To develop and deploy genetic and genomic resources and tools for structural, comparative, translational and functional genomics approaches for mapping, dissection and characterization of priority target traits leading to marker/allele discovery and their initial validation for deployment in forward breeding to accelerate the rate of genetic gain in ICRISAT mandate crops.

1. Genomics & Trait Discovery (GTD)
@ICRISAT
Rajeev Gupta, PhD (Cantab)
& TEAM
Principal Scientist & Theme Leader
Genomics & Trait Discovery,
ICRISAT, Patancheru
g.rajeev@cigar.org
CGIAR Research Program on Grain Legumes & Dryland Cereals (CRP-GLDC)
Flagship Program 5 (Pre-Breeding & Trait Discovery) Leader

2. GTD: Mission & Vision
“To develop and deploy genetic and genomic resources and tools
for structural, comparative, translational and functional
genomics approaches for mapping, dissection and
characterization of priority target traits leading to marker/allele
discovery and their initial validation for deployment in forward
breeding to accelerate the rate of genetic gain in ICRISAT
mandate crops”

3. Genomics & Trait Discovery (GTD) Team
An Excellent Team!
TL-GTD
Rajeev G
Groundnut
Manish P
Chickpea
Mahendar T
Pigeon pea
Rachit S
Pearl millet
Rakesh S
Sorghum
Finger millet
Santosh/RG

4. GTD Team: Major Areas aka ‘Big Lifts’
 Genomic tools & resources
 Genetic tools & resources
 Trait discovery, mapping, characterization & development
 Candidate gene discovery for target traits
 Marker discovery, assay development, and validation
leading to traits SNPs panels for HTPG platform
 QC and mid-density panels for global breeding applications
 Genomic assisted breeding activities such as MABC, MAS,
MARS, GS etc.
 Capacity building

5. Understanding Germplasm, Genomes, & Genes
 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
 Connecting phenome with genome using
transcriptome, proteome and metabolome
 Capturing the genetic variation present in diverse
germplasm through whole genome re-sequencing

6. Next-Gen 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
 Candidate gene discovery and functional
validation
 Development and validation of diagnostic
markers
Diagnostic markers
QTL and gene discovery
Multi-parent populations

7. Genomics-Assisted Breeding
 MAS, MARS, MAPI 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
 QC, mid-density panels
Genomic selection

8. Genome to Field: Downstream Applications
 Strengthening seed-chain system through
 Marker-based purity testing
 DNA finger-print 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

9. Trait Stage & Gateway: Discovery Phase
Stage 1: Scoping
Question: Why is
development for this trait
necessary?
Key outcomes:
• Demonstrate the need for
trait development pipeline
(aligned with PP).
Stage 2: Discovery
Question: How and where
can improved trait be sourced
from?
Key outcomes:
• Demonstrate a reliable,
relevant phenotyping
protocol; establishing
required trait variation;
prioritized list of
QTLs/donors
Stage 3: Development
Question: How stable are key
trait loci in various background
and environments?
Key outcomes:
• Demonstrate a clear, well-
established loci contributing
to definite improvement in
the target trait.
New donor
× Elite1
(Rc2 )22
× Elite 2 × Elite 3 × Elite 4
‘Looking forward

10. Trait Stage & Gateway: Deployment Phase
Stage 4: Deployment
Question: How and where to
deploy key loci in breeding
program?
Key outcomes:
• Elite breeding material
containing the validated loci
Stage 5: Testing
Question: Is locus successful?
Key outcomes:
• Confidence in field performance
• Effect across
backgrounds/environments
Stage 6: Introduction
Question: Who/how to distribute?
Key outcomes:
• Use in the breeding programs

11. GTD: Opportunities
Aligning with EiB, One CG and other platforms for best practices &
better integration of GTD with Crop Improvement programs
Genomic assisted transformation of product development by
enhancing rate of genetic gains in climate change scenarios
Next generation genomic and trait discovery for crop improvement
Wider acceptability of native genetic discovery approaches
Further strengthening of global networks and partnerships
Knowledge sharing with global scientific community and partners

12. Issues & Challenges
Conflicts
Funding
Transparency
Team spirit
Uncertainty
Donor driven research
Career progression
Retain best talent

