Research Program Genetic Gains (RPGG) Review Meeting 2021: Forward Breeding: tools and technologies for accelerating rate of genetic gain By Dr Manish Roorkiwal
Integration of various molecular breeding approaches (MABC, MARS, and GS) in the product development process at ICRISAT. Accelerated rate of genetic gain across all mandate crops by leveraging expertise from various groups inside and outside ICRISAT.
Heterotic group “is a group of related or unrelated genotypes from the same or different populations, which display similar combining ability and heterotic response when crossed with genotypes from other genetically distinct germplasm groups.”
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
FERTILITY RESTORATION IN MALE STERILE LINES AND RESTORER DIVERSIFICATION PROG...Rachana Bagudam
1. FERTILITY RESTORATION IN MALE STERILE LINES AND RESTORER DIVERSIFICATION PROGRAMMES.
2. CONVERSION OF AGRONOMICALLY IDEAL GENOTYPES INTO MALE STERILES.
3. GENERATING NEW CYTONUCLEAR INTERACTION SYSTEM FOR DIVERSIFICATION OF MALE STERILES.
Association genetics‟ or ‟association studies,” or ‟linkage disequilibrium mapping”.
Tool to resolve complex trait variation down to the sequence level by exploiting historical and evolutionary recombination events at the population level.
Natural population surveyed to determine MTA using LD.
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
Heterotic group “is a group of related or unrelated genotypes from the same or different populations, which display similar combining ability and heterotic response when crossed with genotypes from other genetically distinct germplasm groups.”
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
FERTILITY RESTORATION IN MALE STERILE LINES AND RESTORER DIVERSIFICATION PROG...Rachana Bagudam
1. FERTILITY RESTORATION IN MALE STERILE LINES AND RESTORER DIVERSIFICATION PROGRAMMES.
2. CONVERSION OF AGRONOMICALLY IDEAL GENOTYPES INTO MALE STERILES.
3. GENERATING NEW CYTONUCLEAR INTERACTION SYSTEM FOR DIVERSIFICATION OF MALE STERILES.
Association genetics‟ or ‟association studies,” or ‟linkage disequilibrium mapping”.
Tool to resolve complex trait variation down to the sequence level by exploiting historical and evolutionary recombination events at the population level.
Natural population surveyed to determine MTA using LD.
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
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.
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.
Role of Pangenomics for crop ImprovementPatelSupriya
It describes about the role of pangenomics in the crop improvement.It includes pangenome,superpangenome,databases,tools used in pangenomics,utilisation in crop improvement
Quantitative trait loci (QTL) analysis and its applications in plant breedingPGS
Abstract
Many agriculturally important traits such as grain yield, protein content and relative disease resistance are controlled by many genes and are known as quantitative traits (also polygenic or complex traits). A quantitative trait depends on the cumulative actions of many genes and the environment. The genomic regions that contain genes associated with a quantitative trait are known as quantitative trait loci (QTLs). Thus, a QTL could be defined as a genomic region responsible for a part of the observed phenotypic variation for a quantitative trait. A QTL can be a single gene or a cluster of linked genes that affect the trait. The effects of individual QTLs may differ from each other and change from environment to environment. The genetics of a quantitative trait can often be deduced from the statistical analysis of several segregating populations. Recently, by using molecular markers, it is feasible to analyze quantitative traits and identify individual QTLs or genes controlling the traits of interest in breeding programs.
Access to large-scale omics datasets i.e. genomics, transcriptomics, proteomics, metabolomics, phenomics, etc. has revolutionized biology and led to the emergence of systems approaches to advance our understanding of biological processes. With decreasing time and cost to generate these datasets, omics data integration has created both exciting opportunities and immense challenges for biologists, computational biologists, biostatisticians and biomathematicians. Genomics, transcriptomics, proteomics, and metabolomics together they help to bring out the best of characters in plants.
Speed Breeding is new technology to develop plants or breeding materials within a short possible time without affect seed viability and yield performance.
Genomic aided selection for crop improvementtanvic2
In last Several years novel genetic and genomics approaches are expended. Genetics and genomics have greatly enhanced our understanding of the structural and functional aspects of plant genomes.
Research Program Genetic Gains (RPGG) Review Meeting 2021: Current status and...ICRISAT
SNPs designed for validated in mapping populations and breeding lines, Intertek platform. A set of 20 SNP set useful for screening early generation breeding population will be finalized 800 breeding lines from SA, ESA and WCA breeding programs; 2350 lines from ICAR-IIMR-AICRPS Current season -F2s from RxR nurseries from SA program, on-going discussion with ESA and WCA.
Research Program Genetic Gains (RPGG) Review Meeting 2021: Groundnut genomic ...ICRISAT
These high quality genomes are global resource and are being used by all the genomics and breeding researchers across the world including ICRISAT. High density genotyping assays developed and currently been deployed for generating high throughput and high density genotyping data on germplasm and breeding lines.
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.
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.
