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ICRISAT Global Planning Meeting 2019:Research Program - Genetic Gains by Dr Rajeev Varshney and Team

  1. ICRISAT Science RP- Genetic Gains By: Rajeev Varshney & Team
  2. Integration of RP-Genetic Gains with other RPs 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 Mapping homologous environments to target varieties/ quantity of seed MIND analysis to maximize outcomes Sequencing and Informatics Services Consumers Systems Biology Research Initiative Genebank Rt = irsA y
  3. • Focus- Climate resilience, nutrition and market traits • Large-scale germplasm sequencing & value addition • Novel trait pre-breeding lines and compressing pre-breeding time • Candidate genes, QTLs and diagnostic markers for must-have traits • Novel breeding approaches tested, validated and deployed • Biotechnology and genomics approaches for aflatoxin in groundnut, Striga resistance in sorghum, rancidity in pearl millet • Doubled haploidy and speed breeding methods optimized • Strengthening & modernization of seed systems • Linking agriculture (our crops) with human health thru systems biology • New sequencing and genotyping platforms • Resource mobilization, enhanced capacity building & communication Forward-looking synopsis
  4. Germplasm Research Promotion of the use – Molecular Characterization • Collection management • Collection rationalization (duplicates) • Use of molecular markers linked to important traits. Big objective: • Genotype entire collection; • Estimate diversity within and among accessions; • Development of thematic subsets DArT-seq Pilot Projects 1 and 2 • Genotyping: 12,000 samples, three crops, 8-25 plants/crop • Phenotyping: ~ 5,000 samples in field and 12,000 samples – nutritional traits
  5. Blast Drought Heat  Four advanced backcross populations (BC2F6)developed from Pennisetum violaceum  Evaluated in multilocation trials over years PearlMilletGroundnut Stem rot LLS Rust  Three advanced backcross populations developed from A. duranensis , A. ipaensis, A. kempff-mercadoi and A. hoehnei  Evaluated in multilocation trials over years PigeonpeaChickpea • Blast • Terminal drought • Flowering-stage heat • Phytophthora blight • SMD and wilt • Pod Borer • Stem rot • LLS • Rust • Botrytis gray mould (BGM) • Dry root rot (DRR) • Ascochyta blight (AB) Global Crop Diversity Trust funded project  Multiloation trials of high-yielding ILs in India and Myanmar  Four advanced backcross populations ( BC2F3, & 4-way BC1F3) consisting of ~2321ILs developed for improving pod borer tolerance using C. scarabaeoides and c. acutifolius  Four advanced backcross populations developed using C. reticulatum and C. echinospermum for BGM and DRR tolerance Global Crop Diversity Trust funded project Blight Wilt Pod Borer BGM ABDRR Bringing wild species alleles thru Pre-breeding
  6. Sharing new pre-breeding materials and knowledge to 8 countries in Asia and Africa Crop Shared Lines Country Groundnut 87 Malawi, Niger, Mali, India Pearl millet 105 Niger, India Pigeonpea 86 Myanmar, Kenya, India Chickpea 1091 Ethiopia, Turkey, India
  7. Compressing pre-breeding time frame Chickpea Studied the effect of vernalization and photoperiod treatments on flowering and identified wild Cicer species and cultivated chickpea genotypes responsive to vernalization and extended-photoperiod treatments (Sharma & Upadhyaya 2015; Crop Science 55: 1-8) Identified critical day length required by wild Cicer species and cultivated chickpea (Sharma & Upadhyaya 2018; Crop Science) Studied the effect of light quality & response of ovule culture versus immature seed germination (Manuscript under preparation) Extended-photoperiod treatment in chickpea White light Yellow light Response of ovule culture versus immature seeds germination in chickpea & groundnut 8 days immature seeds of chickpea White light Yellow light Photoperiod treatments in pigeonpea Immature seed germination in groundnut 11 days immature seeds of chickpea in soil
