over several generations. This increases recombination and genetic diversity. Key points:
- MAGIC populations allow more precise mapping of QTLs controlling quantitative traits compared to biparental populations.
- Two case studies describe the development of MAGIC populations in rice with 8 founders each, and tomato with 8 founders. Traits like yield, disease resistance, and abiotic stress tolerance were evaluated.
- Advantages include exploiting more genetic variation, developing varieties with favorable trait combinations, and more accurate gene mapping. Limitations include requiring more time, resources for phenotyping and breeding.
Genotyping by Sequencing is a robust,fast and cheap approach for high throughput marker discovery.It has applications in crop improvement programs by enhancing identification of superior genotypes.
This document discusses gene pyramiding as a tool for developing durable resistance in crops. It defines gene pyramiding as combining two or more genes from multiple parents to develop elite lines with simultaneous expression of multiple genes. The objectives of gene pyramiding are to enhance traits, meet deficits in elite cultivars, and increase durability. Types of gene pyramiding include conventional pedigree breeding and backcrossing as well as molecular marker-assisted selection and transgenic methods. Gene pyramiding provides advantages like wider disease resistance and improved elite cultivars, while limitations include difficulty achieving multiple gene incorporation. Examples and applications in rice, wheat and other crops are also provided.
The document discusses various types of mapping populations that can be used for linkage mapping of genetic markers and quantitative trait loci (QTL) in plants. It describes biparental populations like F2, backcross, recombinant inbred lines (RILs), and doubled haploids. It also discusses multiparental populations like immortalized F2 and MAGIC (Multi-parent Advanced Generation Intercross) populations. The key properties, advantages, and disadvantages of different mapping populations are summarized. Mapping populations are crucial resources that enable the construction of dense genetic linkage maps and identification of genomic regions associated with traits.
This document summarizes three case studies on using marker-assisted breeding techniques:
1) Introgressing rice QTLs controlling root traits from donor Azucena into recipient Kalinga III. Five target QTLs were introgressed over three backcrosses using foreground, background, and recombinant selection with RFLPs and SSRs.
2) Introgressing the submergence tolerance Sub1 QTL from donor IR49830 into popular rice variety Swarna. The QTL was introgressed over three backcrosses and a BC3F2 line identified with minimal donor DNA.
3) Introgressing drought tolerance QTLs from donor CML247 into
This document discusses applying genomic selection to a rice breeding program using a synthetic population and recurrent selection. Key points:
- Genomic selection was tested on 343 rice families from a synthetic population with 10 cycles of recombination to estimate its feasibility. Various regression models were evaluated.
- Accuracy of genomic selection was found to depend on trait architecture, heritability, and marker selection. Flowering date saw improved accuracy when markers were selected based on linkage disequilibrium.
- The results indicate genomic selection is feasible for this rice breeding program, though further data across sites and years is still needed to develop stronger prediction models. Genomic selection could help increase selection intensity and reduce time in the recurrent selection scheme.
A new era of genomics for plant science research has opened due the complete genome sequencing projects of Arabidopsis thaliana and rice. The sequence information available in public database has highlighted the need to develop genome scale reverse genetic strategies for functional analysis (Till et al., 2003). As most of the phenotypes are obscure, the forward genetics can hardly meet the demand of a high throughput and large-scale survey of gene functions. Targeting Induced Local Lesions in Genome TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identity point mutations in regions of interest (McCallum et al., 2000). This strategy works with a mismatch-specific endonuclease to detect induced or natural DNA polymorphisms in genes of interest. A newly developed general reverse genetic strategy helps to locate an allelic series of induced point mutations in genes of interest. It allows the rapid and inexpensive detection of induced point mutations in populations of physically or chemically mutagenized individuals. To create an induced population with the use of physical/chemical mutagens is the first prerequisite for TILLING approach. Most of the plant species are compatible with this technique due to their self-fertilized nature and the seeds produced by these plants can be stored for long periods of time (Borevitz et al., 2003). The seeds are treated with mutagens and raised to harvest M1 plants, which are consequently, self-fertilized to raise the M2 population. DNA extracted from M2 plants is used in mutational screening (Colbert et al., 2001). To avoid mixing of the same mutation only one M2 plant from each M1 is used for DNA extraction (Till et al., 2007). The M3 seeds produce by selfing the M2 progeny can be well preserved for long term storage. Ethyl methane sulfonate (EMS) has been extensively used as a chemical mutagen in TILLING studies in plants to generate mutant populations, although other mutagens can be effective. EMS produces transitional mutations (G/C, A/T) by alkylating G residues which pairs with T instead of the conservative base pairing with C (Nagy et al., 2003). It is a constructive approach for users to attempt a range of chemical mutagens to assess the lethality and sterility on germinal tissue before creating large mutant populations.