Role of Pangenomics for crop ImprovementPatelSupriya
It describes about the role of pangenomics in the crop improvement.It includes pangenome,superpangenome,databases,tools used in pangenomics,utilisation in crop improvement
Quantitative trait loci (QTL) analysis and its applications in plant breedingPGS
Abstract
Many agriculturally important traits such as grain yield, protein content and relative disease resistance are controlled by many genes and are known as quantitative traits (also polygenic or complex traits). A quantitative trait depends on the cumulative actions of many genes and the environment. The genomic regions that contain genes associated with a quantitative trait are known as quantitative trait loci (QTLs). Thus, a QTL could be defined as a genomic region responsible for a part of the observed phenotypic variation for a quantitative trait. A QTL can be a single gene or a cluster of linked genes that affect the trait. The effects of individual QTLs may differ from each other and change from environment to environment. The genetics of a quantitative trait can often be deduced from the statistical analysis of several segregating populations. Recently, by using molecular markers, it is feasible to analyze quantitative traits and identify individual QTLs or genes controlling the traits of interest in breeding programs.
Access to large-scale omics datasets i.e. genomics, transcriptomics, proteomics, metabolomics, phenomics, etc. has revolutionized biology and led to the emergence of systems approaches to advance our understanding of biological processes. With decreasing time and cost to generate these datasets, omics data integration has created both exciting opportunities and immense challenges for biologists, computational biologists, biostatisticians and biomathematicians. Genomics, transcriptomics, proteomics, and metabolomics together they help to bring out the best of characters in plants.
Speed Breeding is new technology to develop plants or breeding materials within a short possible time without affect seed viability and yield performance.
Genomic aided selection for crop improvementtanvic2
In last Several years novel genetic and genomics approaches are expended. Genetics and genomics have greatly enhanced our understanding of the structural and functional aspects of plant genomes.
Similar to Research Program Genetic Gains (RPGG) Review Meeting 2021: Forward Breeding: tools and technologies for accelerating rate of genetic gain By Dr Manish Roorkiwal
Research Program Genetic Gains (RPGG) Review Meeting 2021: Current status and...ICRISAT
SNPs designed for validated in mapping populations and breeding lines, Intertek platform. A set of 20 SNP set useful for screening early generation breeding population will be finalized 800 breeding lines from SA, ESA and WCA breeding programs; 2350 lines from ICAR-IIMR-AICRPS Current season -F2s from RxR nurseries from SA program, on-going discussion with ESA and WCA.
Research Program Genetic Gains (RPGG) Review Meeting 2021: Groundnut genomic ...ICRISAT
These high quality genomes are global resource and are being used by all the genomics and breeding researchers across the world including ICRISAT. High density genotyping assays developed and currently been deployed for generating high throughput and high density genotyping data on germplasm and breeding lines.
ICRISAT Global Planning Meeting 2019:Research Program - Genetic Gains by Dr R...ICRISAT
The Global Planning Meeting 2019 focused on implementation plans for modernisation of ICRISAT crop improvement and to review and enhance the existing crop breeding programs, discuss modernization of crop improvement, and strategize how to harness new tools to maximize genetic gains. Innovation systems research was also discussed in detail to ascertain how all the different disciplines in crop improvement, innovation systems and other global and regional programs can work together to contribute to ICRISAT’s mission.
Research Program Genetic Gains (RPGG) Review Meeting 2021: From Discovery to ...ICRISAT
A number of advances in genetics and genomics research of pigeonpea. These advances have enhanced our understanding of structural and functional aspects of genome and also provided us opportunities to deal with constraints impeding production of pigeonpea in precise and faster manner. Availability of the draft genome sequence and large-scale molecular markers has made it possible to map traits of interest in speedy manner. Although germplasm re-sequencing has already been started in pigeonpea, large-scale germplasm including elite breeding line, landraces and wild species is expected to be fully sequenced very soon.
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference DatabaseNathan Olson
"Development of FDA MicroDB: A Regulatory-Grade
Microbial Reference Database" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Heike Sichtig, PhD from the FDA and Luke Tallon from IGS UMSOM.
High data quality and accuracy are recognized characteristics of Sanger re-sequencing projects and are primary reasons that next generation sequencing projects compliment their results by capillary electrophoresis data validation. We have developed an on-line tool called Primer Designer™ to streamline the NGS-to-Sanger sequencing workflow by taking the laborious task of PCR primer design out of the hands of the researcher by providing pre-designed assays for the human exome. The primer design tool has been created to enable scientists using next generation sequencing to quickly confirm variants discovered in their work by providing the means to quickly search, order and receive suitable pre-designed PCR primers for Sanger sequencing. Using the Primer Designer™ tool to design M13-tailed and non-tailed PCR primers for Sanger sequencing we will demonstrate validation of 28-variants across 24-amplicons and 19-genes using the BDD, BDTv1.1 and BDTv3.1 sequencing chemistries on the 3500xl Genetic Analyzer capillary electrophoresis platform.
We recently developed MVRSION for the purpose of using 16S to define microbiome bacterial populations from human, animal, or environmental sources. It is is a methodology that statistically leverages 8, rather than one, 16S hyper-variable regions.
