No. 1556 01 February 2013

Global research team decodes genome sequence of 90 chickpea lines

Decoded genome of chickpea, a leading grain legume for many poor smallholder farmers, promises improved livelihoods in marginal environments

In a scientific breakthrough that promises improved grain yields and quality, greater drought tolerance and disease resistance, and enhanced genetic diversity, a global research team has completed high-quality sequencing of not one but ninety genomes of chickpea.

(L-R) Dr Swapan Datta, DDG (Crop Science), ICAR; Mr Ashish Bahuguna, Secretary, Ministry of Agriculture, GoI; Dr William Dar, Director General, ICRISAT; and Dr Rajeev Varshney, coordinator of ICGSC and Director – Center of Excellence in Genomics, ICRISAT during the press conference announcing the decoding of the chickpea genome sequence at Krishi Bhavan, New Delhi.

Nature Biotechnology, the highest ranked journal in the area of biotechnology, featured the reference genome of the CDC Frontier chickpea variety and genome sequence of 90 cultivated and wild genotypes from 10 different countries, as an online publication on 27 January 2013. The paper provides a map of the structure and functions of the genes that define the chickpea plant. It also reveals clues on how the sequence can be useful to crop improvement for sustainable and resilient food production toward improved livelihoods of smallholder farmers particularly in marginal environments of Asia and sub-Saharan Africa.

The research milestone was the result of years of genome analysis by the International Chickpea Genome Sequencing Consortium (ICGSC) led by ICRISAT, involving 49 scientists from 23 organizations in 10 countries.

The global research partnership succeeded in identifying an estimated 28,269 genes of chickpea after sequencing CDC Frontier, a kabuli (large-seeded) chickpea variety. Re-sequencing of additional 90 genotypes provided millions of genetic markers and low diversity genome regions that may be used in the development of superior varieties with enhanced drought tolerance and disease resistance. This will help chickpea farmers become more resilient to emerging challenges brought about by the threat of climate change. The genome map can also be used to harness genetic diversity by broadening the genetic base of cultivated chickpea genepool.

“ICRISAT and its partners have once again demonstrated the power of productive partnerships by achieving this breakthrough in legume genomics,” said Director General William Dar.  “Under the CGIAR Research Program (CRP) on Grain Legumes led by ICRISAT along with other CGIAR Consortium members and program as well as national partners, genome sequencing will play a crucial role in speeding up the development of improved varieties for smallholder farmer crops such as chickpea.”

“In the face of growing global hunger and poverty amid the threat of climate change, the chickpea genome sequence will facilitate the development of superior varieties that will generate more income and help extricate vulnerable dryland communities out of poverty and hunger for good, particularly those in the drylands of Asia and sub-Africa for whom ICRISAT and our partners are working,” Dr Dar added.

“Genetic diversity, an important prerequisite for crop improvement, is very limited and has been a serious constraint for chickpea improvement. This study will provide not only access to ‘good genes’ to speed up breeding, but also to genomic regions that will bring genetic diversity back from landraces or wild species to breeding lines,” explained Dr Rajeev Varshney, coordinator of ICGSC and Director – Center of Excellence in Genomics, ICRISAT.

“Currently, it takes 4-8 years to breed a new chickpea variety. This genome sequence could reduce by half the time to breed for a new variety with market-preferred traits,” he added.

Highlighting the importance of the research, renowned agricultural scientist Prof MS Swaminathan, Member of Indian Parliament, said, “I would like to compliment the excellent scientific work done by Rajeev Varshney of ICRISAT and his colleagues in developing a high-quality genome sequence of chickpea. I am confident that the knowledge provided by this study will help accelerate the improvement of this crop through marker-assisted breeding.”

Recognizing the efforts of the global research team, Mr Ashish Bahuguna, Secretary, Ministry of Agriculture, Government of India said, “Decoding of the chickpea genome would facilitate the development of improved varieties with higher yields and greater tolerance to biotic and abiotic stresses. This would help chickpea farmers to increase productivity, reduce cost of inputs and realize higher incomes.” He added: “This development is of great importance to India, the largest producer and consumer of chickpea.”