13. Thank You!
Happy New Year 2021!

14. CINTRIN, TIGR2ESS, MillNETi,
FP5-CRP GLDC……
Rajeev Gupta, PhD (Cantab)
& TEAM
Principal Scientist & Theme Leader
Genomics & Trait Discovery,
ICRISAT, Patancheru
g.rajeev@cigar.org
CGIAR Research Program on Grain Legumes & Dryland Cereals (CRP-GLDC)
Flagship Program 5 (Pre-Breeding & Trait Discovery) Leader

15. Name Designation Organisation Role
Dr Rajeev Gupta Prinicipal Scientist ICRISAT PI
Dr R.K. Srivastava Senior Sceintist ICRISAT co-I
Dr S. Deshpande Senior Sceintist ICRISAT co-I
Dr A. Rathore Senior Sceintist ICRISAT co-I
Dr Praveen Chhuneja Director, SAB PAU co-I
Dr Satinder Kaur Assistant Mol. Biol. PAU co-I
Dr Varinder Pal Singh Senior Soil Chemist PAU co-I
Dr Manoj Prasad Staff Scientist NIPGR co-I
Dr D. Chattopadhayay Senior Sceintist NIPGR co-I
Dr Kiran Romana PDRA ICRISAT PDRA
Dr Srikanth Bollam Visiting Scientist ICRISAT PDRA
Dr P Vijayalakshmi PDRA ICRISAT PDRA
Dr T Bandyopadhyay PDRA NIPGR PDRA
Dr Amritpal Kaur PDRA PAU PDRA
Name Designation Organisation Role
Dr Tina Barsby CEO & Director NIAB PI
Dr Alison Bentley Director, GPB NIAB Co-I
Dr Emma Wallington Program Leader NIAB Co-I
Prof Howard Griffith Professor UCAM Co-I
Prof Ottoline Leyser Director, SLCU UCAM Co-I
Dr Stephanie Smith PDRA SLCU PDRA
Dr Stephanie Swarbreck PDRA UCAM PDRA
Dr Alek Legisa Research Scientist NIAB PDRA
Cambridge India Network for
Translational Research in Nitrogen
 Multi-million dollars network recently funded & led by ICRISAT, India and NIAB, UK
 8 partners from India (ICRISAT, PAU, NIPGR) and UK (NIAB, SLCU, UCAM, ADAS Ltd, KisanHub)
 6 Work Packages (WPs) focusing on various objectives and approaches in target crops
 From models (Arabidopsis and Brachypodium) to crops (wheat, sorghum, pearl & foxtail millet)
 Explore natural variation in germplasm of target crops for Nitrogen Use Efficiency (NUE)
 Capacity building and expanding network (exchange visits/technologies, trainings, workshops etc.)
Target Crops Project Launch Review Meeting Training Course PAU Kisan Mela
NUE screens in field & controlled environments in progress
Wheat Sorghum
PIs: Rajeev Gupta, ICRISAT, INDIA & Tina Barsby, NIAB, UK
E-mail: g.rajeev@cigiar.org
Sorghum Pearl millet
http://www.niab.com/cintrin https://twitter.com/CINTRIN_UKIndia http://www.niab.com/pages/id/458/How_to_get_involved
Team Objectives & Approaches
Title & Link of News Media Title & Link of News Media
India, UK to research on crops with nature friendly genesThe Week Magazine New partnership to optimise use of nitrogen in cereal crops for higher yieldsNews Now
Scientists to develop new cereal varieties that check greenhouse gasesThe Times of India New partnership to optimise use of nitrogen in cereal cropsDanik Bhaskar, Hindi
ICRISAT and NIAB, UK join hands to develop cereals that use nitrogen efficiently for higher yieldsThe Economic Times New partnership to optimize use of nitrogen in cereal crops for higher yieldsNamasthe Telangana, Telugu
Research centres to focus on nitrogen efficient cereal varietiesThe Hindu New partnership to optimise use of nitro Eenadu India News
India & UK partner to optimise use of nitrogen in cereal cropsCNBC, Money ControlICRISAT and NIAB, UK join hands to develop cereals that use nitrogen efficiently for higher yieldsNews Fiber
New partnership to optimise use of nitrogen in cereal cropsIndia Today India & UK partner to optimise use of nitrogen in cereal cropsBiz News
New partnership to optimise use of nitrogen in cereal cropsBusiness Standard ICRISAT and NIAB, UK join hands to develop cereals that use nitrogen efficiently for higher yields15minute News
New partnership to optimise use of nitrogen in cereal cropsDaily Excelsior India & UK partner to optimise use of nitrogen in cereal cropsDigital News World
Partnership to work on nitrogen efficiency in cereal cropsRural Marketing magazineCereals that use nitrogen better, pollute lessW3Live News
India-UK Researchers develop cereal crop varieties that cuts greenhouse emissionsThe Hans India ICRISAT and NIAB, UK join hands to develop cereals that use nitrogen efficiently for higher yieldsDaily India News
New partnership to optimize use of nitrogen in cereal crops for higher yields and less environmental pollutionThe Non-Profit Press India & UK partner to optimise use of nitrogen in cereal cropsNews Reality
New partnership to optimize use of nitrogen in cereal crops for higher yields and less environmental pollutionHumanitarian News India & UK partner to optimise use of nitrogen in cereal cropsFinance News Coverage
New partnership to optimise use of nitrogen in cereal crops for higher yieldsNews Now ICRISAT and NIAB, UK join hands to develop cereals that use nitrogen efficiently for higher yieldsPatrika News
New partnership to optimise use of nitrogen in cereal cropsDanik Bhaskar, Hindi ICRISAT and NIAB, UK join hands to develop cereals that use nitrogen efficiently for higher yieldsCEBRA, University of Melbourne
New partnership to optimize use of nitrogen in cereal crops for higher yieldsNamasthe Telangana, TeluguICRISAT and NIAB, UK join hands to develop cereals that use nitrogen efficiently for higher yieldsAgriXchange