Population Calling: a powerful tool for novel mutation detection in larger sa...GENALICE
Population Calling is a powerful tool for novel mutation detection in larger sample pools. The presentation covers different multi-sample variant calling strategies, infrastructure setup, a showcase of the 3,000 rice genomes project, and a comparison study with other industry tools. For more information, please visit http://www.genalice.com/population-calling/
Golden Helix’s SNP & Variation Suite (SVS) has been used by researchers around the world to do association testing and trait analysis on large cohorts of samples in both humans and other species. As samples size increase to do population-scale genomics, the analysis methods need to adapt to remain computable on your analysis workstation.
One of the most popular methods for determining population structure in SVS is Principal Component Analysis. In this webcast, we review the fundamentals of this methodology, as well as how we have advanced the state of the art by implementing a new “Large Data PCA” capability in SVS, handling over 10 times as many samples as previously possible at a fraction of the time. Join us as we cover:
A review of SVS association testing and trait analysis capabilities
Usage of Principle Component Analysis to discern population structure
Scaling PCA beyond the limitations of computer hardware Other SVS improvements based on ongoing feedback from the user community
SVS continues to move forward as a flexible and powerful tool to perform genotype and Large-N variant analysis. We hope you enjoy this webcast highlighting the exciting new features and select enhancements we have made.
Bioanalytical Capabilities - Thought-Leading Science Armed with the Latest Te...Covance
Helping your drug development program succeed is what we do. Keeping your timeline on track requires scientific expertise, operational experience and up-to-date knowledge of the regulatory environment. Whether you need preclinical or clinical bioanalysis, local support or global capabilities, Covance is the partner that you can trust to help deliver on your bioanalytical timelines every day, every time.
Bioanalytical Capabilities -- Thought-Leading Science Armed with the Latest T...Covance
Helping your drug development program succeed is what we do. Keeping your timeline on track requires scientific expertise, operational experience and up-to-date knowledge of the regulatory environment. Whether you need preclinical or clinical bioanalysis, local support or global capabilities, Covance is the partner that you can trust to help deliver on your bioanalytical timelines every day, every time.
Accelerate Delivery of High Producing Cell LinesMilliporeSigma
Watch the interactive recording here: https://bit.ly/30FTDG0
The quest for a viable upstream process relies on generation of a cell line expressing the protein of interest. Unfortunately, the search for the best-producing clone is often compared with looking for a needle in a haystack. Making this more challenging is the pressure to get it right the first time, quickly and while mitigating risk and costs.
Although a lot of efforts are made on the clonal selection, there is often few to none optimization done on the expression cassette, including promoter and enhancer selection, or signal peptide. The statistical approach on how many clones should be screened to get to a good producer is often overlooked as well.
We combined a new generation of promoters and enhancers to improve strategies on pool and mini pool screening with both CHO-K1 and our own CHOZN® GS which helped deliver high-producing clones in an accelerated timeline. In addition, we are able to begin process development in parallel with cell line development, further reducing timelines.
In this webinar, you will learn:
* How the strategy approach can help reducing the overall timeline of cell line generation
* How we have expanded our platform by designing a completely new vector/cell/process template
* How we have worked on promoters, enhancers, pool/mini-pool approach as well as on timelines from DNA to clone
Watch the interactive recording here: https://bit.ly/30FTDG0
The quest for a viable upstream process relies on generation of a cell line expressing the protein of interest. Unfortunately, the search for the best-producing clone is often compared with looking for a needle in a haystack. Making this more challenging is the pressure to get it right the first time, quickly and while mitigating risk and costs.
Although a lot of efforts are made on the clonal selection, there is often few to none optimization done on the expression cassette, including promoter and enhancer selection, or signal peptide. The statistical approach on how many clones should be screened to get to a good producer is often overlooked as well.
We combined a new generation of promoters and enhancers to improve strategies on pool and mini pool screening with both CHO-K1 and our own CHOZN® GS which helped deliver high-producing clones in an accelerated timeline. In addition, we are able to begin process development in parallel with cell line development, further reducing timelines.
In this webinar, you will learn:
* How the strategy approach can help reducing the overall timeline of cell line generation
* How we have expanded our platform by designing a completely new vector/cell/process template
* How we have worked on promoters, enhancers, pool/mini-pool approach as well as on timelines from DNA to clone
Similar to Research Program Genetic Gains (RPGG) Review Meeting 2021: Forward Breeding: tools and technologies for accelerating rate of genetic gain By Dr Manish Roorkiwal (20)
ICRISAT’s soil laboratory registers with FAO’s International Network on Ferti...ICRISAT
The Charles Renard Analytical Laboratory at ICRISAT has been officially registered with the International Network on Fertilizer Analysis – a network created in December 2020, to build and strengthen the capacity of laboratories in fertilizer analysis and harmonize fertilizer quality standards. Dr Pushpajeet L Choudhari, Manager of the soil laboratory, said that testing serves as a preventive measure to avoid the misuse of fertilizers leading to better soil management.