  8. Understanding genes, genomes, and germplasm • Development of key genetic and genomic resources • Improved and high quality genome assemblies for cultivated and wild species • Deciphering the core and dispensable genome through PAN Genome • Capturing the genetic variation present in diverse germplasm through whole genome re-sequencing • Connecting phenome with genome using transcriptome, proteome and metabolome
  9. Next-generation trait discovery • Family-based and natural populations • High-medium-low density genotyping assays • Linkage and LD-based high resolution mapping • Identification of QTLs and MTAs for target traits as per PCNs and other global challenges • Candidate gene discovery and functional validation • Development and validation of diagnostic markers Diagnostic markers QTL and gene discovery Multi-parent populations
  10. Genomics-assisted breeding • MAS, MARS and MABC for target traits • Development of super donors for multiple traits • Development, optimization and deployment of GS breeding • Understanding and development of heterotic pools for crop improvement Genomic selection
  11. Genome to field: downstream applications • Strengthening seed-chain system through • Marker-based purity testing • DNA fingerprints database for elite cultivars and founder parents • Diagnostic markers for target traits • Genomics-assisted improved lines • Enabling NARS partners in genomics-based crop improvement • DNA-fingerprinting support for varietal release • Socio-genomics for impact assessment • Influencing national/international agriculture, science and research policies
  12. Rice $306,058 Wheat $153,378 Maize $137,549 Potato $89,232 Cassava $183,766 Groundnut $79,640 Common Bean $37,824 Sorghum $37,438 Cowpea $25,528 Finger Millet $16,123 PigeonPea $11,400 Pearl Millet $9,984 Soybean $7,104 Yam $4,800 Chickpea $4,680 Overall Investment by Crop (Routine + Verification) Genotyping: $1,104,505 High throughput genotyping (HTPG) project
  13. $83,160 $144,462 $104,638 $592,234 Year 1 AUG 2016 to JUL 2017 Year 2 AUG 2017 to AUG 2018 2016 to 2018 volume to date New genotyping platform •Expected offering in 2019 •Mid - High density genotyping (100 to 5K SNPs) •Global access though service provider •All crops included •Cost: < $10 per sample •Includes: DNA, Genotyping, Bioinformatics •Data interoperability & scalability
  14. P1 × P2 P1 × P2 P1 × P2 P1 × P2 P1 × P2 P1 × P2 F2 F5 Practical Haplotype Graph Genotyping 6000 F5 plants Allele calling Training population (320 lines) Selection of lines based on GEBV lines in field for evaluation Oct 18-Mar 19 Compare field evaluation vs GEBV lines Apr-May 19 Genomic selection in chickpea
  15. Line/ variety* No. of lines selected Varieties 69 Landrace 15 Hybrids 29 Donor/ recipient parent (bmr, shoot fly, Anthracnose & Leaf bligh, biomass, QTL donor lines) 17 B lines 59 R lines 36 A2 Hybrids 2 A3 Hybrids 1 A4 Hybrids 1 BC2F4 (ILs) 3 TOTAL 232 *Panel of 232 lines planted in 2018 Rainy season at three locations in India: Parbhani, Akola and Patancheru • Training population encompassing parent material for all important traits • Participation of two AICSIP centres - Parbhani, Akola • Varieties/ lines/ hybrids from NARS (both from India and Africa) • Phenotyping for morphological and agronomical traits along with key traits for tolerance/resistance • Multi-location data Genomic selection in sorghum Implementing GS in sorghum breeding