Current Status of TILLING and EcoTILLING:
TILLING and EcoTILLING technique have been adapted in diverse species including rice, maize, Lotus, poplar, Arabidopsis, wheat, barley, potato, tomato, sunflower, common bean, Field Mustard, clover, melon, pea, peanut, sorghum, rapeseed, soybean, melon, poplar, sugarcane, brassica and other for the purpose of gene detection, functional genomics, polymorphism assessment, plant breeding as described in case study part.
Ecotilling:
EcoTILLING is similar to TILLING, except that its objective is to identify natural genetic variation as opposed to induced mutations.
Many species are not amenable to chemical mutagenesis; therefore, EcoTILLING can aid in the discovery of natural variants and their putative gene function
This approach allows one to rapidly screen through many samples with a gene of interest to identify naturally occurring SNPs and / or small INs/DELS
iTILLING:
A new approach to the TILLING method that reduces costs and the time necessary to carry out mutation screening was developed for Arabidopsis and it is called iTILLING, individualized TILLING
The document discusses MAGIC (Multi-parent Advanced Generation Inter-Cross) populations, which are created by intercrossing multiple parent lines over several generations. This increases recombination and genetic diversity. Key points:
- MAGIC populations allow more precise mapping of QTLs controlling quantitative traits compared to biparental populations.
- Two case studies describe the development of MAGIC populations in rice with 8 founders each, and tomato with 8 founders. Traits like yield, disease resistance, and abiotic stress tolerance were evaluated.
- Advantages include exploiting more genetic variation, developing varieties with favorable trait combinations, and more accurate gene mapping. Limitations include requiring more time, resources for phenotyping and breeding.
Genotyping by Sequencing is a robust,fast and cheap approach for high throughput marker discovery.It has applications in crop improvement programs by enhancing identification of superior genotypes.
This document discusses gene pyramiding as a tool for developing durable resistance in crops. It defines gene pyramiding as combining two or more genes from multiple parents to develop elite lines with simultaneous expression of multiple genes. The objectives of gene pyramiding are to enhance traits, meet deficits in elite cultivars, and increase durability. Types of gene pyramiding include conventional pedigree breeding and backcrossing as well as molecular marker-assisted selection and transgenic methods. Gene pyramiding provides advantages like wider disease resistance and improved elite cultivars, while limitations include difficulty achieving multiple gene incorporation. Examples and applications in rice, wheat and other crops are also provided.
The document discusses various types of mapping populations that can be used for linkage mapping of genetic markers and quantitative trait loci (QTL) in plants. It describes biparental populations like F2, backcross, recombinant inbred lines (RILs), and doubled haploids. It also discusses multiparental populations like immortalized F2 and MAGIC (Multi-parent Advanced Generation Intercross) populations. The key properties, advantages, and disadvantages of different mapping populations are summarized. Mapping populations are crucial resources that enable the construction of dense genetic linkage maps and identification of genomic regions associated with traits.
This document summarizes three case studies on using marker-assisted breeding techniques:
1) Introgressing rice QTLs controlling root traits from donor Azucena into recipient Kalinga III. Five target QTLs were introgressed over three backcrosses using foreground, background, and recombinant selection with RFLPs and SSRs.
2) Introgressing the submergence tolerance Sub1 QTL from donor IR49830 into popular rice variety Swarna. The QTL was introgressed over three backcrosses and a BC3F2 line identified with minimal donor DNA.
3) Introgressing drought tolerance QTLs from donor CML247 into
Marker Assisted Selection in Crop BreedingPawan Chauhan
Marker Assisted Selection is a value addition to conventional methods of Crop Breeding. It has been gaining importance in plant breeding with new generation of plant breeders and to get accurate and fast desired result from plant breeding.
Multiple inbred founder lines are inter-mated for several generations prior to creating inbred lines, resulting in a diverse population whose genomes are fine scale mosaics of contributions from all founders.
This document discusses marker-assisted backcrossing (MAB) for introgressing traits from a donor parent into a recipient line. MAB uses DNA markers linked to target genes/QTLs to aid in selection. Markers can be used for foreground selection of target genes, background selection to recover the recipient genome, and recombinant selection to minimize linkage drag. A case study is described where MAB was used over multiple generations to introgress 5 drought resistance QTLs from a donor rice variety into a recipient variety. Through foreground, background, and recombinant selection using DNA markers, lines were developed with the target QTLs and most of the recipient genetic background.
