This document discusses crop genetic resources and genomic resources. It provides background on plant genetic resources, genetic diversity, genetic erosion, and conservation efforts. It then shifts to discussing genomic resources, including sequenced crop plant genomes and genomic tools. Examples of comparative and translational genomics are also presented. The document concludes with a case study on promoter analysis of the PDI gene in wheat and related species.
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.
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.
An overview of agricultural applications of genome editing: Crop plantsOECD Environment
The presentation gives an overview of genome editing applications in relation to crop plants. The aim is to have a better understanding of the specific features of genome editing in comparison with classical breeding and genetic engineering techniques. It will give an overview of some examples of agricultural applications that may be on or close to the market or under research and development. It will also consider the possibility of foreseeing future applications (e.g. variations in CRISPR/Cas applications, DNA-free application, agricultural pest control), if possible.
Molecular Breeding in Plants is an introduction to the fundamental techniques...UNIVERSITI MALAYSIA SABAH
This slide describe the process of molecular breeding in plants which involves the application of molecular markers for Marker Assisted Selection and Marker Assisted Breeding.
Presentation delivered by Dr. Jesse Poland (Kansas State University, USA) at Borlaug Summit on Wheat for Food Security. March 25 - 28, 2014, Ciudad Obregon, Mexico.
http://www.borlaug100.org
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
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.
A concise and well fabricated presentation the current techniques used for plant genome editing including CRISPER/cas9 system, TALENS, TELES, ZINC FINGER NUCLEASES(ZFN), HEJ (homologous endjoing) and many other high throughout techniques along references.
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)
Gene stacking is a type of gene cloning that refers to the process of combining two or more genes of interest into a single plant. The emerging combined traits from this process are called stacked traits. A genetically engineered crop variety that bears stacked traits is called a biotech stack or simply stack.
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
The presentation was done as part of the course STAT 504 titled Quantitative Genetics in Second Semester of MSc. Agricultural Statistics at Agricultural College, Bapatla under ANGRAU, Andhra Pradesh
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
An overview of agricultural applications of genome editing: Crop plantsOECD Environment
The presentation gives an overview of genome editing applications in relation to crop plants. The aim is to have a better understanding of the specific features of genome editing in comparison with classical breeding and genetic engineering techniques. It will give an overview of some examples of agricultural applications that may be on or close to the market or under research and development. It will also consider the possibility of foreseeing future applications (e.g. variations in CRISPR/Cas applications, DNA-free application, agricultural pest control), if possible.
Molecular Breeding in Plants is an introduction to the fundamental techniques...UNIVERSITI MALAYSIA SABAH
This slide describe the process of molecular breeding in plants which involves the application of molecular markers for Marker Assisted Selection and Marker Assisted Breeding.
Presentation delivered by Dr. Jesse Poland (Kansas State University, USA) at Borlaug Summit on Wheat for Food Security. March 25 - 28, 2014, Ciudad Obregon, Mexico.
http://www.borlaug100.org
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
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.
A concise and well fabricated presentation the current techniques used for plant genome editing including CRISPER/cas9 system, TALENS, TELES, ZINC FINGER NUCLEASES(ZFN), HEJ (homologous endjoing) and many other high throughout techniques along references.
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)
Gene stacking is a type of gene cloning that refers to the process of combining two or more genes of interest into a single plant. The emerging combined traits from this process are called stacked traits. A genetically engineered crop variety that bears stacked traits is called a biotech stack or simply stack.
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
The presentation was done as part of the course STAT 504 titled Quantitative Genetics in Second Semester of MSc. Agricultural Statistics at Agricultural College, Bapatla under ANGRAU, Andhra Pradesh
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
Ewa Zimnoch-Guzowska's presentation in the framework of the expert consultati...cwr_use
The expert consultation on the use of crop wild relatives for pre-breeding in potato was a workshop organized by the Global Crop Diversity Trust in collaboration with CIP and took place from the 22nd – 24th of February 2012.