Uzbek delegation explores climate-resilient crop options for arid, degraded e...ICRISAT
A delegation from Uzbekistan visited ICRISAT headquarters in India in search of a short-duration second crop suited to arid ecologies that mature before winter. The visit aligns with the Government of Uzbekistan’s efforts to increase agricultural production through double cropping. The visitors were briefed on dryland crop options and expressed interest in academic exchanges and internships based on the Institute’s expertise in genomic technologies and dryland agri-food systems.
Indian Ambassador to Niger explores opportunities for South-South cooperationICRISAT
The Ambassador of India to Niger, His Excellency Mr Prem K Nair, visited ICRISAT’s research station at Sadore, to explore opportunities for South-South collaboration. He said that the objective of his visit was to learn about ICRISAT’s activities in Niger and to identify possible areas of cooperation for implementing agri-development initiatives introduced by India.
WFP, ICRISAT to partner on climate-resilience, food security, nutrition and l...ICRISAT
The United Nations World Food Programme (WFP) and the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) will partner on programs and research to improve food, nutrition security and livelihoods in India against the impacts of climate change. A Memorandum of Understanding (MoU) was signed today between Mr. Bishow Parajuli, WFP India Representative and Country Director, and Dr. Jacqueline Hughes, Director General, ICRISAT.
Visit by Sri Lankan Deputy High Commissioner to ICRISAT opens opportunities f...ICRISAT
Dr Doraiswamy Venkateshwaran, Sri Lankan Deputy High Commissioner stationed in Chennai, recently visited the ICRISAT campus in Hyderabad to learn more about the Institute’s science-backed research for dryland agriculture. Along with his team, he visited the genebank and toured the pigeonpea and finger millet field plots, where Dr Prakash Gangashetty and Dr Sobhan Sajja explained to him the research focus and various traits of hybrids and varieties developed by ICRISAT.
UK Ambassador to Niger discusses climate change adaptation and humanitarian i...ICRISAT
Niger needs support for the implementation of climate change adaptation measures,” said Her Majesty’s Ambassador to the Republic of Niger, Ms Catherine Inglehearn while on a recent visit to ICRISAT-Niger. She spoke about the ongoing discussion with the government regarding Niger’s participation at the 26th UN Climate Change Conference of the Parties (COP26) meeting in November 2021 in Glasgow.
New climate-resilient, disease-resistant chickpea varieties coming farmers’ wayICRISAT
Three new chickpea varieties, with enhanced drought tolerance, disease resistance and increased yield, are set to become available to the Indian farmers. These have been notified to be available for cultivation by the Central Varietal Release Committee. Calling for the deployment of ‘fast-forward breeding’, a newly conceived framework that promises faster delivery of varieties to farmers, Dr Rajeev Varshney, Research Program Director – Accelerated Crop Improvement, ICRISAT, who coordinated the integration of genomics-assisted breeding activities for developing these varieties
Deputy Collector gets training on agriculture research at ICRISAT HyderabadICRISAT
Mrs Bikumalla Santoshi, Deputy Collector of Yadadri Bhuvanagiri district in Telangana, India, visited ICRISAT, Hyderabad recently as part of her orientation and training in agricultural research. Mrs Santoshi toured the campus and learnt about the research done on dryland cereals and legumes at ICRISAT’s centers in India as well as Africa.
Cereal-legume value chain stakeholders in WCA meet to develop demand-driven a...ICRISAT
ICRISAT’s Gender Research Program recently brought together breeders, value chain stakeholders and social scientists from Mali, Ghana, Burkina Faso and Nigeria to define priority traits of cultivars of sorghum, millet and groundnut during a 4-day workshop. Prior to the workshop, studies were carried out with the national agricultural research systems (NARS) partners in the above countries, to examine and assess the trait preferences of key stakeholders, especially taking into account the specificity of traits with respect to gender-related needs. The results of these studies were presented during the workshop. The expected output is priority trait demands translated into new market-driven and gender-responsive product profiles for the breeding programs at ICRISAT and NARS.
ICRISAT to share expertise on sorghum production with farmers in SomaliaICRISAT
ICRISAT is collaborating with the Somali Agricultural Technical Group (SATG) to provide technical support for sorghum production in Somalia. The expertise provided includes identification of sorghum varieties suitable for Somalia, provision of breeder seed of the identified varieties and training of SATG staff and their partners in sorghum seed production.
4CAST: New digital tool to enhance farmers’ access to modern varietiesICRISAT
To improve smallholder farmers’ access to new improved varieties, a digital variety catalog tool created by ICRISAT in partnership with public and private institutions was recently launched. Called 4CAST, the tool is a user-friendly data driven platform that gives information about new improved varieties, quality and availability of seeds nationally and regionally. 4CAST, which stands for Digital Tools 4 Cataloguing and Adopting Improved Seed Technologies, also provides stakeholders in seed value chains a digital workflow, decentralized access, real-time tracking of progress, private catalogues as well as seed roadmaps.