Diversity array technology (DArT) is a high-throughput marker system that does not require sequence information. DArT arrays have been developed for chickpea, pigeonpea, and groundnut comprising 15,360 clones each. DArT markers showed 35% and 9% polymorphism in chickpea and pigeonpea mapping populations, but are not cost-effective for detecting variation in cultivated germplasm. DArT may be useful for introgressing segments from wild species into elite varieties, as seen with introgressing resistance genes from C. platycarpus into pigeonpea. Next-generation sequencing has also been used to develop SSR markers for trait mapping in these
This document summarizes a seminar on breeding concepts and crop improvement in chickpea. It discusses the floral biology of chickpea, including emasculation and pollination techniques. Breeding objectives for chickpea include increasing yield, biotic and abiotic stress resistance, and quality traits. Key breeding techniques used are mass selection, pure line selection, and hybridization methods like bulk hybridization and pedigree breeding. Varieties developed through these techniques with important traits are mentioned. The document provides information on the present uses of chickpea and production constraints.
QTL is a gene or the chromosomal region that affects a quantitative trait, which should be polymorphic (have allelic variation) to have an effect in a population, must be linked to a polymorphic marker allele to be detected. The QTL mapping consists of 4 steps, like the development of mapping population, generation of polymorphic marker data set among the parents, construction of linkage map, and finally the QTL analysis
All the above steps are described in these slides very briefly along with two case studies.
Introduction:
Proposed by Meuwissen et al. (2001)
GS is a specialized form of MAS, in which information from genotype data on marker alleles covering the entire genome forms the basis of selection.
The effects associated with all the marker loci, irrespective of whether the effects are significant or not, covering the entire genome are estimated.
The marker effect estimates are used to calculate the genomic estimated breeding values (GEBVs) of different individuals/lines, which form the basis of selection.
Why to go for genomic selection:
Marker-assisted selection (MAS) is well-suited for handling oligogenes and quantitative trait loci (QTLs) with large effects but not for minor QTLs.
MARS attempts to take into account small effect QTLs by combining trait phenotype data with marker genotype data into a combined selection index.
Based on markers showing significant association with the trait(s) and for this reason has been criticized as inefficient
The genomic selection (GS) scheme was to rectify the deficiency of MAS and MARS schemes. The GS scheme utilizes information from genome-wide marker data whether or not their associations with the concerned trait(s) are significant.
GEBV: GenomicEstimated Breeding Values-
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Gene-assisted genomic selection:
A GS model that uses information about prior known QTLs, the targeted QTLs were accumulated in much higher frequencies than when the standard ridge regression was used
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Population used:
Training population: used for training of the GS model and for obtaining estimates of the marker-associated effects needed for estimation of GEBVs of individuals/lines in the breeding population.
Breeding population: the population subjected to GS for achieving the desired improvement and isolation of superior lines for use as new varieties/parents of new improved hybrids.
Training population-
large enough: must be representative of the breeding population: max. trait variance with marker : by cluster analysis
should have either equal or comparable LD, LD decay rates with breeding populations
Updated by including individuals/lines from the breeding population
Training more than one generation
Low colinearity between markers is needed since high colinearity tends to reduce prediction accuracy of certain GS models. (colinearity disturbed by recombination)
Within the last twenty years, molecular biology has revolutionized conventional breeding techniques in all areas. Biochemical and Molecular techniques have shortened the duration of breeding programs from years to months, weeks, or eliminated the need for them all together. The use of molecular markers in conventional breeding techniques has also improved the accuracy of crosses and allowed breeders to produce strains with combined traits that were impossible before the advent of DNA technology
This document discusses quantitative trait loci (QTL) mapping. It explains that QTL mapping can identify the genomic regions linked to quantitative traits, analyze the effects of QTLs, and provide information on the number, location, effects, and interactions of QTLs. The key aspects of QTL mapping covered are the objectives, principles, analysis methods, required resources like mapping populations, and applications in plant breeding and genetics research.
MARKER-ASSISTED BREEDING FOR RICE IMPROVEMENTFOODCROPS
This document discusses marker-assisted breeding for rice improvement. It begins with an outline of the topics to be covered, which include the theory and practice of marker-assisted selection, marker-assisted breeding schemes, and a case study of marker-assisted backcrossing done at IRRI. The first section defines marker-assisted selection and describes its advantages over phenotypic selection, such as earlier selection and greater reliability. Subsequent sections discuss specific marker-assisted breeding schemes like backcrossing, pyramiding traits, and early generation selection. The document concludes with details of IRRI's case study using markers to backcross a submergence tolerance gene into popular rice varieties.
I would like to share this presentation file.
Some basics information regarding to molecular plant breeding, hope this help the beginner who start working in this field.
Thanks for many original source of information (mainly from slideshare.net, IRRI, CIMMYT and any paper received from professor and some over the internet)
This document discusses allele mining as a technique for improving crops. It defines allele mining as identifying allelic variation within genetic resources collections to find superior alleles. There are two main approaches - TILLING based allele mining which uses mutagenized populations and enzymatic cleavage to find mutations, and sequencing-based allele mining which uses PCR and sequencing to identify natural variation. Both have benefits and limitations. Applications of allele mining include finding alleles for resistance, abiotic stress tolerance, and improved yield and quality. Overall, allele mining is a promising approach for utilizing genetic resources to discover variants that can aid crop breeding.
