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Research Program Genetic Gains (RPGG) - Review Meeting 2021: Overview By Dr Rajeev K Varshney

  1. Research Program: Genetic Gains Program profile: 70 staff: 24 women (34%) and 46 men including 20 IRS/SMG Rajeev K Varshney
  2. RP Genetic Gains • Harnessing the full potential of modern genomics, molecular biology, and advanced breeding approaches • Generating trait knowledge, tools/technologies and platforms for integrating with crop improvement programs towards increasing crop productivity, profitability, and improving nutrition. • Empowering national programs for adopting modern technologies in their crop improvement programs 2
  3. Delivering genetic gains in farmers fields 1. Genomics & Trait Discovery 2. Forward Breeding 3. Pre-breeding 4. Cell, Mol. Biology & Genetic Engineering 5. Biotechnology – Eastern & Southern Africa 6. Seed Systems Sequencing & Informatics Services Unit
  4. Farmers fields Research Program Genetic Gains Research Program ISD Research Programs Asia, ESA, WCA Crop Improvement Int. Crop Management Breeding Population Selfing and selection Advanced breeding lines Parental lines Varieties Hybrids NARS/ Pvt. Sector Pre-breeding Genomics & Trait discovery Forward Breeding Marker Cell, Molecular Biology & Genetic Engineering Seed Systems Agribusiness and Innovation Platform Systems analysis for Climate Smart Agriculture Phenotyping Diversity Trait specific lines Strategies Lessons MIND analysis to maximize outcomes Sequencing and Informatics Services Consumers Systems Biology Research Initiative Rt = irsA y ESA- Biotechnology Statistics, Bioinformatics & Data Management Genebank DDG-R office Synergy and collaboration
  5. Discovery science for a strong foundation 5 Enhancing trait knowledge • Developing genomic resources- reference genome, gene expression atlas, genotyping arrays, etc. • Understanding genome architecture and genetic variations • Molecular basis, identification of genes and metabolic pathways for breeding product profile traits • Molecular mapping and development of diagnostic markers for ‘must have traits’ and ‘nice to have traits’ Developing tools, technologies and platforms • Diagnostic markers on high-throughput genotyping platform • Mid-density arrays and QC panel for enhancing breeding efficiency • Computational genome infrastructure and databases like GOBii to manage and archive high-density genotyping data • Linking genotyping data to tools and pipelines for routine use in modern breeding • RapidGen platform for reducing breeding cycle time
  6. Accelerating and delivering genetic gains 6 Optimization of advanced breeding approaches and genetic material to breeding programs • New sources for stress tolerance (striga, late leaf spot, drought) and nutrition traits through pre-breeding • Integration of traits through genomics-assisted breeding approaches • Optimizing genomic prediction, haplotype-based breeding, optimal contribution selection (OCS) approaches for modernizing breeding programs • Host-induced gene silencing, transgenics and genome editing approaches Serving and empowering breeding/ national programs • Documenting learning and guiding seed delivery systems to NARS • Modernizing breeding programs by providing genotyping/ sequencing services and training national programs • Making sequencing/genotyping data and research outputs publicly available through databased/ publications • Organizing training courses/ conferences/ webinars, etc. for knowledge dissemination
  7. Key highlights and achievements • Genomic foundation: Reference genome sequence for all crops, genome sequence diversity, gene expression atlases and functional genomics platforms; and genomics research network with >180 partners from 35 countries of 6 continents • Trait discovery pipeline: Mapping for 20-30 traits, markers for ca. 10 traits for breeding • Trait deployment pipeline: marker-assisted backcrossing approach developed, validated and made available to breeding programs • Genetic engineering products: Bt- chickpea, Bt- pigeonpea, low aflatoxin contamination groundnut • Optimization of novel breeding approaches: Genomic prediction, haplotype-based breeding, optimal contribution selection, gene editing and speed breeding • High-throughput low-cost genotyping marker platform serving CGIAR, NARS and private sector partners
  8. • Success stories of modernization of breeding: 6 legume varieties in India and Ethiopia in 2019 and 2020- Geletu and Pusa 10216 drought tolerant chickpea varieties, SuperAnnigeri1 and Pusa Chickpea Manav Fusarium Wilt resistant chickpea varieties, and Girnar 4 and Girnar 5, high-oleic groundnut varieties • New pre-breeding lines to 8 countries in Asia and sub-Saharan Africa • TLIII project: Facilitated development and release of 312 drought tolerant, nutrient dense varieties in >15 countries • HTPG project: provided 7.5 M datapoints (US$ 2 M) to 30+ NARS, 8 CGIAR centers in 28 countries • Sequencing/ genotyping data: 4400 GB sequencing data, 61824 SSR datapoints for 15.5 K lines and shared > 12 Tb genomic data • Shared knowledge and research outputs through research publications/ databases/ presentations • Capacity building by hosting students/ scientists & organizing training courses/ conferences/ webinars Key highlights and achievements
  9.  Focus- Climate resilience, nutrition and market traits  Large-scale germplasm characterization & value addition  Novel trait pre-breeding lines and compressing pre-breeding time  Candidate genes, QTLs and diagnostic markers for must-have traits  Implementation of markers in forward breeding, MABC/MAS and QC.  DNA markers for impact assessment  Novel breeding approaches testing, validation & deployment
  10.  Biotechnology and genomics approaches for aflatoxin in groundnut, Striga resistance in sorghum, rancidity in pearl millet  Doubled haploidy and speed breeding methods optimization  Strengthening & modernization of seed systems  Avail new sequencing and genotyping platforms  Resource mobilization, capacity building & communication
  11. Budget trend in RPGG
  12. Tools & technologies made available, some breeding programs are embracing them for modernizing their breeding programs, others need to be motivated Representation and contribution of RP GG in modernization of crop improvement agenda of the institute- e.g. Task Force on Modernization of Crop Improvement, Breeding Strategies, BPAT, EiB, and other initiatives. Integration and budgeting of RP GG disciplines / staff in institutional programs e.g. CRP-GLDC, CtEH, AVISA Supp Grant, ICAR- ICRISAT, etc. Staff salary is an important issue, several projects bring resources for operations, but not salary. Need more fungible funding from institutional initiatives. Need for a better coordination among several ongoing activities across programs ESA- Biotechnology (and WCA) and Pre-breeding disciplines are important to identify and bring novel alleles and modernized breeding programs using genomics tools and technologies- need institutional support Challenges & opportunities
  13. RP GG has diverse skill sets and competencies, global recognition for cutting edge upstream research and excellent infrastructure and technological support Developed large scale genomic resources, genomic and biotechnology tools and technologies, pre-breeding and seed system platforms. Several success stories on contribution to modernize crop improvement available in many countries Breeding programs at ICRISAT and NARS can be heavily benefitted by adopting the available tools and technologies RP GG is contributing and fully committed to modernization of crop improvement agenda, needs suggestions, guidance and support for improvement/ changes, as and when required. Summary
  14. Thank You
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