16. CINTRIN 1: Summary
 Large genetic variations exit for NUE in global association panels
NS and NIS lines identified from multi-years/seasons screens in various N regimes
MTA/SNPs/genomic regions identified for various direct/indirect traits related to NUE
with direct implication in crop breeding in future
Temporal and spatial N regulation of differentially expressed genes in NS and NIS lines
CINTRIN provided a great avenue for capacity building, knowledge sharing, low cost
technology (e. g., LCC) validation and strengthening the professional networks resulting
in attracting funds in crop improvement and nutritional areas
CINTRIN 2 developed and submitted for funding

17. CINTRIN 1: Network Activities
 Review meeting cum workshop of all CINTRIN partners at ICRISAT.
 Review meeting cum ‘Long Look’ workshop of all 4 VJCs conducted
by CINTRIN at ICRISAT, 2018. Also attended by DBT/BBSRC
 BBSRC dissemination workshop, London, December 2019
 Short term exchange visits, 6 ICRISAT scientists visited various
laboratories in UK to further foster the on-going collaborations
 Training course on quantitative methods in plant breeding (30
participants from UK and India) from conducted by NIAB, UK team.
 Training course on “Quantitative Methods in Plant Breeding”
(QMPB’2018) on March 12-23, 2018 at NIAB, Cambridge, UK, was
attended by two CINTRIN PDRAs from ICRISAT.

18. Cambridge India Network for
Translational Research in
Nitrogen
Cover Story from CINTRIN

19. Vision and Objectives: Key Research Questions, Cross-disciplinary
Partnerships and Collaborations bridging Science and Society
TIGR2ESS (2018-2022) will integrate these four thematic questions
through 6 fully interlinked Flagship Projects:
 FP1: Defining a Second Green Revolution for India
 FP2 (Lead-Rajeev G): Crop Sciences- Water use and
Photosynthesis
 FP3: Crop Sciences- Heat and Drought Resilience in Wheat
 FP 4: Water use and Management in a Changing Monsoon Climate
 FP5: Supply Chains: modelling water use for sustainable
livelihoods
 FP6: Impacting Well-being in Rural & Urban communities
TIGR2ESS
Transforming India’s Green Revolution by Research and
Empowerment for Sustainable food Supplies

20. TIGR2ESS: Summary
Explored natural variation in global diversity germplasm
collections (~250 in sorghum and ~400 in pearl millet lines)
for water use efficiency and its component traits
(transpiration efficiency, water extraction capacity etc.)
Collected data on ~20 direct and derived traits with
physiology team
Sorghum panel screens completed for 2 seasons, GWAS in
progress
Pearl millet 1st season screening completed, 2nd season
screen delayed due to Covid 19.
FP2/3 workshop for Sep 2020 postponed due to Covid
Deep-diving in a set of contrasting lines using physiological,
molecular and bio-informatics tools with UK and NIPGR
partners
Knowledge sharing and capacity building by training
students, researchers, impacted due to Covid
General assembly organized at ICRISAT in Jan 2020