Association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of linkage disequilibrium to link phenotypes to genotypes.Varioius strategey involved in association mapping is discussed in this presentation
Genomics refers to the study of the entire genome of an organism. It deals with mapping genes on chromosomes and sequencing entire genomes. While work on genomics began with prokaryotes like bacteria, research has now been conducted on crop plants like rice and Arabidopsis thaliana. Genomics is an interdisciplinary field that uses tools from molecular biology, robotics, and computing to study genomes. It provides information on genome size, gene number, gene function, and evolution. Genomics has applications in crop improvement through gene mapping, marker-assisted selection, and transgenic breeding. However, genomic research also faces limitations due to high costs, technical challenges, and complexity of traits.
Molecular Breeding in Plants is an introduction to the fundamental techniques...UNIVERSITI MALAYSIA SABAH
The document discusses molecular genetics and breeding in plants. It begins by introducing Arabidopsis thaliana as a model plant and describes its small genome size, which was advantageous for early genome sequencing efforts. It notes that the A. thaliana genome contains 5 chromosomes totaling 115 Mbp and encodes 25,498 genes. The document then discusses various aspects of the A. thaliana genome structure, organization, and chromosomes. It also briefly describes the chloroplast and mitochondrial DNA structures. The remainder of the document focuses on introducing concepts in plant genetics and molecular breeding techniques.
MARKER ASSISTED SELECTION IN CROP IMPROVEMENTVinod Pawar
The document summarizes a presentation on marker assisted selection in crop improvement. It begins with an introduction to MAS and its advantages over conventional breeding. It then discusses key aspects of MAS including marker genotyping platforms, MAS breeding schemes such as foreground and background selection to minimize linkage drag, and case studies on MAS for trait pyramiding in rice and introgressing stay-green QTLs in sorghum. The conclusion emphasizes that MAS can be a useful supplement to conventional breeding programs for developing new crop varieties in a time-efficient manner.
molecular markers ,application in plant breedingSunil Lakshman
1. The document discusses a seminar on applying molecular markers in plant breeding. It defines different types of markers including morphological, cytological, biochemical, and DNA/molecular markers.
2. It describes various molecular marker techniques like RFLP, RAPD, AFLP, and SSR. The techniques differ in characteristics like being dominant or co-dominant.
3. Molecular markers have important applications in plant breeding like marker-assisted selection, genetic diversity analysis, germplasm characterization, variety identification, and gene pyramiding.
4. Two case studies demonstrate the use of SSR markers to study genetic diversity in aromatic rice accessions and identify hybrids in sunflower. Specific markers were
This document discusses the use of marker-assisted selection (MAS) in plant breeding. It begins by outlining some key challenges in plant breeding, then describes how MAS can accelerate the breeding cycle by allowing selection at early generations. It provides details on different types of MAS, including marker-assisted backcrossing, pyramiding of multiple genes, and early generation selection. Examples are given of MAS being used to introgress submergence tolerance and salinity tolerance genes into rice varieties. The document also discusses some reasons for the low impact of MAS to date, such as insufficient linkage between markers and traits.
Marker assisted selection (MAS) uses DNA markers linked to traits of interest to assist plant breeders in selecting desirable plants. MAS can increase the efficiency and precision of plant breeding by allowing selection at early generations or at the seedling stage before phenotypic selection. It also reduces the influence of environmental effects and allows selection of homozygous plants. While MAS has advantages over conventional breeding, its use in actual breeding programs remains limited due to technical and cost constraints. Further optimization and integration of molecular genetics with plant breeding is needed to fully realize the potential of MAS.
Marker assisted selection (MAS) is a technique used in animal breeding that uses genetic markers linked to traits of interest to indirectly select desirable individuals. MAS can improve traits more efficiently than traditional breeding by selecting early in an individual's life. The key advantages of MAS are that it allows selection based on traits that are difficult to measure, for recessive genes, and faster than phenotypic selection. Future challenges include reducing costs and developing methods for large-scale genotyping to implement MAS in large breeding populations.
Marker Assisted Selection in Crop BreedingPawan Chauhan
Marker Assisted Selection is a value addition to conventional methods of Crop Breeding. It has been gaining importance in plant breeding with new generation of plant breeders and to get accurate and fast desired result from plant breeding.
Multiple inbred founder lines are inter-mated for several generations prior to creating inbred lines, resulting in a diverse population whose genomes are fine scale mosaics of contributions from all founders.
This document discusses marker-assisted backcrossing (MAB) for introgressing traits from a donor parent into a recipient line. MAB uses DNA markers linked to target genes/QTLs to aid in selection. Markers can be used for foreground selection of target genes, background selection to recover the recipient genome, and recombinant selection to minimize linkage drag. A case study is described where MAB was used over multiple generations to introgress 5 drought resistance QTLs from a donor rice variety into a recipient variety. Through foreground, background, and recombinant selection using DNA markers, lines were developed with the target QTLs and most of the recipient genetic background.