  16. 2017 • Upload files from local computer • BGLR models and allow model specification • K fold cross validation 2018 (green= in active testing) • Enhanced encoding and sample matching tools • PCA and similarity matrix, clustering tools • BLUP and BLUE calculator • GEBV calculators, including GBLUP • Consistent input and output formats to connect between tools • User defined cross validation within and across groups • Crop-specific GS workflow 2019+ • Galaxy to pull dataset from GOBii through livelink • Direct query data and access to data sources GOBii or BDMS/BMS • User friendly UI • Include G x E • Push BLUP/BLUE, GEBV, and selection results to store in databases GS-Galaxy analysis pipeline functionalities Start Stop
  17. Experimental design Capture Collate/ organize Curate AnalyzeArchive Planting and labeling in field DNA Assay 38474037 38668738 38748270 38867490 MSU7_12_17391484_G/TMSU7_12_17391872_A/GMSU7_2_10003379_C/A Plate 01-A01 G:G G:G T:T T:T T:T A:A A:A Plate 01-A02 G:G G:G T:T T:T T:T A:A C:A Plate 01-A03 G:G G:G T:T T:T T:T A:A C:A Plate 01-A04 A:G A:G C:T G:T T:T A:A C:A Plate 01-A05 A:G A:G C:T G:T T:T A:A C:C Plate 01-A06 A:A A:A C:C G:G T:T A:A A:A Plate 01-A07 A:G A:G C:T G:T T:T A:A C:C Plate 01-A08 A:G A:G C:T G:T T:T A:A C:A Plate 01-A09 A:A A:A C:C G:G T:G A:A A:A Plate 01-A10 G:G G:G T:T T:T T:T A:A C:A Plate 01-A11 A:A A:A C:C G:T T:T A:A A:A Plate 01-A12 A:G A:G C:T G:T T:G A:A C:A Plate 01-B01 A:G A:G C:T G:T T:T A:A C:A Plate 01-B02 G:G G:G T:T T:T T:T A:A C:A Plate 01-B03 A:A A:A C:C G:G T:T A:A C:A Plate 01-B04 G:G G:G T:T T:T T:T A:A C:A Plate 01-B05 A:A A:A C:C G:G T:T A:A C:C Plate 01-B06 A:G A:G C:T G:T T:T A:A C:A Plate 01-B07 A:A A:A C:C G:G T:T A:A C:C Plate 01-B08 A:A A:A C:C G:G T:T A:A C:A Plate 01-B09 A:A A:A C:C G:G T:T A:A A:A Order form Genotyping data GOBii – HTPG integration • Notify Intertek of upcoming orders • Assign plate and sample IDs • Provide barcodes • Load raw data into GOBII • Store genotypic data • Facilitate data extraction • Genotypic data in ready-to- analyze formats Connect data to visualization and analysis tools HTPG
  18. Biotechnological approaches for groundnut for resistance to aflatoxin contamination ICGV 15083 x 4EC 26-2 ICGV 86015 x 4EC 26-2ICGV 86015 Inoculated Control ICGV 15083 Inoculated Control Construct Event# AFB1 (ppb) Def4Ec ICGV 15083 x Def4Ec 26-2-3 3.72 Def4Ec ICGV 15083 x Def4Ec 26-2-20 2.90 Def4Ec ICGV 15083 x Def4Ec 26-2-25 5.66 Def4Ec ICGV 15083 x Def4Ec 26-2-28 1.71 Def4Ec ICGV 15083 x Def4Ec 26-2-31 2.60 Def4Ec ICGV 15083 x Def4Ec 26-2-32 8.34 Def4Ec ICGV 15083 x Def4Ec 26-2-33 1.09 Def4Ec ICGV 86015 x Def4Ec 26-2-2 9.50 Def4Ec ICGV 86015 x Def4Ec 26-2-5 1.95 Def4Ec ICGV 86015 x Def4Ec 26-2-11 3.37 Def4Ec ICGV 86015 x Def4Ec 26-2-14 5.45 Def4Ec ICGV 86015 x Def4Ec 26-2-15 6.82 Def4Ec ICGV 86015 x Def4Ec 26-2-19 7.67 Def4Ec ICGV 86015 x Def4Ec 26-2-20 6.10 WT Parent AFB1 (ppb) ICGV 15083 IC1 771.14 ICGV 15083 IC2 512.03 ICGV 15083 IC3 654.54 ICGV 15083 IC4 566.73 ICGV 15083 IC5 680.00 ICGV 86015 IC1 636.15 ICGV 86015 IC2 378.88 ICGV 86015 IC3 450.00 ICGV 86015 IC4 388.26 ICGV 86015 IC5 350.00 Selected F2 progeny ICGV 15083 x Def4Ec 26 & ICGV 86015 x Def4Ec 26 CMBGE, Groundnut breeding, Groundnut Pathology ICGV 15083 ICGV 03043 ICGV 86015
  19. carlactone MAX3, MAX4,: MAX1 STRIGOLACTONES CCD7 CCD8 (P450) D27 (β-carotene-9-isomerase) CCD7 edited lines HIGS- Striga PMEI Pectin-Methyl-Estrase Inhibitor HIGS- Cell Wall Degradation Enzymes Types of resistances 1. Germination & haustoria induction 2. Attachment 3. Post-attachment haustoria formation strigolactones Orobanche - Striga Germination stimulants PARASITIC INTERACTION Root exudates (secondary metabolites) Striga resistance in sorghum CMBGE, Corteva Agriscience, Kenyatta University, U of Sheffield