New ‘one-stop shop’ team formed to take ICRISAT’S plant breeding program in W...ICRISAT
ICRISAT West and Central Africa has reorganized all disciplines of agronomic research (agronomy, breeding, biotechnology/ genomics, integrated crop management, physiology, sociology, agroeconomics, etc.) under one umbrella called the Crop Improvement Operations Team (CIOT). A “one-stop shop” for all crop improvement operations, the CIOT was launched on Tuesday 24 August 2021 at ICRISAT’s Samanko research station in Mali.
The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) has been awarded the 2021 Africa Food Prize, for work that has improved food security across 13 countries in sub-Saharan Africa. ICRISAT, a CGIAR Research Center, is a non-profit, non-political public international research organization that conducts agricultural research for development in Asia and sub-Saharan Africa with a wide array of partners throughout the world.
Rooting for strong partnerships and participatory extension in Nigeria for ro...ICRISAT
To enhance partnerships and make the extension systems for cereals and legumes production technologies in Nigeria more participatory, the International Institute of Tropical Agriculture (IITA) and ICRISAT recently organized a workshop for agencies implementing the Kano State Agro Pastoral Development Project.
Understanding consumption preferences for sorghum and millets globallyICRISAT
In support of the objectives of the International Year of Millets (2023), a global study, “Prioritizing Regular Intake of Sorghum and Millets (PRISM)”, is being conducted to understand the potential drivers of sorghum and millets consumption. PRISM is a collaborative effort of researchers in the Markets, Institutions and Policy team at ICRISAT, Massachusetts Institute of Technology (MIT) and ICAR-Indian Institute of Millets Research (IIMR) to understand the choices that drive the consumption of these nutricereals and to explore their increased inclusion in diets globally for the good of dryland farmers, human health and the environment.
ICRISAT introduces an invigorated research structure (The research structure ...ICRISAT
A robust, more efficient research structure is part of the reorganization initiative at ICRISAT that aims at building a cohesive and interconnected body of work in agricultural research. The revitalized framework is expected to seamlessly integrate and deliver agricultural research outputs across the drylands of Asia and Africa. The strength of this framework is the deeply interlinked global and regional programs working towards common and interdependent goals.
Training on science communication to engage funders and stakeholdersICRISAT
Communicating research findings to policy makers, peers and civil society is crucial for research uptake and development. To meet this goal, a one-day training session on messaging through newsletters and journal articles was held for participants of the International Training Programme on Climate Change – Mitigation and Adaptation of the Swedish Meteorological and Hydrological Institute (SMHI) at ICRISAT, Mali.
Virtual training in the use of remote sensing for the agriculture sector in P...ICRISAT
A virtual hands-on training program on developing geospatial maps for supporting insurance products using Google Earth Engine and semi-automatic techniques was conducted for participants in Pakistan as part of the project “Strengthening Post-COVID-19 Food Security and Locust Attacks”. The nine participants were from the PARC Agrotech company (PATCO) technical team and crop reporting service teams from Punjab and Sindh in Pakistan. They were introduced to remote sensing and its applications in agriculture. Hands-on training using Google Earth Engine (GEE), Image Processing Software – ERDAS 2015 and various automatic classification techniques was provided along with several applications for using these modern tools.
ICRISAT pleased to share this five-year Strategic Plan 2021-2025 which builds on our extensive partnerships, networking and our understanding of the needs on the ground and sets out our current expertise with our vision for the next five years of a streamlined, targeted research for development institution, working closely with our partners and stakeholders in the private and public sectors.
ICRISAT and HarvestPlus to collaborate on mainstreaming nutrition research an...ICRISAT
ICRISAT and HarvestPlus signed an agreement for scientific and technical collaboration between the two global organizations. Mr Arun Baral, CEO, HarvestPlus, and Dr Jacqueline d’Arros Hughes, Director General, ICRISAT, signed the Memorandum of Understanding, which is made and entered into by IFPRI on behalf of its HarvestPlus Program. On the occasion, Dr Hughes said, After 17 years of fruitful collaboration on biofortification research, we have now decided to elevate this partnership. ICRISAT and HarvestPlus will work together more closely, making available micronutrient-rich varieties, high-quality seed and related technologies to the farming communities and consumers. This will contribute to eliminating micronutrient malnutrition in the drylands.
Jennifer Schaus and Associates hosts a complimentary webinar series on The FAR in 2024. Join the webinars on Wednesdays and Fridays at noon, eastern.
Recordings are on YouTube and the company website.
https://www.youtube.com/@jenniferschaus/videos
RFP for Reno's Community Assistance CenterThis Is Reno
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Preliminary findings _OECD field visits to ten regions in the TSI EU mining r...OECDregions
Preliminary findings from OECD field visits for the project: Enhancing EU Mining Regional Ecosystems to Support the Green Transition and Secure Mineral Raw Materials Supply.