Diversity array technology (DArT) is a high-throughput marker system that does not require sequence information. DArT arrays have been developed for chickpea, pigeonpea, and groundnut comprising 15,360 clones each. DArT markers showed 35% and 9% polymorphism in chickpea and pigeonpea mapping populations, but are not cost-effective for detecting variation in cultivated germplasm. DArT may be useful for introgressing segments from wild species into elite varieties, as seen with introgressing resistance genes from C. platycarpus into pigeonpea. Next-generation sequencing has also been used to develop SSR markers for trait mapping in these
This document summarizes a seminar on breeding concepts and crop improvement in chickpea. It discusses the floral biology of chickpea, including emasculation and pollination techniques. Breeding objectives for chickpea include increasing yield, biotic and abiotic stress resistance, and quality traits. Key breeding techniques used are mass selection, pure line selection, and hybridization methods like bulk hybridization and pedigree breeding. Varieties developed through these techniques with important traits are mentioned. The document provides information on the present uses of chickpea and production constraints.
QTL is a gene or the chromosomal region that affects a quantitative trait, which should be polymorphic (have allelic variation) to have an effect in a population, must be linked to a polymorphic marker allele to be detected. The QTL mapping consists of 4 steps, like the development of mapping population, generation of polymorphic marker data set among the parents, construction of linkage map, and finally the QTL analysis
All the above steps are described in these slides very briefly along with two case studies.
Introduction:
Proposed by Meuwissen et al. (2001)
GS is a specialized form of MAS, in which information from genotype data on marker alleles covering the entire genome forms the basis of selection.
The effects associated with all the marker loci, irrespective of whether the effects are significant or not, covering the entire genome are estimated.
The marker effect estimates are used to calculate the genomic estimated breeding values (GEBVs) of different individuals/lines, which form the basis of selection.
Why to go for genomic selection:
Marker-assisted selection (MAS) is well-suited for handling oligogenes and quantitative trait loci (QTLs) with large effects but not for minor QTLs.
MARS attempts to take into account small effect QTLs by combining trait phenotype data with marker genotype data into a combined selection index.
Based on markers showing significant association with the trait(s) and for this reason has been criticized as inefficient
The genomic selection (GS) scheme was to rectify the deficiency of MAS and MARS schemes. The GS scheme utilizes information from genome-wide marker data whether or not their associations with the concerned trait(s) are significant.
GEBV: GenomicEstimated Breeding Values-
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Gene-assisted genomic selection:
A GS model that uses information about prior known QTLs, the targeted QTLs were accumulated in much higher frequencies than when the standard ridge regression was used
The sum total of effects associated with all the marker alleles present in the individual and included in the GS model applied to the population under selection
Calculated on a single individual basis
Population used:
Training population: used for training of the GS model and for obtaining estimates of the marker-associated effects needed for estimation of GEBVs of individuals/lines in the breeding population.
Breeding population: the population subjected to GS for achieving the desired improvement and isolation of superior lines for use as new varieties/parents of new improved hybrids.
Training population-
large enough: must be representative of the breeding population: max. trait variance with marker : by cluster analysis
should have either equal or comparable LD, LD decay rates with breeding populations
Updated by including individuals/lines from the breeding population
Training more than one generation
Low colinearity between markers is needed since high colinearity tends to reduce prediction accuracy of certain GS models. (colinearity disturbed by recombination)
Within the last twenty years, molecular biology has revolutionized conventional breeding techniques in all areas. Biochemical and Molecular techniques have shortened the duration of breeding programs from years to months, weeks, or eliminated the need for them all together. The use of molecular markers in conventional breeding techniques has also improved the accuracy of crosses and allowed breeders to produce strains with combined traits that were impossible before the advent of DNA technology
This document discusses quantitative trait loci (QTL) mapping. It explains that QTL mapping can identify the genomic regions linked to quantitative traits, analyze the effects of QTLs, and provide information on the number, location, effects, and interactions of QTLs. The key aspects of QTL mapping covered are the objectives, principles, analysis methods, required resources like mapping populations, and applications in plant breeding and genetics research.
MARKER-ASSISTED BREEDING FOR RICE IMPROVEMENTFOODCROPS
This document discusses marker-assisted breeding for rice improvement. It begins with an outline of the topics to be covered, which include the theory and practice of marker-assisted selection, marker-assisted breeding schemes, and a case study of marker-assisted backcrossing done at IRRI. The first section defines marker-assisted selection and describes its advantages over phenotypic selection, such as earlier selection and greater reliability. Subsequent sections discuss specific marker-assisted breeding schemes like backcrossing, pyramiding traits, and early generation selection. The document concludes with details of IRRI's case study using markers to backcross a submergence tolerance gene into popular rice varieties.