Root genetic research and its application in plant breeding or crop improvementOm Prakash Patidar
UNIVERSITY OF AGRICULTURAL SCIENCES, DHARWAD
DEPARTMENT OF GENETICS AND PLANT BREEDING Master’s seminar-II
Root genetic research and its applications in plant breeding
Speaker: Om Prakash Patidar Date: 20/03/2015 ID No.: PGS13AGR6140 Time: 3:00 PM
Synopsis
Roots play an essential role in the acquisition of water and minerals from soils. Root system architecture (RSA), the spatial configuration of a root system in the soil, is used to describe the shape and structure of root system. Its importance in plant productivity lies in the fact that major soil resources are heterogeneously distributed in the soil, so that the spatial deployment of roots will substantially determine the ability of a plant to secure edaphic resources. Measuring crop root architecture and assaying for changes in function can be challenging, but examples have emerged showing that modifications to roots result in higher yield and increased stress tolerance.1
A marker-assisted back-crossing (MABC) breeding programme was conducted to improve the root morphological traits, and thereby drought tolerance, of the Indian upland rice variety, Kalinga III. The donor parent was Azucena, an upland japonica variety from Philippines. Five segments on different chromosomes were targeted for introgression; four segments carried QTLs for improved root morphological traits and the fifth carried a recessive QTL for aroma. It significantly increased root length under both irrigated and drought stress treatments.2
Alteration of root system architecture improves drought avoidance through the cloning and characterization of DEEPER ROOTING 1 (DRO1), a rice quantitative trait locus controlling root growth angle. Higher expression of DRO1 increases the root growth angle, whereby roots grow in a more downward direction. Introducing DRO1 into a shallow-rooting rice cultivar by backcrossing enabled the resulting line to avoid drought by increasing deep rooting, which maintained high yield performance under drought conditions relative to the recipient cultivar.3
GmEXPB2, A vegetative -expansin gene, clone from a Pi starvation-induced soybean cDNA library. GmEXPB2 was found to be primarily expressed in roots, and was highly induced by Pi starvation, and the induction pattern was confirmed by GUS staining in transgenic soybean hairy roots. Results from intact soybean composite showed that GmEXPB2 is involved in hairy root elongation, and subsequently affects plant growth and P uptake, especially at low P levels.4
Candidate Aluminum tolerance proteins include organic acid efflux transporters, with the organic acids forming non-toxic complexes with rhizosphere aluminum. ge
The role of ex situ crop diversity conservation in adaptation to climate changeLuigi Guarino
Keynote delivered on behalf of Cary Fowler at international conference on Food Security and Climate Change in Dry Areas -- 1-4 February 2010 -- Amman, Jordan. Thanks to Colin Khoury for putting this together.
Genetic Variability, Heritability And Genetic Advance For Vegetable Yield And...Premier Publishers
The present study was carried out to estimate the genetic variability for vegetable yield and yield-related traits among Ethiopian kale accessions. The experiment was carried out using 7x7 simple lattice design at Debre zeit Agricultural Research Center during 2017 main cropping season. The analysis of variance revealed highly significant differences (p<0.01) among accessions for all traits except days to second leaf picking. High genotypic coefficient of variation and phenotypic coefficient of variation were estimated for the number of leaves per plant, fresh leaf weight, dry leaf matter content, fresh biomass and leaf yield. High broad sense heritability coupled with high Genetic advance as the percent of mean were obtained for the number of leaves per plant, fresh leaf weight, dry leaf matter content, leaf width, leaf petiole length, leaf petiole thickness, fresh biomass and leaf yield. It can be concluded that variation generated for these traits is mainly due to genetic and moderate role of environmental factors and these were the most important for selection criteria in developing high yielding Ethiopian kale accession. In general, the present study revealed the presence of variability among accession for most studied traits.
International Journal of Engineering and Science Invention (IJESI)inventionjournals
International Journal of Engineering and Science Invention (IJESI) is an international journal intended for professionals and researchers in all fields of computer science and electronics. IJESI publishes research articles and reviews within the whole field Engineering Science and Technology, new teaching methods, assessment, validation and the impact of new technologies and it will continue to provide information on the latest trends and developments in this ever-expanding subject. The publications of papers are selected through double peer reviewed to ensure originality, relevance, and readability. The articles published in our journal can be accessed online.
Life on earth is dependent on plants, which are a crucial component of all ecosystems. Not only they are the basis of world food, but also can provide us fuel, clothes and medicine and play a major role in atmosphere and water purification and prevention of soil erosion. Plants are part of our natural heritage and it is our responsibility to preserve and protect them for future generations.