Monitoring Health for the SDGs - Global Health Statistics 2024 - WHOChristina Parmionova
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Working with data is a challenge for many organizations. Nonprofits in particular may need to collect and analyze sensitive, incomplete, and/or biased historical data about people. In this talk, Dr. Cori Faklaris of UNC Charlotte provides an overview of current AI capabilities and weaknesses to consider when integrating current AI technologies into the data workflow. The talk is organized around three takeaways: (1) For better or sometimes worse, AI provides you with “infinite interns.” (2) Give people permission & guardrails to learn what works with these “interns” and what doesn’t. (3) Create a roadmap for adding in more AI to assist nonprofit work, along with strategies for bias mitigation.
Research Program Genetic Gains (RPGG) Review Meeting 2021: Forward Breeding: tools and technologies for accelerating rate of genetic gain By Dr Manish Roorkiwal
1. Forward Breeding: tools and
technologies for accelerating rate
of genetic gain
Manish Roorkiwal
Senior Scientist, Forward Breeding
Research Program- Genetic Gains
5 Jan, 2021
2. Establish and use of high throughput and cost-effective genotyping platforms
Forward breeding-based breeding solutions to crop improvement
Deploy molecular breeding approaches e.g. MAS/MARS/GS in collaboration with the themes on Crop
Improvement and Genomics and Trait Discovery
Collaborate with the theme on Genomics and Trait Discovery to validate identified markers
Convert candidate molecular markers to high-throughput enable marker system
Lead/engage in developing analytical tools, platforms and databases for molecular breeding
Meta-analysis using sequencing data for haplotypes-based selection
Forward Breeding
Integration of various molecular breeding approaches (MABC, MARS, and GS)
in the product development process at ICRISAT.
Accelerated rate of genetic gain across all mandate crops by leveraging
expertise from various groups inside and outside ICRISAT.
Key responsibilities:
4. Forward Breeding
Many lines having undesirable alleles are discarded
Opportunity to the evaluation of fewer lines in later generations
Provides tools, technologies and platforms to deploy markers in breeding
programs for developing improved lines in cost- and time-effective manner
5. Gene Pyramiding
Single gene/QTL introgression
Single backcross DH Scheme
Multi-trait introgression
MES: Marker-evaluated selection
SLS-MAS: Single large scale MAS
Forward Breeding based solutions
6. building a global community of knowledge through workshops, hackathons and cross-training to
transform breeding http://cbsugobii05.tc.cornell.edu/wordpress/
GOBii: A Global Community
A stable, high quality, easy to deploy, genomic data management system,
with a web service layer incorporating BrAPI for integration
Developed and released key tools for breeders
To improve data availability, working to integrate GOBii with breeding
management systems and tools
7. GOBii Tools
GOBii Genomics Data Manager (GDM)
Scalable genomic data management system, and
a marker tools portal to access all GOBii-GDM
tools for data loading, QC, extract & breeding.
GOBii DArT Tools
The GOBii-QC (quality control)
module run by KDCompute is fully
integrated with the GOBii-GDM
system.
GOBii Genomic Selection (GS)
Genomic Selection (GS-Galaxy) Analysis
Pipeline is under active development by
GOBii team and CGIAR contributors using
open-source Galaxy platform.
GOBii JHI Tools
Marker-Assisted Back Crossing (MABC)
module is an open-source platform for
conducting marker-assisted backcross
visualization and selection analysis.
http://cbsugobii05.tc.cornell.edu:6084/x/GQDcAQ
MABC module:
http://flapjack.hutton.ac.uk/en/latest/mabc.html
F1 pedigree verification module:
http://flapjack.hutton.ac.uk/en/latest/pedver_f1s_known_
parents.html
http://galaxy-demo.excellenceinbreeding.org/
10. Circa. 2.0 Million USD
Genotyping Volume
Circa. 7.5 Million
Data points
AUG 2016 -
DEC 2019
With 4 million US$ investment,
HTPG saved significant resources
for CGIAR & NARS and enabled
generation of genotyping data at
1/3rd- 1/4th price.
By assuming a minimum cost of
US$1 per data point, CG and
NARS might have spent about
US$ 7.5 Million on the data
generation.