I would like to share this presentation file.
Some basics information regarding to molecular plant breeding, hope this help the beginner who start working in this field.
Thanks for many original source of information (mainly from slideshare.net, IRRI, CIMMYT and any paper received from professor and some over the internet)
This document discusses allele mining as a technique for improving crops. It defines allele mining as identifying allelic variation within genetic resources collections to find superior alleles. There are two main approaches - TILLING based allele mining which uses mutagenized populations and enzymatic cleavage to find mutations, and sequencing-based allele mining which uses PCR and sequencing to identify natural variation. Both have benefits and limitations. Applications of allele mining include finding alleles for resistance, abiotic stress tolerance, and improved yield and quality. Overall, allele mining is a promising approach for utilizing genetic resources to discover variants that can aid crop breeding.
Association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of linkage disequilibrium to link phenotypes to genotypes.Varioius strategey involved in association mapping is discussed in this presentation
Genomics refers to the study of the entire genome of an organism. It deals with mapping genes on chromosomes and sequencing entire genomes. While work on genomics began with prokaryotes like bacteria, research has now been conducted on crop plants like rice and Arabidopsis thaliana. Genomics is an interdisciplinary field that uses tools from molecular biology, robotics, and computing to study genomes. It provides information on genome size, gene number, gene function, and evolution. Genomics has applications in crop improvement through gene mapping, marker-assisted selection, and transgenic breeding. However, genomic research also faces limitations due to high costs, technical challenges, and complexity of traits.
Molecular Breeding in Plants is an introduction to the fundamental techniques...UNIVERSITI MALAYSIA SABAH
The document discusses molecular genetics and breeding in plants. It begins by introducing Arabidopsis thaliana as a model plant and describes its small genome size, which was advantageous for early genome sequencing efforts. It notes that the A. thaliana genome contains 5 chromosomes totaling 115 Mbp and encodes 25,498 genes. The document then discusses various aspects of the A. thaliana genome structure, organization, and chromosomes. It also briefly describes the chloroplast and mitochondrial DNA structures. The remainder of the document focuses on introducing concepts in plant genetics and molecular breeding techniques.
MARKER ASSISTED SELECTION IN CROP IMPROVEMENTVinod Pawar
The document summarizes a presentation on marker assisted selection in crop improvement. It begins with an introduction to MAS and its advantages over conventional breeding. It then discusses key aspects of MAS including marker genotyping platforms, MAS breeding schemes such as foreground and background selection to minimize linkage drag, and case studies on MAS for trait pyramiding in rice and introgressing stay-green QTLs in sorghum. The conclusion emphasizes that MAS can be a useful supplement to conventional breeding programs for developing new crop varieties in a time-efficient manner.
molecular markers ,application in plant breedingSunil Lakshman
1. The document discusses a seminar on applying molecular markers in plant breeding. It defines different types of markers including morphological, cytological, biochemical, and DNA/molecular markers.
2. It describes various molecular marker techniques like RFLP, RAPD, AFLP, and SSR. The techniques differ in characteristics like being dominant or co-dominant.
3. Molecular markers have important applications in plant breeding like marker-assisted selection, genetic diversity analysis, germplasm characterization, variety identification, and gene pyramiding.
4. Two case studies demonstrate the use of SSR markers to study genetic diversity in aromatic rice accessions and identify hybrids in sunflower. Specific markers were
This document discusses the use of marker-assisted selection (MAS) in plant breeding. It begins by outlining some key challenges in plant breeding, then describes how MAS can accelerate the breeding cycle by allowing selection at early generations. It provides details on different types of MAS, including marker-assisted backcrossing, pyramiding of multiple genes, and early generation selection. Examples are given of MAS being used to introgress submergence tolerance and salinity tolerance genes into rice varieties. The document also discusses some reasons for the low impact of MAS to date, such as insufficient linkage between markers and traits.
Marker assisted selection (MAS) uses DNA markers linked to traits of interest to assist plant breeders in selecting desirable plants. MAS can increase the efficiency and precision of plant breeding by allowing selection at early generations or at the seedling stage before phenotypic selection. It also reduces the influence of environmental effects and allows selection of homozygous plants. While MAS has advantages over conventional breeding, its use in actual breeding programs remains limited due to technical and cost constraints. Further optimization and integration of molecular genetics with plant breeding is needed to fully realize the potential of MAS.
Marker assisted selection (MAS) is a technique used in animal breeding that uses genetic markers linked to traits of interest to indirectly select desirable individuals. MAS can improve traits more efficiently than traditional breeding by selecting early in an individual's life. The key advantages of MAS are that it allows selection based on traits that are difficult to measure, for recessive genes, and faster than phenotypic selection. Future challenges include reducing costs and developing methods for large-scale genotyping to implement MAS in large breeding populations.