It is estimated that up to 100,000 plants, representing more than one third of all the world's plant species, are currently threatened or face extinction in the wild. In Europe, particularly, biodiversity is seriously threatened. Biotechnological approaches offer several conservation possibilities which have the potential to support in situ protection strategies and provide complementary conservation options.
Estimate of Genetic Variability Parameters among Groundnut (Arachis hypogaea ...Premier Publishers
Sixteen groundnut genotypes (including local check) were evaluated for quantitative parameters. The crop was sown during 2015 wet season in Ethiopia across four locations. The experiment was laid out in Randomized Complete Block Design with three replications. Twelve quantitative parameters were studied. The analysis of variance revealed the prevalence of significant difference among the genotypes for all studied parameters. Based on mean performance of genotypes Beha gudo, Manipeter and Werer-962 were found to be best for grain yield in kg/ha. High to moderate estimates of genotypic coefficient of variation (GCV) and phenotypic coefficient of variation (PCV) were exhibited by all characters except for SHP and NSP indicating that those characters could be used as selection indices for crop improvement. High heritability was observed for 100SW (91.2%), AGBP (90.3%), NBP (90.2%), PH (89.4%), NMP (86.8%), NSPOD (85.7%), HI (83.7%) and KY (79.7%) accompanied by high genetic advance indicating the predominant role of additive gene action and the possibilities of effective selection for the improvement of groundnut genotypes based on these characters. Low broad sense heritability and low genetic advance was observed only for SHP and NSP indicating low genetic potentials for these characters and non-additive gene effect prevails.
Underutilized Legumes: Global Status, Challenges and Opportunities for Harnes...apaari
Underutilized Legumes: Global Status, Challenges and Opportunities for Harnessing Potential Benefits by JC Rana, Bioversity International, Central and South Asia Office - Regional Expert Consultation on Underutilized Crops for Food and Nutritional Security in Asia and the Pacific November 13-15, 2017, Bangkok
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
Exploiting Artificial Intelligence for Empowering Researchers and Faculty, In...Dr. Vinod Kumar Kanvaria
Exploiting Artificial Intelligence for Empowering Researchers and Faculty,
International FDP on Fundamentals of Research in Social Sciences
at Integral University, Lucknow, 06.06.2024
By Dr. Vinod Kumar Kanvaria
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
A Strategic Approach: GenAI in EducationPeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
A workshop hosted by the South African Journal of Science aimed at postgraduate students and early career researchers with little or no experience in writing and publishing journal articles.
This slide is special for master students (MIBS & MIFB) in UUM. Also useful for readers who are interested in the topic of contemporary Islamic banking.
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
1. Crop Plants Genetic and Genomic
Resources - Two Sides of the Same Coin
Arun Prabhu Dhanapal
[Fritschi Lab]
2. Outline of today‟s talk
• Plant Genetic Resources
• Genetic Diversity
• Genetic Erosion
• Conservation of PGR
• Value of CGR
• Genomic Resources
• Genomic Tools
• Sequencing Technologies
• Comparative and Translational Genomics
• Promoter study in PDI gene
3. Total Number of Plants
Name of Plant Species Purpose
250,000-400,000 Identified as higher plant species
7000 Cultivated plant species
150 Grown commercially
30 Feeding the world
12 75% of food
4 50 % of food we eat
The Guardian, 2010; FAO, 2007
4. Plant Genetic Resources (PGR)
• The PGR include primitive forms of cultivated plant
species and landraces, modern cultivars, obsolete
cultivars, breeding lines and genetic stocks, weedy
types and related wild species
(FAO, 1983; IPGRI, 1993).
• Crop genetic resources are used by breeders to
develop new and improved varieties for farmers.
• Genetic resources are constantly required as inputs
into the continuing process of enhancement through
selective breeding.
5. Genetic Diversity
• Genetic diversity is defined as variations in the genetic
composition of individuals within or among species.
• Diversity of genes within species increases its ability
to adapt to adverse environmental conditions. When
varieties or populations of these species are destroyed,
the genetic diversity within the species is diminished.
• Conservation of crop genetic resources is needed,
given their critical role in agricultural production.
6.
7. Genetic erosion
• The loss of genetic diversity in a species is called as
genetic erosion, and reason for this decline in
diversity has been the loss of landraces and wild
relatives of cultivated crops.