Highlighting the importance of the breakthrough to India, Dr Swapan Datta, Deputy Director General – Crop Science, Indian Council of Agricultural Research (ICAR), said, “The chickpea genome sequence is expected to help in the development of superior varieties with enhanced tolerance to drought and resistance to several biotic stresses. India will benefit most from this genome sequence, our country being the largest producer of chickpea. This, in my opinion, is by far the most significant collaboration between ICAR, ICRISAT and the global genomics community.”

Drs Dar and Varshney addressing the media during the press conference.

According to Professor Jun Wang, Director of BGI, “The collaboration between BGI and ICRISAT has yielded significant achievements in orphan crops research, like the pigeonpea genome before and now, the chickpea genome. I believe that our partnership will revolutionize research on orphan crops, which are key staple crops in many low-income countries and are extremely important to smallholder farmers worldwide.

“The importance of this new resource for chickpea improvement cannot be overstated. This genome sequence will provide the basis for a wide range of studies, from the important goal of accelerated breeding, to identifying the molecular basis of a range of key agronomic traits, to basic studies of chickpea biology,” said Professor Doug Cook from the University of California-Davis, USA.

“Making the chickpea genome available to the global research community is an important milestone in bringing chickpea improvement into the 21st century to address nutritional security of the poor – especially the rural poor in South Asia. We look forward to seeing how researchers around the globe will harness this resource to increase chickpea productivity against the backdrop of climate change in the developing world,” according to Dr David Bergvinson, Senior Programme Manager, Science & Technology, Global Development, Bill & Melinda Gates Foundation.

The chickpea genome sequencing project was undertaken by the ICGSC led by ICRISAT, the University of California-Davis (USA) and BGI-Shenzhen (China) with key involvement of national partners in India, USA, Canada, Spain, Australia, Germany and Czech Republic.

The initiative was funded by the CGIAR Generation Challenge Programme (GCP), US National Science Foundation (NSF), Saskatchewan Pulse Growers (Canada), Grains Research  & Development Corporation (Australia), Indo-German Science Technology Corporation (Germany and India), National Institute for Agricultural and Food Research and Technology (Spain), National Research Initiative of US Department of Agriculture’s National Institute of Food and Agriculture (USA), Ministry of Education, Youth and Sports of the Czech Republic and the European Regional Development Fund, University of Cordoba, ICAR (India), BGI (China) and ICRISAT.

Link to full paper on Nature Biotechnology Journal:

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Project on recycling wastewater to improve agricultural production and farmers’ livelihoods launched

(L-R) Mr Dinakar Babu, Dr Antonio Lopez, Dr Dar and SP Wani during the project’s kick-off meeting at Patancheru.

Aiming to address issues of water scarcity, poverty and food insecurity through wastewater reuse for agriculture, ICRISAT is now leading a consortium of national partners in the implementation of India’s component of the project “Integrating bio-treated wastewater reuse with enhanced water-use efficiency to support the green economy in EU and India.” The project, also known as ‘Water4Crops-India’, is a mirror of EU’s Water4Crops project composed of 21 consortium partners led by the Istituto di Ricerca Sulle Acque – Consiglio Nazionale delle Ricerche (IRSA-CNR), Department of Bari, Italy.

At the inaugural session of the project’s kick-off meeting on 29 January at the ICRISAT headquarters in Patancheru, Director General William Dar said, “Water reuse is of critical importance to the semi-arid regions of the world. Following ICRISAT’s successes with rainwater harvesting and management, we will now lead the Indian consortium in venturing into recycling industrial and domestic wastewater for agricultural use to improve the livelihoods of the rural poor, particularly those in the country’s dryland areas.”

Also speaking at the inaugural session, Mr Dinakar Babu, Collector, Medak district, Government of Andhra Pradesh, highlighted the need for recycling and reusing water and promised to extend support in setting up the site in Medak district for industrial wastewater recycling.

The two-day kick-off meeting, attended by EU and Indian consortia partners from state agricultural universities, national research institutes, nongovernment organizations (NGOs), and private industrial partners, aimed to discuss India’s side of the workplans; prepare detailed activity plans with milestones and  timelines; identify opportunities for collaboration among the Indian partners and develop package-wise ties with EU partners; build the consortium team; and discuss the project’s dissemination and communication strategy.

