Researchers of the International Peanut Genome Initiative (IPGI) with 39 scientists from 26 organizations in 6 countries, including CEG-ICRISAT, were instrumental in cracking the first genome of cultivated peanut (Nature Genetics 2016). A team of 51 scientists from 9 institutes in China, India, USA and Australia, including ICRISAT, successfully decoded the complete DNA sequence of the ancestor genome of groundnut (Proc Natl Acad Sci USA 2016), the diploid A-genome (Arachis duranensis), providing insights into geocarpy – a unique reproductive process, oil biosynthesis and allergens.

1. ICRISAT-led global
team cracks
pigeonpea genome
1. Years of genome analysis by a global research partnership led by CEG-ICRISAT decoded the pigeonpea genome
(Nature Biotechnology, 2012). 48,680 pigeonpea genes were identified. A couple of these were found unique
to the crop in terms of drought tolerance, a key trait that can be transferred to other legume crops.
2. The first SSR marker kit was developed to detect genetic purity in pigeonpea hybrid ICPH 2438.
3. One “QTL-hotspot” containing 45 QTLs for 12 drought tolerance traits exlaining 58.2% phenootypic varition
was identified in chickpea. This “QTL-hotspot” has been introgressed widely in genetic backgrounds of several
elite varieties by sevearl breeding programs in India, Kenya and Ethiopia.
4. Jointly initiated by the CGIAR-GCP and Bill & Melinda Gates Foundation (BMGF), CEG-ICRISAT organized the
Molecular Breeding Platform (MBP, subsequently renamed the Integrated Breeding Platform) workshop. It
provided a foundation for developing world scientists, allowing their countries to take advantage of advanced
plant breeding technologies to meet the challenge of food security.
5. A US$ 1.7 million research grant was awarded by the National Science Foundation (NSF), USA to UC Davis and
CEG- ICRISAT, to propel research on nitrogen fixation in legumes, reviving the long discontinued/slow pace of
N-fixation research at ICRISAT. It provided a platform to identify genes controlling nitrogen fixation to develop
more efficient legume crops.
First molecular
markers kit for
purity assessment of
hybrids in pigeonpea
Molecular
Breeding Platform
(MBP) workshop
to harness
genomics tools
“QTL-hotspot” for
drought tolerance traits
in chickpea
1. An estimated 28,269 genes of chickpea were identified after sequencing CDC Frontier, a kabuli (large-seeded)
chickpea variety. Also completed high-quality sequencing of 90 additional genomes of chickpea (Nature
Biotechnology, 2013).
2. A “QTL-hotspot” containing QTLs for several root and drought tolerance traits was transferred through MABC
into JG 11, a leading variety of chickpea in India from the donor parent ICC 4958. This has enhanced 12-24%
higher yield in JG 11. Several lines, after multi-location testing , have entered in varietal release trials of ICAR
in India.
3. BGI and ICRISAT signed an MoU on 24 April 2012 in Shenzhen, China, for long-term collaborative genomics
research on ICRISAT’s mandate crops. This has been crucial to decode genome sequences of pearl millet,
groundnut as well as germplasm resequencing, epigenomics and proteomics studies.
4. To effectively enhance precision and efficiency of breeding programs, ICRISAT and IBP initiated the
‘digitalization’ of crop breeding. It was a first and crucial step towards enhancing genetic gains in breeding
programs of ICRISAT’s mandate crops.
5. CEG-ICRISAT hosted the sixth International Conference on Legume Genetics and Genomics (ICLGG) in
collaboration with ICAR in Hyderabad. The event brought together 500 delegates representing different
disciplines of legume biology from 44 countries, showcasing 60 talks and 290 poster presentations over 13
sessions.
Chickpea reference
genome and 90
chickpea lines
sequenced
First molecular
breeding product
for drought tolerance
in chickpea
BGI and ICRISAT sign
MoU to boost genomics
research in dryland crops
Digitalization of
crop breeding
Sixth ICLGG with
over 500 participants
from 44 countries
organized
2012-2013
1. Introgression lines using Marker-assisted backcrossing (MABC) for foliar fungal disease resistance were bred in
groundnut by the efforts of ICRISAT and Indian NARS partners. A pod yield increase of 20-96% in introgression
lines over their respective recurrent parents and a disease score similar to resistant donor GPBD 4 was recorded in
evaluation trials.
2. In MABC programs undertaken to introgress resistance to Fusarium wilt and Ascochyta blight in C 214, an elite cultivar
of chickpea, 3 lines resistant to Fusarium Wilt and 7 lines resistant to Ascochyta blight were identified. NARS partners
including ICAR-IIPR, ARS-Gulbarga of UAS-Raichur, Jawahar Nehru Krishi Vishwavidyalaya started such molecular
breeding efforts and developed several superior lines for these diseases.
3. The ‘3000 Chickpea Genome Sequencing Initiative’ was launched. An advanced sequencing facility that included
Illumina HiSeq 2500 and a high performance computational genome analysis (HPCGA) facility were established in CEG.