• In many cases, habitat destruction has narrowed the
genetic variability of species lowering the ability to
adapt to changed environmental conditions.
• The use of land to preserve habitats for wild relatives
remains undervalued compared with alternative uses
such as clearing for agricultural or urban use.
8. Conservation of genetic resources
• Agriculture is becoming more and more intensified
and location specific, crop improvement objectives
are also becoming more and more complex.
• All aspects related to genetic resources
(collection, conservation, evaluation, management
and utilization) are however needed and to be done
eminently.
1) Ex situ conservation – Off-site conservation
Germplasm in a gene bank
2) In situ conservation - On-site conservation
Nature or biosphere reserves and national parks
12. Value of Crop Genetic Resources
• Conserved genetic resources may also have economic
value even if the resources are not currently being
used.
• For example, we may not currently need to use a
particular species of potato occurring naturally in the
Andes. However, information about that species (for
example, that it has genes adapted for high altitudes)
may be of value to agricultural producers in the
future.
• Widespread adoption of genetically uniform crop
varieties makes the crop population more susceptible
to a widespread disease or pest infestation. Genetic
uniformity itself, mean that a variety is more
vulnerable to pest and diseases.
13. • The introgression of genes that reduced plant height and
increased disease resistance in wheat provided the
foundation for the „„Green Revolution‟‟ and demonstrated
the tremendous impact that genetic resources on crop
production.
• „„Norin 10,‟‟ a cultivar from Japan, provided two very
important genes, Rht1 and Rht2, that resulted in the
reduced height (or dwarf) of wheats.
• The incorporation of the Sr2 (Fontana) and Lr34 (Hope)
genes from genetic resources into cultivated wheat varieties
represent milestones in the grain‟s genetic advancement.
> 50% of the wheat varieties has stable resistance.
14. • In USA (1970) the uniformity of the maize crop enabled a
Southern leaf blight to destroy almost US $1,000 million of
maize and reduced yields by as much as 50 percent.
• Resistance to the blight was finally found in the genes of an
African maize variety called Mayorbella (National
Research Council, 1972).
• National Research Council (1993) determined that genetic
uniformity of rice, beans, and many minor crops is still a
major concern.
• > 85 percent of wheat production is susceptible to Ug99
and its variants (CIMMYT & BGRI).
15. Consultative Group of International Agricultural Research
(CGIAR)
• CIAT - Centro Internacional de Agricultura
Tropical, Cali, Colombia. Founded in 1967 to focus on crop
improvement in Latin American lowland tropical agriculture.
Research covers rice, beans, cassava, forages and pasture.
• CIMMYT - Centro Internacional de Mejoramiento de Maíz y
Trigo, Mexico D.F., Mexico. Founded 1966. Focus on crop
improvement in maize, wheat, barley and triticale.
• CIP - Centro Internacional de la Papa, Lima, Peru. Founded 1971.
Focus on potato and sweet potato improvement with special
attention to the ecology of specific mountain regions.
• IPGRI - International Plant Genetic Resources Institute, Rome.
Founded 1974. Conservation of gene pools for crops and
forages.
16. • ICARDA - International Center for Agricultural Researach in the Dry
Areas. Aleppo, Syria. Founded 1977. Focus on improving farming
systems for North Africa and West Asia. Research covers wheat, barley,
chickpea, lentils, pasture legumes and small ruminants.
• ICRISAT - International Crops Research Institute for the Semi-Arid
Tropics, Patancheru, Andhra Pradesh, India. Founded 1972. Focus on
crop improvement, cropping systems in sorghum, millet, chickpea,
pigeonpea and groundnut.
• IITA - International Institute of Tropical Agriculture, Ibadan, Nigeria.
Founded 1967. Focus on crop improvement and land management in
humid and sub-humid tropics, farming systems in maize, cassava,
cowpea, plantain, soybean, rice and yam.
• IRRI - International Rice Research Institute, Manila, The Philippines.
Founded 1960. Research on global rice improvement.
• WARDA - West Africa Rice Development Association, Bouake, Côte
d'Ivoire. Founded 1970. Focus on rice improvement in West Africa, with
research on rice in mangrove and inland swamps, upland conditions,
irrigated conditions.