21. TIGR2ESS: Network Activities
Happenings, Dec 31, 2020
Happenings, Jan 24, 2020

22. TIGR2ESS: Networking with Policy Makers
1 to 1 Discussions With Mr Anirudh Tewari, Additional Chief Secretary, Government of Punjab, India
With Dr Arbind Mitra, Science Secretary, GOI With International Advisory Board (IAB) TIGR2ESS

23. MillNETi
Millets and Nutritional Enhancement Traits for Iron bioavailability
• FP1: Growth
• FP2: Bioavailability
• FP3: Processing
• FP4: Outreach and extension
MillNETi (2019-2021) brings together a multidisciplinary team of
researchers from the University of Cambridge (Departments of
Plant Sciences, Development Studies, MRC Bone Health group,
Pathology, the Global Food Security IRC, the Cambridge Global
Challenges SRI and the Cambridge-Africa initiative), the Centre
for Global Equality, NIAB, the NIAB Innovation
Farm, Rothamsted Research, MRC The Gambia, Bahir Dar
University (Ethiopia) and ICRISAT (India, Ethiopia, Malawi),
working with partner institutions HarvestPlus, King's College
London and JeCCDO.

24. THE PROCESS
FP4: Variety/ hybrid
development
FP1: Priority setting,
impact acceleration
FP2: Transforming
Agri-Food Systems
FP5: Pre-breeding &
Trait Discovery
FP3: Farm, household
management
Five Flagship Programs deliver
into two impact pathways
• 9 crops (including all ICRISAT
mandate crops)
• M&E with key indicators
• Prioritize women and youth
CRP-GLDC

25. FP5: Vision & Mission
“To develop and deploy modern genetic, omics, molecular
resources and tools for structural, comparative, translational and
functional genomics approaches for mapping, dissection and
characterization of target traits by exploring natural and induced
diversity leading to marker/allele/events discovery and improved
processes for deployment in breeding to accelerate the rate of
genetic gain in GLDC crops”

26. FP5: Core Team
Flagship Program 5 (FP5): Pre-breeding & Trait Discovery
FP5 Leader Rajeev Gupta (ICRISAT, India)
CoA 5.1 Pre-Breeding Ousmane Boukar (IITA, Kano)
Jean-Francois Rami (CIRAD, France)
CoA 5.2 Trait Discovery Damaris Odeny (ICRISAT, Nairobi)
Laurent Laplaze (IRD, France)
CoA 5.3 Enabling Technologies Pooja Bhatnagar (ICRISAT)
Aladdin Hamwieh (ICARDA)
An Excellent Team!

27. FP5: Cluster of Activities (CoAs)
Cluster of activities Major activity
CoA 5.1: Pre-breeding Use of natural (e. g., in un-adapted germplasm)
or induced (e. g. mutants populations,
transgenic) diversity available in key priority
traits in GLDC crops
CoA: 5.2: Trait discovery Trait discovery, dissection and elucidation with
molecular, omics, biochemical and
physiological tools to provide
markers/alleles/events/knowledge for use in
breeding
CoA 5.3: Enabling technologies Modern enabling tools, technologies, and
platforms to facilitate efficient trait discovery
and breeding
• 80 activities funded in 2020
• Significant progress in all CoAs since start of CRP in 2018
• Highlighted in recent CAS Review

28. FP5: Activity Leaders 2020
FP5 Activity Lead Lead Centre
Daniel Foncéka CIRAD
David Pot CIRAD
Jean-Francois Rami CIRAD
Aladdin Hamwieh ICARDA
Shiv Kumar Agrawal ICARDA
Abhishek Rathore ICRISAT
Damaris Odeny ICRISAT
Hari Kishan Sudini ICRISAT
K Himabindu ICRISAT
Mahendar Thudi ICRISAT
FP5 Activity Lead Lead Centre
Mamta Sharma ICRISAT
Manish Pandey ICRISAT
Manish Roorkiwal ICRISAT
Pooja Bhatnagar ICRISAT
Rachit Saxena ICRISAT
Rajan Sharma ICRISAT
Rajeev Gupta ICRISAT
Rajeev K Varshney ICRISAT
Rakesh K Srivastava ICRISAT
S Gopalkrishnan ICRISAT
FP5 Activity Lead Lead Centre
Santosh Deshpande ICRISAT
Shivali Sharma ICRISAT
Sobhan Sajja ICRISAT
Boukar, Ousmane IITA
Chigeza, Godfree IITA
Chigeza, Godfree IITA
G. Chigeza IITA
Laurent Laplaze IRD
Rémy Pasquet IRD
Yves Vigouroux IRD
Super 30 Teams!!!