TILLING (Targeting Induced Local Lesions IN Genomes) is a reverse genetics technique that uses chemical mutagenesis and screening to identify point mutations in genes of interest. It involves mutagenizing an organism's genome with chemicals like EMS, pooling DNA from mutagenized individuals, amplifying target genes via PCR, treating products with enzymes like CEL1 to detect mutations, and analyzing cleavage products on gels to find mutations. TILLING has been used to identify mutations in many crops to determine gene function and discover traits like disease resistance. It provides an efficient way to study gene function without transgenic approaches.
The document discusses various biotechnological interventions for improving fruit crops. It begins with an introduction to fruit production and its economic importance. It then discusses limitations of traditional breeding methods and how biotechnology can help overcome these limitations. Various biotechnological techniques for fruit crop improvement are described, including genetic engineering techniques like transgenics, cisgenics, and genome editing using CRISPR-Cas. Molecular marker techniques like marker-assisted selection are also discussed. Examples of using these techniques in crops like apple, pear, and papaya are provided.
1. The document discusses biotechnological interventions for crop improvement in fruit crops. It describes various conventional and biotechnological methods for fruit crop breeding including molecular markers, genetic engineering, and marker-assisted selection.
2. Molecular markers like SSRs, SNPs, and RAPDs can be used for genetic mapping, marker-assisted selection, and gene cloning in fruit crops. The document provides examples of using SSR markers for mapping genes controlling fruit traits in papaya and strawberry.
3. Marker-assisted selection allows shortening the breeding cycle by selecting genotypes with desired traits based on their marker profile, without needing to wait for phenotypic evaluation.
B4FA 2012 Nigeria: Cassava Research in Nigeria - Emmanual Okogbeninb4fa
Presentation by Dr Emmanuel Okogbenin, National Root Crops Research Centre, Umudike, Nigeria
Delivered at the B4FA Media Dialogue Workshop, Ibadan, Nigeria - September 2012
www.b4fa.org
This document provides an outline for a presentation on Targeting Induced Local Lesions In Genomes (TILLING). TILLING is a technique that combines chemical mutagenesis with high-throughput screening to induce and identify point mutations in genes of interest. The presentation covers the principle, steps, applications, merits, and demerits of the TILLING technique. It involves chemically mutagenizing an organism using EMS, screening pooled DNA samples to detect mutations using enzymes like CEL1, and identifying mutant individuals. TILLING has applications in functional genomics, genetic engineering, and evaluating genetic diversity. It provides a way to study gene function without transgenics.
This document provides an overview of transgenic fruit plants. It discusses the history of transgenic plants, how they differ from traditional breeding methods, and why transgenic fruit crops are developed. The document outlines the process of plant transformation and lists some deregulated transgenic fruit crops. It also discusses production and adoption rates of transgenic fruits and provides case studies on papaya and plum. The document notes both advantages and constraints of transgenic plants and concludes by discussing alternative technologies.
Targeting Induced Local Lesions IN Genomes (TILLING) is a combined tool of plant mutagenesis and DNA Biology to investigate useful mutations at Genomic level. First time used for cotton improvement.
TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identify point mutations in regions of interest.
This document provides an overview of the TILLING (Targeted Induced Local Lesions IN Genome) technique. TILLING combines chemical mutagenesis with PCR screening to identify point mutations in genes of interest. It has been used successfully in plants like Arabidopsis thaliana and Lotus japonicus to generate allelic series and study gene function. The document discusses the TILLING methodology, including EMS mutagenesis to generate populations, DNA pooling, PCR amplification of target regions, detection of mutations via CEL1 enzyme cleavage, and sequencing. Advantages of TILLING include its applicability to any organism and ability to saturate genes with mutations without excessive DNA damage. Eco-TILLING is also
TILLING AND ECO TILLING IN CROP IMPROVEMENT.pptxrushitahakik1
TILLING AND ECO TILLING in crop Improvement
A Reverse genetics Tool that enhences the potential to introduce specific mutation in oplants in order to improve crop diversity. i.e. Biotechnology beyound Genetically Modified crops.
Marker-assisted selection (MAS) uses molecular markers linked to genes or traits of interest to select desirable plants. MAS can reduce the time needed for variety development compared to conventional breeding by allowing early generation selection. The success of MAS depends on the close linkage between markers and target genes. MAS has been used successfully in crops like rice, maize, and chickpeas to develop varieties with improved disease resistance and other traits. While powerful, MAS also has limitations like the need for accurate marker-trait linkage and potential recombination between markers and genes.