17. Genomic Resources
• Crop Plant genome sequences and related data
presently with us are valuable Genomic resources.
• Genomics is a discipline in genetics that applies
recombinant DNA, DNA sequencing methods, and
bioinformatics to sequence, assemble, and analyze the
function and structure of genomes (the complete set of
DNA within a single cell of an organism).
• Crop Genomics potentially carries the strength to shape
the future of agriculture and its sustainability
• The better prediction of the phenotype that a particular
genotype will produce is a primary goal of genomics
based breeding
18. Application of Genomics for Genomic Resources
• Mapping the genome of an crop/plant
• Sequencing a single individual or several individuals from a
given species
• Studying genetic variability within species
• Studying genetic similarities across species
• Discovering gene function, and the relationship between
gene structure, protein synthesis, and metabolic pathways
• Studying gene regulation, including gene activation and
gene silencing
• Studying gene interaction and phenomena dependent on
many genes.
19. Genomic Resources
Name of crop plants References
Arabidopsis thaliana and The Arabidopsis Genome Initiative, 2000;
Arabidopsis lyrata Cao et al. 2011; Hu et al. 2011
Oryza sativa ssp indica and japonica Yu et al. 2002; Goff et al. 2002
Poplar (Populus trichocarpa) Tuskan et al. 2006
Grape (Vitis vinifera) Jaillon et al. 2007
Mosses (Physcomitrella patens) Rensing et al. 2007
Lotus (Lotus japonicas) Sato et al. 2008
Papaya (Carica papaya) Ming et al. 2008
Maize (Zea mays) Schnable et al. 2009
Sorghum (Sorghum bicolor) Paterson et al. 2009
Cucumber (Cucumis sativus) Huang et al. 2009
Potato (Solanum tuberosum) The Potato Genome Sequencing Consortium, 2011
Rape seed (Brassica napus) Wang et al. 2011
Cucumber (Cucumis sativus) Wóycicki et al. 2011
Crucifer (Thellungiella parvula) Dassanayake et al. 2011
Cacao (Theobroma cacao) Argout et al. 2011
Castor bean (Ricinus communis) Chan et al. 2011
Apple (Malus domestica) Velasco et al. 2010
Cannabis (Cannabis sativa) van Bakel et al. 2011
Strawberry (Fragaria vesca) Shulaev et al. 2011
Soybeans (Glycine max) Schmutz et al. 2010
Pigeon pea (Cajanaus cajan) Varshney et al. 2011
Alfalfa (Medicago sativa), Young et al. 2011
Date palm (Phoenix dactylifera) Al-Dous et al. 2011
Model Grass (Brachypodium distachyon) International Brachypodium Initiative, 2011
Spike mosses (Selaginella moellendorffii) Banks et al. 2011
20. Update in 2013
Name of Crop Plants References
Tomato(Solanum lycopersicum) The Tomato Genome Consortium 2012
Water Melon (Citrullus lanatus) Guo et al 2013
Peach (Prunus persica) Ahmad et al 2012 and Jun et al 2012
Cotton (Gossypium raimonddi Wang et al 2012
Barley (Hordeum vulgare) The International Barley Genome Sequencing
Consortium (2012)
Foxtail Millet (Setaria italica) Zheng G et al. (2012) Bennetzen J et al. (2012)
Banana (Musa acuminate) D'Hont et al (2012)
• These genomes reveals numerous species-specific details,
including genome size, gene number, patterns of sequence
duplication, a catalog of transposable elements, and syntenic
relationships.
• To understand the complex instructions contained in all these
raw sequence information of the plant genome, large-scale
functional genomics projects are required.
21. Genomic Tools
• Marker Assisted Selection (MAS)
• Quantitative Trait Loci Mapping (QTL Mapping and e QTL Mapping)
• Candidate Gene Mapping & Allele mining
• Targeting induced Local Lesions In Genomes (TILLING) & Eco TILLING
• Association Mapping (GWAS)
• Nested Association Mapping (NAM)
• Multiparental advanced generation intercross (MAGIC)
• Recombinant inbred advanced intercross lines (RIAIL)
• Development in crop genomics play key role in crop improvement in two
general ways.
• A better understanding of the biological mechanisms can lead to new or
improved screening methods for selecting superior genotypes more
efficiently.
• New knowledge can improve the decision-making process for more
efficient breeding strategies.