Under the project, ICRISAT along with its consortium partners will embark on recycling treated wastewater (grey water) from domestic use and industrial wastewater. The consortium is unique as national and international research organizations and universities have joined hands with private entrepreneurs to find a win-win solution to wastewater disposal using bio-treatments for reuse in agriculture. This initiative will benefit farmers, industries, researchers as well as government organizations.

Among the Indian consortium partners are: The Energy Research Institute (TERI); National Environmental Engineering Research Institute (NEERI); Euro India Research Centre (EIRC), University of Agricultural Sciences Bangalore (UASB); University of Agricultural Sciences Dharwad (UASD); MS Swaminathan Research Foundation (MSSRF); SABMiller, India; and Jain Irrigation Systems Limited (JISL).

Through this initiative, Europe and India will share experiences, technologies and knowledge to benefit farmers, researchers and policy makers. The consortium will be working on three types of industrial waste water mainly from the Charminar Breweries of SABMiller, India in Andhra Pradesh; the Onion and Fruit Processing Plant at JISL, Jalgaon in Maharashtra; and the Sugar Factory from Ugar Sugar in Karnataka.

Treatment of domestic wastewater will be studied and used in Hyderabad, Andhra Pradesh; Kolar, Karnataka; and Nagpur, Maharashtra; and saline wastewater from industries in the coastal regions. The consortium will also address the issue of rehabilitating degraded lands using untreated wastewater at certain sites to be identified.

The project is led in India by Dr S P Wani, ICRISAT Principal Scientist (Watersheds) and in Europe by   Dr Antonio Lopez, Head of Unit, National Research Council, Water Research Institute, Italy.

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USAID supports project to apply genomics research to pigeonpea improvement

Releasing the ICRISAT-USAID project document during the project launch at Patancheru.

In the fight against poverty and hunger amid the threat of climate change, highly nutritious and drought-tolerant crops are the best bets for smallholder farmers. To assist pigeonpea breeders develop such improved cultivars more efficiently using genomic tools, a three-year, US$2-million pigeonpea molecular breeding project was launched on 30 January at ICRISAT-Patancheru.

The project “Pigeonpea Improvement using Molecular Breeding” supported by the United States Agency for International Development (USAID) India Mission will be implemented by ICRISAT along with the National Bureau of Plant Genetic Resources (NBPGR), New Delhi; the University of Agricultural Sciences (UAS), Raichur, Karnataka; Acharya NG Ranga Agricultural University (ANGRAU), Hyderabad; and other partners in India and Africa.

“I am very pleased to announce this new partnership between the Governments of India and the United States, and ICRISAT – a partnership that will take new studies in pigeonpea genomics to the next stage of scientific research. This collaboration will improve the agricultural productivity of pigeonpea, a main source of protein for more than a billion people in Asia, Africa, Latin America, and the Caribbean,” said Ms Elizabeth Warfield, Deputy Mission Director, USAID, New Delhi during the project launch.

Acknowledging USAID’s commitment to the project, Director General William Dar said, “USAID has always been an advocate of the agricultural research-for-development continuum. Thus, this project has a research component in Phase I and an application component in Phase II. This project is another testament to USAID’s commitment to improve the lot of resource-poor farmers particularly in the pigeonpea growing countries of the world.”

“Under the CGIAR Research Program (CRP) on Grain Legumes led by ICRISAT along with other CGIAR Consortium members and program as well as national partners, genomics research will play a crucial role in speeding up the development of improved varieties for smallholder farmer crops such as pigeonpea,” he added.

Dr Swapan Datta, Deputy Director General (Crop Science), ICAR said, “We are very excited to see the launch of this USAID project.” Speaking on the occasion, Dr Rajeev Varshney, Project Coordinator and Director, Center of Excellence in Genomics, said the primary objective of the project was to translate genome information into the farmers’ fields. “The project team is quite confident and looks forward to working with different partners and stakeholders in enhancing pigeonpea crop productivity to ensure food security in India and generate more incomes for farmers in Africa,” he added.

