VI NEXT GENERATION GENOMICS & INTEGRATED BREEDING FOR CROP IMPROVEMENT CONFERENCE ON CROP GENOMICS: PRESENT & FUTURE n Genomics (CE CELEBRATING THE 10TH ANNIVERSARY OF CEG ence i G) cell ANNIVERSARY Ex of (2007-2017) tre en C ICRISAT, HYDERABAD, INDIA CROP GENOMICS: PRESENT & FUTURE CROP GENOMICS: DECEMBER 6-8, 2017 Accelerating Genetic Gains in Crop Breeding Programs throughAccelerating Center Genetic of Excellence Gains in inCrop Genomics Breeding (CEG) Programs throughAccelerating Center Genetic of Excellence Gains in inCrop Genomics Breeding (CEG) Programs through Center of Excellence in Genomics (CEG) Integrated genomics and breeding activities Integrated genomics and breeding activities Integrated genomics and breeding activities Genetic resources Genetic Genetic resources Genetic Genetic resources Genetic Wild species, Landraces, Cultivars, breeding lines, Mapping populations breeding Cultivars, Wild species, Landraces, Superior lines with enhanced tolerance/resistance to abiotic and biotic stress lines, Mapping populations breeding Cultivars, Wild species, Landraces, Superior lines with Wild species, Landraces, Cultivars, breeding lines, Mapping populations breeding Cultivars, Wild species, Landraces, enhanced tolerance/resistance to abiotic and biotic stress Superior lines with Genome sequences enhanced tolerance/resistanceMarker resources to abiotic and biotic stress Genome• Pigeonpea sequences (Nature Biotech 2012, 30:83-89) Marker• Diagnostic resources markers for key traits Genome• PigeonpeaChickpea (Naturesequences (Nature Biotech Biotech 2013, 2012, 31:240-246) 30:83-89) Marker• Diagnostic>10,000 resourcesSSRs markers across formandate key traits crops • Groundnut – A & B genomes • PigeonpeaChickpea (Nature (Nature Biotech Biotech 2013, 2012, 31:240-246) 30:83-89) • Diagnostic>10,000 SSRsSNPs markers acrossacross for mandatemandate key traits cropscrops (Nature Genetics 2016, 48:438-446), (PNAS 2016, 113: 6785-6790) • ChickpeaGroundnut (Nature – A & BBiotech genomes 2013, 31:240-246) • >10,000High density SSRsSNPs DArT acrossacross arrays mandatemandate for chickpea, cropscrops pigeonpea and groundnut • (NatureSorghum Genetics (Nature 2009,2016, 457:551-556)48:438-446), (PNAS 2016, 113: 6785-6790) • Groundnut – A & B genomes • Pearl millet (Nature Biotech 2017, 35:969-976) • >10,000HighAffymetrix density SNPs 50K+SNP DArT across arrays mandatearrays for in chickpea, cropschickpea, pigeonpea pigepnpea and and groundnut groundnut • (NatureSorghum Genetics (Nature 2009,2016, 457:551-556)48:438-446), (PNAS 2016, 113: 6785-6790) • High throughput & low cost genotyping platform • Pearl3000 chickpeamillet (Nature genome Biotech sequencing 2017, 35:969-976) • HighAffymetrix density 50K+SNP DArT arrays arrays for in chickpea, chickpea, pigeonpea pigepnpea and and groundnut groundnut • Sorghum (Nature 2009, 457:551-556) (US$ 1.5 per sample including DNA sample for 10 markers) • 1000 pearl millet genome sequencing • Pearl3000 chickpeamillet (Nature genome Biotech sequencing 2017, 35:969-976) • AffymetrixHigh throughput 50K+SNP & low arrays cost ingenotyping chickpea, platformpigepnpea and groundnut (Nature Biotech 2017, 35:969-976) (US$ 1.5 per sample including DNA sample for 10 markers) • 30001000 chickpeapearl millet genome genome sequencing sequencing •High High performancethroughput & low costcomputational genotyping platform genome analysis • Re-sequencing initiatives in sorghum, groundnut and pigeonpea (Nature Biotech 2017, 35:969-976) (US$ 1.5 per sample including DNA sample for 10 markers) • (Nature1000 pearl Genetics millet genome2017b, 49:1082-1088)sequencing High• Number performance of cores 408 computational genome analysis • (NatureRe-sequencing Biotech initiatives 2017, 35:969-976) in sorghum, groundnut and pigeonpea (Nature Genetics 2017b, 49:1082-1088) High• NumberStorage performance ~805 of cores TB 408 computational genome analysis •Molecular Re-sequencing breeding initiatives in sorghum, groundnut and pigeonpea (Nature Genetics 2017b, 49:1082-1088) • NumberStorageRAM 6 TB ~805 of cores TB 408 Molecular• Chickpea: drought breeding tolerance and resistance to Fusarium wilt and • StorageRAM 6 TB ~805 TB Aschochyta blight Decision support tools Molecular• Chickpea: drought breeding tolerance and resistance to Fusarium wilt and • ISMABRAM 6 forTB molecular breeding • AschochytaGroundnut: blightresistance to rust and oil quality Decision support tools • Chickpea: drought tolerance and resistance to Fusarium wilt and • GDMS for data management • AschochytaGroundnut:Sorghum: drought blightresistance tolerance, to rust resistance and oil quality to shoot fly and Striga Decision• ISMAB for supportmolecular breeding tools • ISMU for mining SNPs based on NGS • Groundnut:Sorghum:Pearl millet: drought