  20. New Breeding Techniques (NBTs) for addressing rancidity in pearl millet Knocking down FA biosynthesis genes through gene editing Low rancid line Functional flour market projected to reach USD 954 billion by 2022* Pearl millet has inherent challenges due to rancidity CMBGE, Pearl millet Breeding, GTD, CEGSB, NutriPlus & Corteva Agriscience
  21. Doubled Haploidy for accelerated plant breeding Inducing Double Haploids in commercial germplasm CMBGE, GTD - Sorghum INRA, Corteva Agriscience Founder line 1 x Founder line 2 F1Selfing Inbred line DH Inbred line W MTarget 1 Target 2 Sobic.001G348600 Sorghum phenotype Candidate genes identified for generation of pre breeding material that has potential to be used to induce Double Haploids in commercial germplasm
  22. Biotechnology in Africa- i • Validation of QTL regions for Striga detected by GWAS through transcriptome analysis • Characterizing sorghum for pre-germination Striga resistance • GWAS for resistance to blast disease in cultivated finger millet accessions at seedling stage • Development of essential genetic and genomic resources for finger millet
  23. • Genome wide Association studies (GWAS) to map to genomic regions responsible for Striga resistance in pearl millet, sorghum • Characterizing a NAM population for Striga, anthracnose, midge and drought tolerance • Molecular characterization of groundnut accessions in Africa • Screening diverse sorghum genotypes for response to anthracnose with or without Lr34 Biotechnology in Africa- ii
  24. Delivery of nutritious grain legumes and dryland cereals Creating demand for quality seed: Product advancement criteria and process to prioritize varieties Seeds to business (S2B) operational model of the Syngenta foundation for sustainable agriculture
  25. Seed value chain: what drives seed purchase? 64% of legume farmers are buying ‘seed’ from grain traders (McGuire and Sperling, 2016) Affecting farm decisions: • Allocation of resources • Choice of crop • Choice of variety  Varietal turnover • Choice of seed source  Seed replacement rate
  26. Engaging the private sector: breeding and seed systems Operations Type 1 Type 2 Type 3 Type 4 Type 5 Variety development Breeding Testing Seed Production Breeder Foundation Certified Seed Marketing Packaging Selling Resources Private Staff + Land + Equipment + Varieties Staff + Land + Equipment Staff + Equipment Staff None Public (CGIAR; NARS) Breeding lines (co- developme nt and release) Varieties (co- developme nt and release; Licensing) Varieties + Land (Licensing; contractual seed production with seed producer groups) Varieties + Land + Equipment (contractu al seed productio n with seed producer groups) Varieties + Land + Equipment + Staff
  27. Genotypingandsequencingplatforms WGRS GBS RNA-Seq Genome Assembly Epigenomics Microarrays High Performance Computational Genome Analysis facility  600 cores  ~ 830 TB storage  7.5 TB RAM SISU- partnering in accelerating genomics research
  28. SSR 6M data points 1.5M samples DArT 75K data points 2K samples KASPar 1.5M data points 4K samples VeraCode 75K data points 1K Samples GBS 3TB data 14K samples RNA-seq 1.6TB data 243 Samples Small RNA 130 GB data 132 Samples WGRS 40TB data 4K samples 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017  Sequencing Costs may vary according to the genome size & coverage  DNA extraction costs are not included Cost-effective sequencing technologies
  29. Bringing DNA extraction cost down… NaOH DNA extraction • Where no refrigerator, no centrifuge • 5 min/plate, < $0.10/sample + = Zou et al. (2017) PLoS Biology • 30 seconds/sample, < $0.10/sample • Modifying to scale to full-plate extractions Conventional Phenol-Chloroform Macherey Nagel DNA Extraction