22. Sequencing Technologies
• Sanger dideoxy sequencing and its modifications
dominated the DNA sequencing field for nearly 30 years.
• In the past 10 years sequence reads has increased from 450
bases to more than 1 kb in the length of Sanger
sequencing.
Varshney, 2009
• The term NGS is used to collectively describe technologies
other than Sanger sequencing that have the potential to
sequence the human and plant genome.
• Sequencing machine are constantly increasing sequence
output in terms of number of reads (bp-base pair), in-
creasing read length, as well as working to improve read
quality.
23. Quick transition of Equipment's
HiSeq2000
ABI 3130 Genome Analyzer IIx
Genetic Analyser Miseq
Genome Analyzer IIx HiSeq2000 Miseq
Output (Gb) 95 600 >1
Yield of error-free data (Gb) 67 400-480 >0.8
Single-end reads 320 Million 2.5 -3 Billion 3.4 Million
Paired-end reads 640 Million 5-6 Billion 6.8 Million
Required input 50 ng with Nextra 50 ng with Nextra 50 ng with Nextra
100ng-1 ug with TrueSeq 100ng-1 ug with 100ng-1 ug with TrueSeq
TrueSeq
Read length 2 x 150 bp 2 x 100 bp 2 x 150 bp
Applications supported Genome, epigenome, Genome, epigenome, Amplicon, small genome,
transcriptome transcriptome clone checking
24. Comparative Genomics
• It is the study of the relationship of genome structure and
function across different species.
• It has advantage in providing information of signatures of
selection to understand the function and evolutionary
processes that act on genomes.
Translational Genomics
• Implies the translation of gene functions from a model
species (Arabidopsis) to a cultivated crop species.
• Genes with a proven or predicted function in a “model”
species (functional candidate genes) or genes that are co-
localized with a trait-locus (positional candidate genes)
could control a similar function or trait in an target crop of
interest.
25.
26. Promoter Study in Classical / Typical PDI Gene
• The Protein Disulfide Isomerase (PDI) gene family
encodes several PDI and PDI-like proteins containing
thioredoxin domains and controlling diversified metabolic
functions, including disulfide bond formation and
isomerisation during protein folding.
• Study of variability in partial promoter region of 700 bp
(Comprising 600 bp of 5‟ upstream putative promoter
region and 100 bp of the first exon of the typical PDI gene.)
• Five accessions, eight plants per accession.
• Triticum uratu (AA)
• Aegilops speltoides (BB)
• Aegilops tauschii (DD)
• Total Number of Sequences = (3×5×8=120)
28. Phylogenetic tree of PDI gene sequences (partial promoter and
partial part of first exon) of Triticum uratu (AA), Aegilops
speltoides (BB) and Aegilpos taushcii (DD)
51
BBC S+EX
IG48766-1 Le banon
IG46812-3 Turke y Aegilops speltoides (BB)
97
80 IG46811-2 Turke y
89
IG46597-5 Syria
69
IG46593-4 Syria
100
DDC S+EX
AE525-1 Iran
AE526-2 Iran Aegilops taushcii (DD)
98
AE527-3 Iran
AE541-4 Iran
71
AE1068-5 Syria
100
AAC S+EX
IG45475-1 Le banon
IG115817-2 Jordan
Triticum uratu (AA)
98
IG44831-3 Syria
IG45108-4 Turke y
IG45477-5 Iran
29.
30. Take Home Message !!
• Present day crop cultivars has led to increased
productivity of crop species, but at the same time has
narrowed their genetic basis.
• Fortunately, wild relatives of crop plants exhibit vast
genetic diversity for adaptation to stressful
environments such as frost, drought and high salt and
metal etc..
THANK YOU
Editor's Notes
It is the process of protecting an endangered species of plant outside its natural habitat; for example, by removing part of the population from a threatened habitat and placing it in a new locationOn-site conservation or the conservation of genetic resources in natural populations of plantspecies, such as forest genetic resources in natural populations of tree species.
"orthodox" desiccation-tolerant seeds and those that have "recalcitrant", desiccation-sensitive seeds
The seed vault is managed under terms spelled out in a tripartite agreement between the Norwegian government, the Global Crop Diversity Trust (GCDT) and the Nordic Genetic Resource Center (NordGen).