resistanceresistance tolerance, toto rustblast, resistance and downy oil quality mildew to shoot and fly Fe and and Striga Zn • ISMABGDMS forfor datamolecular management breeding • ISMU v 2 for deploying Genomic Selection • Sorghum:PearlPigeonpea: millet: drought markers resistance tolerance, for to enhancing blast, resistance downy precision mildew to shoot and and efficiencyfly Fe and and Striga Zn of • GDMSISMU for for mining data management SNPs based on NGS hybrid breeding • GOBII for high-density genotyping data • PearlPigeonpea: millet: markers resistance for to enhancing blast, downy precision mildew and and efficiency Fe and Zn of • ISMU forv 2 miningfor deploying SNPs based Genomic on NGS Selection • Pigeonpea:hybrid breeding markers for enhancing precision and efficiency of • ISMUGOBII vfor 2 forhigh-density deploying genotyping Genomic Selection data hybrid breeding • GOBII for high-density genotyping data Dec 2017 About ICRISAT: www.icrisat.org ICRISAT’s scientific information: http://EXPLOREit.icrisat.org Dec 2017 About ICRISAT: www.icrisat.org ICRISAT’s scientific information: http://EXPLOREit.icrisat.org Dec 2017 About ICRISAT: www.icrisat.org ICRISAT’s scientific information: http://EXPLOREit.icrisat.org i ii On behalf of the Governing Board I would very much like to welcome you both to ICRISAT and to the “Crop Genomics: Present and Future” conference. We hope that your participation in the conference and stay at ICRISAT will be stimulating and rewarding. Please accept my sincere apologies for being unable to attend the conference and meet with you in person but I believe that the conference (together with the CEG alumni meeting) will lead to the strengthening old partnerships and the development of new ones. The Crop Genomics: Present and Future Conference celebrates 10 outstandingly productive years of the Centre of Excellence in Genomics (CEG) at ICRISAT. The CEG has made some very important findings which are significantly helping ICRISAT and its partners modernise their breeding programmes. While the CEG is celebrating its tenth anniversary, this year ICRISAT is celebrating its 45th anniversary. During these 45 years, ICRISAT together with our partners, have transformed the lives and livelihoods of many of the world’s most vulnerable people. The title of our conference Crop Genomics: Present and Future made me consider what genomics was like 45 years ago and what it might be like in 45 years. In 1972 when I was an undergraduate studying Botany, Walter Fiers and his team at the University of Ghent were the first to establish and publish in Nature the complete nucleotide sequence of a gene (bacteriophage MS2 coat protein). Since 1995 we have witnessed an exponential growth in the number of genomes that have been sequenced due to improved techniques and massive cost reductions. Today genomics is helping us understand both agricultural and human traits with applications in human and animal disease and enhancing agricultural productivity. The pace of technological advances will continue and significantly impact diverse disciplines such as synthetic biology and species conservation as well as revolutionising plant and crop breeding to address the challenges of future sustainable food security, hunger and malnutrition. During the last 10 years and facilitated by its CEG, ICRISAT has become a leading international CGIAR centre that has championed the sequencing (and re-sequencing) of genomes of several crops like chickpea, pigeonpea, groundnut and pearl millet. A plethora of genotyping platforms have been established that cater for the different needs of researchers both in ICRISAT and NARS programs for both understanding plant biology as well as modernising breeding approaches. I believe that 10 years from today, we will have genome blue prints of all of our germplasm collections that will enable the tailoring of nutritionally rich climate smart (resilient) crops. The combination of mobile ICT technologies and genomics may well allow us to predict varietal performance at farm, field and within field scales, maximising resources. We must through the meeting of minds and disciplines continue to significantly accelerate the conversion of genetic information into knowledge and the translation of this knowledge into new and better products and services that are “good for the consumer, producer and environment. We need to consider new thinking and approaches and will need to forge enduring partnerships to realise our collective potential. Genome projects have played an important role in developing systems thinking. Systems Biology with its integrative approach will in the next 10 years significantly increase the impact of our knowledge. I am delighted that ICRISAT is pursuing such approaches. Congratulations