$0.26 per data
point
The project has saved about US$
5.0 Million, with total
investment of about US$ 3.25
Million by 2019
Groundnut,
662160
Pigeon Pea,
49104Chick Pea,
82320
Finger Millet,
145536
Pearl Millet,
193536
Sorghum,
348768
ICRISAT Crops - Data point
AUG 2016 - JUNE 2020
Barley, 46080 cassava,515040
Common Bean,
736512
Cowpea,166272
Maize,837792
Potato,306720Rice, 2316576
Wheat,1137120
Other CGIAR Crops - Data point
AUG 2016 - DEC 2019
High Throughput Genotyping Project (HTPG)
11. 1.8 Tb sequence data generated (5 X to 14 X)
4.9 million SNPs, 596K Indels, 4.9K CNVs, 60.7K PAVs & 70K SVs
Domestication analysis reported 122 CDR regions that underwent
selection
Selection sweep analysis reported a significant reduction in diversity
from wild to landraces to breeding lines
Candidate genes for yield, heat and flowering time identified
15. Mid Density – Targeted GBS with AgriSeqTM
NGS Platform
Targeted GBS—a flexible, powerful,
highly accurate genotyping system
Sequencing based identification
of Novel SNPs in addition to
known SNPs
16. ~4.9 million markers on diverse chickpea lines
Based on different QC criteria, a set of 8654 highly
polymorphic markers tested
5000 markers in 4349 amplicons
Primer panel in manufacturing
Mid Density – Targeted GBS
panel for chickpea
Priority
Total
Markers
Dropped in
preDesignQC
No Design
Available
Remaining Design (not included in the
5000 markers final panel)
Included in Final
Panel
Priority 1 422 53 126 0 243
Priority 2 8232 149 381 2945 4757
Total 8654 202 507 2945 5000
Validation of mid-density panel by Dec 2020
Genotyping of chickpea breeding material for possible deployment in
routine chickpea breeding
ICRISAT chickpea breeding specific panel
17. Sample genotype table: AgriSum Toolkit
17
Sample Matrix
Table Output
Top/Bottom
Output
Sample 1;IonCode_0601 Sample 2;IonCode_0602 Sample 3;IonCode_0603 Sample 4;IonCode_0604 Sample 5;IonCode_0605
Target-1 C/G G/G C/C C/G C/G
Target-2 C/G G/G C/C ./. C/G
Target-3 A/G G/G A/A A/G A/G
Target-5 G/A A/A G/G G/A G/A
Target-6 G/A A/A G/G G/A G/A
Target-9 G/A A/A G/G G/A G/A
Target-11 G/A A/A G/G G/A G/A
Target-14 C/G G/G C/C ./. C/G
Target-17 C/T T/T C/C C/T C/T
Sample 1;IonCode_0601 Sample 2;IonCode_0602 Sample 3;IonCode_0603 Sample 4;IonCode_0604 Sample 5;IonCode_0605
Target-1 AB BB AA AB AB
Target-2 AB BB AA ./. AB
Target-3 AB BB AA AB AB
Target-5 AB AA BB AB AB
Target-6 AB AA BB AB AB
Target-9 AB AA BB AB AB
Target-11 AB AA BB AB AB
Target-14 AB BB AA ./. AB
Target-17 AB AA BB AB AB
Target-20 AB BB AA AB AB
18. Chrom Position Ref Variant Allele Call Filter Frequency Quality Filter Type Allele Source Allele Name
Ca1 389832 T C Heterozygous - 53.2 330.717 - SNP Novel tvc.novel.1
Ca1 389920 C G Heterozygous - 48.5 236.899 - SNP Hotspot Target-1
Ca1 391254 C G Heterozygous - 46.5 166.596 - SNP Hotspot Target-2
Ca1 393860 TGGTC - Heterozygous - 52.8 316.761 - DEL Novel tvc.novel.2
Ca1 393871 G A Heterozygous - 52.8 319.98 - SNP Novel tvc.novel.3
Ca1 393894 A G Heterozygous - 54 346.287 - SNP Hotspot Target-3
Ca1 395378 G C Heterozygous - 48.2 232.03 - SNP Novel tvc.novel.4
Ca1 395496 G A Heterozygous - 48.6 238.193 - SNP Hotspot Target-5
Ca1 396587 G A Heterozygous - 49.2 247.027 - SNP Hotspot Target-6
Ca1 401320 G A Heterozygous - 49.2 250.298 - SNP Hotspot Target-9
Ca1 405686 G A Heterozygous - 49.7 257.24 - SNP Hotspot Target-11
Ca1 407777 G A Heterozygous - 34.8 52.0189 - SNP Novel tvc.novel.5
Ca1 407795 C T Heterozygous - 34.8 51.8514 - SNP Novel tvc.novel.6
Ca1 407849 C G Heterozygous - 33.5 41.8833 - SNP Hotspot Target-14
Ca1 407887 C T Heterozygous - 34.5 49.9275 - SNP Novel tvc.novel.7
Ca1 407897 G A Heterozygous - 37.1 73.0879 - SNP Novel tvc.novel.8
Ca1 407901 T C Heterozygous - 39.6 101.75 - SNP Novel tvc.novel.9
Ca1 407928 CTC AT Heterozygous - 42.3 136.08 - COMPLEX Novel tvc.novel.10
Novel SNP Detection
18
Novel Markers - 2899
19. Chickpea QC (CaQC) SNP panel
Available re-sequencing data on 66 chickpea parental lines
from chickpea breeding (1.9 million markers) were used
Based on different criteria and analysis, a set of 48 markers
selected & used for genotyping
Marker data was analyzed on 94 different cross combination
Set of 14 markers for testing on larger set of lines for
validation
2-12 polymorphic markers polymorphic for all the crosses
except 2 cross combinations
The panel is also being tested on parental lines from NARS
partners
An affordable and effective genotyping platform for hybridity
testing and seed quality control & assurance
SNP panel ready for deployment
during crop season 2020-21
20. Selected 14 SNPs deployed in ICRISAT chickpea breeding
program