29. 2020: Key Highlights of FP5
 Significant progress in trait discovery, markers applications (~2M data points since start of CRP),
molecular assisted breeding products releases (chickpea-3, groundnut-2) and advancements (pearl
millet, sorghum, groundnut etc.)
 Significant progress in upstream trait discovery, characterization and deployment areas resulting in
several publications (~100 in 2020 & a total ~300 since start of CRP-GLDC in 2018) in high impact factor
journals
 Public private partnerships (e. g., ICRISAT-Corteva, IITA-Bayer) for significant advances in traits discovery,
enabling tools & technologies, and crop improvement programs
 Trainings, students/researchers exchanges, workshops, seminars, symposiums, conferences etc. for
knowledge sharing and capacity building
 Progresses from FP5 highlighted in recent CAS review conducted in May-June 2020
 Appreciated the progress by IAC members attached to FP5 in annual review, Oct 2020

30. FP5: Public Private Partnership (PPP)
• ICRISAT-Corteva: Master Alliance Agreement (MAA) for access to various
technologies such as genome editing, next generation transformation (Quick
Transformation), Rapid Generation Turnover (RGT), DH etc.
• ICRISAT-Corteva-EiB consortium: for a comprehensive pearl millet improvement
program. Recent discussion going on to expand this to sorghum
• ICRISAT-Keygene: will work on innovative approaches to trait development in grain
legumes by using KeyGene’s proprietary Keypoint® platform to develop reservoirs
for gene discovery and trait development
• IITA-Bayer-EiB consortium launched in 2020

31. Resource Mobilization: Summary
Project Funder Role Total funding USD Duration
CINTRIN 1 Newton Fund UK/DBT PI ~3.5M 2016-2019
TIGR2ESS GCRF, UK FP2 Lead ~10M 2018-2022
MillNETi GCRF, UK CoPI ~1.7M 2019-2021
Finger millet-GOK GOK CoPI ~1.5M 2016-2020
Chickpea mission project DBT CoPI ~7M 2020-2025
DAC-chickpea, pigeon pea DARE CoPI ~1.6M 2017-2020
Quality Protein GFI (through BMGF) CoPI ~150K 2020-2021
FP5 Leader CRP-GDC CRP-GLDC FP5 Lead ~5M (w1/w2) 2018-2021
CINTRIN 2 DBT PI ~730K 2021-24 Under revision
TIGR2ESS/MillNETi phaseII GCRF, UK, other funders CoPI TBD 2022-Under discussion
Rhizobial symbiosis UM6P, Morroco CoPI ~684K 2021-24, submitted
Beyond CRP- funding SMO TBD 2022-24, to be developed
CLEAR (Climate Livelihoods
& Resilience) (multiple
CGIAR partners)
DFID (now FCDO after
merger of FCO & DFID UK,
in 4Q2020) TBD (~50M)
2021-2026, Under
discussion
Millet Mission Project DBT CoPI TBD 2021-2026 Under discussion

32. Path forward CINTRIN
 CINTRIN 2 revision in progress for next phase of funding
 Finish data analysis and manuscripts
 SNP markers validation and deployment in breeding is proposed in CINTRIN2
 TIGR2ESS
 Finish screens/GWAS in sorghum, pearl mille and manuscripts
 MTAs/SNPs identification, validation, deployment
 2nd phase of TIGRESS for funding
 FP5 CRP-GLDC
 Impactful finish to CRP-GLDC and FP5 as 2021 is last year
 Participate in development of research areas for interim funding from 2022-24
 GTD-Theme
 Alignment with EiB, One CG,
 Best practices (e.g. Stage & Gateway) and integration with CI programs
 More focus on ‘Science of Discovery to Science of Delivery’, i.e., applications

33. Thank You!
Happy New Year 2021!