  30. HiSeq 2500 NovaSeq 6000 Output: 6TB data Duration: 3 days • Cost reduced by million folds • Read length increased • Throughput increased Upgrade Output: 1TB data Duration: 1 Week New sequencing platforms 96-plex assay $60-80/Gb data Nextera Truseq
  31. • Friendly interface • Detailed results • Advance visualization • Prevent data duplication • For scientific community’s inspection • Cross verification • Comprehensive Workflow Tools and Online resources
  32. Impact of ICRISAT crop diet on gut microbiome for curbing malnutrition Anemia & malnutrition in pregnant woman Malnutrition in babies Transmission of gut microbiome Poor nutrition Vicious cycle of malnutrition Does ICRISAT mandate crops play an important role in altering gut microbiota for enhanced nutrient absorption and alleviate malnutrition? Pearl Millet Breeding Asia Program, ICRISAT Anemia in adolescent girls
  33.  Linking soil microbiome structure to function  Association of microbiome structure/function with crop performance  Defining the ‘functional’ microbiome Employing soil microbiome for enhanced crop productivity & environmental sustainability
  34. Capacity Building  Total activities conducted: 23  Participants trained: 598 (M:492 and F: 106)  No. of training conducted country wise o India: 12 o Tanzania: 1 o Mali: 3 o Ethiopia: 3 o Uganda: 3 o Morocco: 1 *Capacity building activities (conducted/facilitated by RP- GG during 2018) including TL III & HOPE- II Annual Meeting
  35. High impact oriented & high impact factor journal articles Thanks to our collaborating partners
  36. Sustainable fund raising • Enhancing the awareness and visibility on impacts of upstream & strategic science in crop improvement  High quality scientific publications  Communicating success stories with potential donors  Establishing a roadmap for impactful communication with grant donors (e. g., brainstorming workshops with donors) • Multi-disciplinary and multi-institutional mega- proposals • Strengthening national and international partnerships through workshops/conferences
  37. Communications… • 12 Stories • 4 Bulletins RP- GG & CEGSB Tropical Legumes III • 15 Stories Key resources for genomics and crop improvement practitioners – series of books released India-Myanmar pigeon pea project gets a research boost ICRISAT working on developing climate-resilient pigeon pea Pre-breeding scientists at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) are exploring possible solutions to increase nutritional value in agriculture produce, sourced from wild species of cajanus. A project funded by Global Crop Diversity Trust (GCDT), would evaluate promising pre-breeding lines in India and Myanmar, bringing them one step closer to cultivation, according to a release here on Thursday. https://www.thehindu.com/sci-tech/india-myanmar-pigeon-pea-projectgets-a- research-boost/article25344041.ece
  38. Social Media… RP Genetic Gains : 94 members, CEGSB: 95 members, and Systems Biology: 88 members ICRISAT RP- GG 580 Followers 133,353 impressions 1,314 Followers 586,546 reach 437 Followers 137,117 impressions 1,875 Followers 2,174,590 reach 389 photos from conferences/workshops 740 Followers 119,862 impressions 970 Followers 583,798 reach CEGSB 933 photos from conferences/workshops received 302,887 hits from more than 123 countries. http://cegsb.icrisat.org/ @coeingenomics@rpgeneticgains @rpgeneticgains @tropicallegumesIII @tropicallegumes@coeingenomics 2,389 Followers 1,032,000 impressions 4,296 Followers 5,333,205 reach @rajvarshney @rajeevkvarshney
  39. Thank You
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