snpCA00171; snpCA00177; snpCA00178; snpCA00181;
snpCA00184; snpCA00188; snpCA00192; snpCA00193;
snpCA00197; snpCA00203; snpCA00206; snpCA00207;
snpCA00209; snpCA00216
32 plates for genotyping (2020-2021 chickpea crop season)
Deployment of CaQC SNP panel
Sequencing of chickpea parental lines with Chickpea
breeding team for identification of more markers
Upload of data on all parental lines to GOBii and provide
access to chickpea team
21. Optimization of genomic prediction based
selection strategy in chickpea
Frontiers in Plant Science 2016;
Scientific Reports 2018
Frontiers in Plant Science 2020
Restructuring training population
Genotyping of new training population with
new mid-density genotyping platform
Optimization and establishment of GS models
22. Total individuals in training set: 315 (162 Desi, 153 Kabuli)
5000 F5 plants from IARI and ICRISAT genotyped using LD DArT
Comparison of visual selection vs selection based on GEBV: two set of
~200 lines (based on GEBVs and visual selection) were evaluated in the
field conditions for yield and yield related traits during crop season
2019-2020
Lines selected based on GEBVs performed better in terms of yield and
100 seed weight as compared to lines selected based on visual selection
Deployment of genomic prediction based
selection strategy in chickpea
All Predict All Desi Predict Desi Kabuli Predict Kabuli Desi Predict Kabuli Kabuli Predict Desi
Seed Yield 0.48 (0.015)a 0.26 (0.029) 0.25 (0.020) 0.08b 0.04c
Seed Weight 0.92 (0.002) 0.76 (0.012) 0.74 (0.014) 0.20 0.58
Biomass 0.50 (0.013) 0.39 (0.019) 0.26 (0.026) 0.11 0.16
Plant Height 0.65 (0.011) 0.75 (0.010) 0.42 (0.038) -0.13 0.16
Days to Flower 0.68 (0.007) 0.63 (0.016) 0.56 (0.031) -0.34 0.07
Days to Maturity 0.70 (0.003) 0.53 (0.021) 0.53 (0.038) -0.16 0.09
Frontiers in Plant Science 2020
23. Based on initial results from pilot experiments AICRP Chickpea
initiated efforts to deploy GS in routine breeding program
Included additional parental lines from national chickpea
breeding program to extend the training population
Training population genotyped using newly developed Mid-
density SNP arrays
Training population evaluated at NARS locations for yield and
quality traits
Based on initial analysis ICRISAT suggested new sets of crosses to
AICRP centres
These crosses are being made in the ongoing crop season
Deployment of Genomic selection in Indian
national chickpea breeding program
24. BGM 10216 a drought tolerant MABC line in field
BGM 10216 First MABC line released in India for
commercial cultivation in central zone
Pusa Chickpea 10216 (BGM 10216) is developed after
introgression QTL-hotspot in “Pusa 372” genetic
background at IARI in coll. with ICRISAT
16% yield advantage over recurrent parent across all
the centers tested under AICRP
It’s grain protein content is 22.6%
Support to NARS: Pusa Chickpea
10216 (BGM 10216), drought
tolerant variety - 2019
25. Support to NARS: Pusa Chickpea Manav (BGM
20211) enhanced fusarium wilt resistance -
2020
Pusa Chickpea Manav developed by introgression
of “QTL region” for wilt resistance from WR 315
to recurrent parent Pusa 391
28 % yield advantage over recurrent parent in
National WRIL Trials under AICRP under wilt
stress conditions
Its average 100-seed weight is 19.5 g.
It’s grain protein content is 18.92%.
28. Wide phenotypic variability observed for the
11 nutritional traits
Trait (PVE %) Candidate gene analysis results for
significant MTAs
Beta carotene (15-20) CA_4 (Ca_03822)
Iron (10-17) CA_6 (Ca_08678)
Phytic acid (12-17) CA_1 (Ca_02905) ; CA_4 (Ca_03574)
Vitamin B1 (25-31) CA_1 (Ca_26128) ; CA_4 (Ca_12127)
CA_4 (Ca_03836) ; CA_5 (Ca_13399)
CA_6 (Ca_09604)
Zinc (11-15) CA_3 (Ca_12279)
Candidate gene analysis
GWAS for nutrition traits in chickpea
Chickpea reference set analyzed for 11 nutritional traits
237K markers from WGRS
29. Data management
All the chickpea genotyping data in stored in GOBii database and public repositories
(NCBI; CEGSB open access)
All the chickpea datasets
uploaded in ICRISAT dataverse
30. Challenges and way forward…
Lack of funding support and recognition in different institutional
initiatives including CRP-GLDC, AVISA and CtEH
No-clarity in activity alignment with GTD and Crop Improvement themes
with defined role and responsibilities and due recognition
Need to support ICRISAT and NARS breeding programs through team of
specialists in genomics and molecular breeding, and information technology
to design breeding process
Primary focus would be cost effective genotyping, pedigree verification
system, genome-wide marker based prediction and haplotype based
breeding through identification of novel superior haplotypes for target
traits