This document discusses current trends in plant breeding. It begins by defining plant breeding as the genetic improvement of crops using both traditional and modern techniques to select for desired traits. It then provides background on the history of plant breeding, including the Green Revolution. The document outlines various modern breeding technologies like phenomics, proteomics, transcriptomics, genetic modification, and the role of bioinformatics in data analysis. It discusses using these omics approaches and genome sequencing to enable a second Green Revolution with crops that are higher yielding, more nutritious, and tolerant of environmental stresses. The goal is to produce more food to feed a growing global population in a sustainable way.
A powerful non-transgenic reverse genetics method that combines chemical mutagenesis with PCR based screening to identify point mutations in regions of interest.
EcoTILLING is a molecular technique that is similar to TILLING, except that its objective is to uncover natural genetic variation as opposed to induced mutations.
This document summarizes a study on marker assisted selection for disease resistance in legume crops. It discusses marker assisted selection (MAS) and its advantages over conventional breeding. MAS allows for indirect selection of traits using DNA markers linked to genes or traits of interest. It also describes specific examples of using MAS to develop disease resistance in pea and common bean crops by mapping genes conferring resistance to powdery mildew in pea and rust resistance in common bean. The studies aimed to validate DNA markers for use in MAS breeding programs to more efficiently develop legume varieties with improved disease resistance.
This document provides an overview of plant biotechnology techniques. It discusses how genes can be manipulated by identifying genes that control traits of interest or modifying existing genes. Genes are then introduced into organisms using transformation methods like Agrobacterium or gene guns. Transformation cassettes containing the gene of interest and selection markers are used. The document explains this process and provides examples like making crops resistant to herbicides or increasing vitamin levels. It also notes there is public controversy around developing and releasing transgenic organisms.
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3. TILLING (Targeting Induced Local Lesion
IN Genome)
TILLING was first developed for Arabidopsis as a novel reverse genetic
technique (Clair McCallum et al. 2000)
It is a method in molecular biology that allows direct identification of
mutation in a specific gene
It is reverse genetic method that combines chemical mutagenesis (EMS,
ENU) with high throughput genome-wide screening for point mutation
detection in gene of interest
Reverse genetics is-
DNA sequence Protein Phenotypes
AGCTCAATCAGATAATC
TCGAGTTAGTCTATTAG
4. Heterozygote mutation were detected at twice the
rate of homozygote mutation
It is the method for finding mutations produced by
chemical mutagen in specific genes
Tilling has since been used as a reverse genetic
method in other organisms such as zebrafish,
corn,wheat, rice soyabean, and tomato etc
5. 1. Seeds (Arabidopsis) treated with chemical mutagens
(EMS, ENU)
2. Development of M1 and M2 generation
3. DNA extracted from individual M2 plant
4. Creation of DNA pool
5. PCR amplification of region of interest (Make primers
flanking gene of interest)
6. Denature DNA from pools of mutant lines
Steps in TILLING
6. 7. Allow to hybridize to wild-type DNA or formation of
heteroduplex
8. Detect mismatches in hybridized DNA
Denaturing HPLC
Cel I enzyme cuts at mismatches
9. Identification of the mutant individuals and
sequencing of the mutant PCR product.
7. WT
mutant
gene Z
gene Z WT
mutant
PCR amplification
from wild type
and mutant
EMS
mutagenize
seed
TILLING Work flow
8. ATGCGGACTG
|||||| |||
TACGCCGGAC
ATGCGG CTG
|||||| |||
TACGCC GAC
+
Denature DNA from
pools of mutant lines
Allow to hybridize to
wild-type DNA
Detect
mismatches in
hybridized DNA
Sequence to identify
site of mutation
DHPLC
Cel 1
9. Mute TILLING- mutagenesis–based reverse genetic
TechTILLING- the TILLING process
Veggie TILLING- TILLING in vegetatively propagated plant
In silico TILLING
I TILLING- individualized TILLING
Eco TILLING
Types of TILLING
10. The Eco TILLING techniques allows polymorphism in target
genes of natural population to be quickly identified
It facilitates the screening of gene bank collections for
desired traits
This process was introduced by Comai.et.al (2004) using A.
thaliana and given the name eco TILLING
Eco TILLING
11. Both natural and mutagenized populations in any
organism can be screened
High throughput screening capacity
99% of mutations from alkylation of guanine induced
by EMS reported as G/C to A/T transition
Small population require to screen several mutation
Time and saving
No transgenic manipulations required.
Advantages of TILLING
30. Introduction
Normal maize - deficiency in two essential amino acids (lysine and
tryptophan) and high leucine–isoleucine ratio.
Breakthrough came in the 1960s, discovery maize mutant opaque2
(Mertz et al., 1964)
Encodes a transcriptional factor that regulates the expression of zein
genes and a gene encoding a ribosomal inactivating protein (Schmidt et
al., 1990)
Reduces the level of 22-kD alpha-zeins while increasing the content of
non zein proteins particularly, EF-1 alpha, which is positively correlated
with lysine content in the endosperm (Habben et al., 1995).