4. A shared industrial scale, low-density SNP genotyping service was established through Intertek Group plc for the CGIAR
and public breeding programs serving sub-Saharan Africa and Southern Africa. The project has been able to aggregate
samples and provide genotyping services at US$ 1.5 per sample.
5. Genomic Open-Source Breeding Informatic Initiative (GOBII) was set up in 2015 with funding from BMGF and global
collaborators from the public and private sectors. The initiative works closely with CGIAR Centers to develop
open-source computational infrastructure and analysis capabilities, enabling the implementation of genomic and
marker-assisted selection as part of routine breeding programs for staple crops in developing world.
6. To accelerate collaborative genome sequencing and other biotechnology applications in peanut, the Shandong Peanut
Research Institute (SPRI) and ICRISAT signed a Memorandum of Agreement (MoA) to set up the “Joint SPRI-ICRISAT
Biotech Lab” in Qingdao, China.
7. Union Minister for Agriculture, Government of India, Mr Radha Mohan Singh appreciates the contribution of CEG
scientists towards helping smallholder farmers.
1. Researchers of the International Peanut Genome Initiative (IPGI) with 39 scientists from 26 organizations in
6 countries, including CEG-ICRISAT, were instrumental in cracking the first genome of cultivated peanut
(Nature Genetics 2016).
2. A team of 51 scientists from 9 institutes in China, India, USA and Australia, including ICRISAT, successfully
decoded the complete DNA sequence of the ancestor genome of groundnut (Proc Natl Acad Sci USA 2016), the
diploid A-genome (Arachis duranensis), providing insights into geocarpy – a unique reproductive process, oil
biosynthesis and allergens.
3. Research co-led by ICRISAT, BGI-Shenzhen, and the French National Research Institute for Sustainable
Development (IRD) decoded the reference genome of pearl millet and resequencing of 1000 pearl millet lines
(Nature Biotechnology, 2017).
4. The genomes of 292 pigeonpea lines from 23 countries were resequenced by a global team of 19 scientists led
by CEG-ICRISAT (Nature Genetics 2017). ‘efl3’ gene was identified for making pigeonpea photo-period insensitive
for wider cultivation. The likely origin of the domesticated pigeonpea was also traced to Madhya Pradesh in
central India.
5. Using MABC and MAS approaches, CEG-ICRISAT and partner institutes developed high oleate introgression lines
in groundnut, many of which are undergoing special trials by ICAR, India. High oleate groundnuts offer two
commercial benefits -- health benefits to consumers and an extended shelf life of groundnut products.
Molecular breeding
lines for disease
resistance in
chickpea
Joint biotech lab
set up in China
Visit of Union Agriculture
Minister to CEG
Launch of the 3000
chickpea genome
sequencing
initiative
First molecular breeding
product for foliar disease
resistance in groundnut
Genomic Open-Source
Breeding Informatic
Initiative (GOBII)
launched
High Throughput
Genotyping (HTPG)
project for low-cost
genotyping launched
2014-2015 2016-2017
Genotyping services
for SSR & DArT
markers started
First workshop
on NGS Data
Analysis
“HHB 67 Improved”
pearl millet hybrid
released
First CEG training
course organized
Center of Excellence
in Genomics
is founded
First SSR-based
genetic map in
groundnut
1. CEG was initially launched with a CoE grant from the Department of Biotechhnology, Government of India to
offer marker genotyping services and train scientists in genetic analysis and modern breeding.
2. HHB 67 Improved was the first marker-assisted breeding product released and notified in India. This joint effort
by ICRISAT’s scientists and partners was aimed at better seed production and upscaling to encourage adoption
among resource-poor dryland farmers to generate higher incomes through better yields.
3. The CEG-hosted two-week course on “Molecular Marker Applications in Crop Genetics and Breeding” to
scientists and breeders from various ICAR institutes, Indian agricultural institutes and research foundations.
4. Genotyping services for SSR and DArT markers at cost-to-cost basis were started for deployment of modern
breeding in crop improvement programs.
5. The CGIAR Generation Challenge Program (GCP)-sponsored international workshop on next generation
sequencing (NGS) data analysis that had 30 scientists from 9 countries (USA, UK, France, Korea, Japan,
Australia, Mexico, India and Philippines).
6. Scientists from ICRISAT and partner institutes in Brazil and USA published the first SSR-based genetic map for
cultivated groundnut in 2009. The map served as a foundation for developing several genetic maps.
First genome of
cultivated peanut
cracked
Global team cracks
ancestor genome
of groundnut
Pigeonpea genome
of 292 lines
sequenced
Molecular breeding
lines for oil quality in
groundnut
Pearl millet reference
genome and 1000
lines sequenced
Partners 2007-2009
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Center of Excellence in
Genomics & Systems Biology
A 10 year journey of Excelence in Science
and Partnership (2007 - 2017)
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NSF-sponsored grant
to boost nitrogen
fixation in legumes
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5Vision: To fully utilize modern
genetic analysis and breeding
methods by undertaking high-
quality genome science and
empowering crop improvement
programs to deliver higher genetic
gains in developing countries
2010-2011