The project launch meeting brought together about 70 delegates from India, Ghana, Mozambique, Uganda, Tanzania and Malawi and private sectors.

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ICRISAT at BioAsia 2013

Dr Dar during his Special Address at the inaugural session of BioAsia 2013 at HICC, Hyderabad.

“Agricultural biotechnology has the potential to reduce crop losses, improve nutrient efficiency of food, extend the postharvest life of fruits and vegetables, and increase the stress tolerance of plants. In developing countries in particular, it has the potential to revitalize the agricultural sector and enhance profitability of farming,” said Director General William Dar, during his Special Address at the inaugural session of BioAsia 2013, held on 28-30 January in Hyderabad. He also stressed on the need for public-private sector partnerships as key to innovations that would help poor farmers get out of poverty.

Speaking as Chief Guest, Union Minister of State for Commerce and Industries, Ms D Purandeswari pointed out that with India emerging as the third largest in the biotechnology sector, around 40-50 percent of global exports in biosimilars could be expected from the country in the next decade.

The tenth edition of BioAsia focused on the next wave in biotechnology, with eminent speakers from the industry and the academe elucidating on diverse topics such as: bio-medical research and regulatory environment; growing partnerships between biologics innovators and biosimilars’ manufacturers; next big trends in healthcare; and the role of emerging markets in the area of global biologics. The event had more than 500 delegates from 45 countries with Spain being the partner country.

ICRISAT co-hosted the AgBioAsia 2013 sessions, which aimed to bring together the power of biotechnology and commerce to help leverage the agricultural sector and achieve sustainable levels of global food security. Andhra Pradesh Chief Minister Mr Kiran Kumar Reddy, speaking at the opening program of AgBioAsia, urged entrepreneurs and scientists to ensure that biotechnology products are within the reach of the common man, acknowledging institutions like ICRISAT for working towards this end.

Joanna Kane-Potaka, Kiran Sharma and Suresh Pande at BioAsia 2013.

Topics discussed at AgBioAsia included: biotechnology and social responsibility; communicating biotechnology; opportunities and challenges in public sector R&D in translational research; food safety regulations; addressing global food security and climate change through biotechnology; and stewardship and liability issues in the deployment of transgenic crops. The sessions were sponsored by the Ministry of Food Processing Industries, Government of India. Representing ICRISAT at the sessions were Joanna Kane-Potaka, KK Sharma and Suresh Pande.

BioAsia 2013 was hosted by the Government of Andhra Pradesh, with the support of the Federation of Asian Biotech Associations (FABA) and Pharmaceutical Export Promotion Council (Pharmexcil).

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Tropical Legumes II Project Management Team meets, finalizes country strategies

Participants of the Project Management Team meeting.

To review project progress and propose alignments with the CGIAR Research Program on Grain Legumes, a Project Management Team meeting of the Gates Foundation-funded Tropical Legumes II project was held on 24-25 January in Nairobi, Kenya. The project aims to enhance the production and productivity of six grain legumes (chickpea, common bean, cowpea, groundnut, pigeonpea and soybean) in the drought-prone areas of sub-Saharan Africa and South Asia.

The meeting sought to: review the complementarities between Phase I and II of the project and the CGIAR Research Program on Grain Legumes and propose the best way to maximize synergies to deliver the project outcomes; review progress of the Tropical Legumes I Database Management Platform being implemented by aWhere consultancy; refine and finalize the legume ‘country x crop’ strategies and seed road maps; review the logframes and milestones; and revisit the project monitoring and evaluation plan.

Country strategies were finalized and a project report on legumes country strategies and seed road maps for all 15 countries will be compiled for publication. Project scientists agreed to develop and implement a common Review and Planning meeting with the Tropical Legume I phase in order to incorporate the products of the first phase research into the Phase II workplans. The first such meeting is planned in May 2013.  Reporting frequencies and formats and templates for data collection were agreed upon. The team will complete a Monitoring, Learning and Evaluation plan to be shared among team members and the donors.

The participants of the meeting included CLL Gowda, ES Monyo, Jupiter Ndjeunga, P Janila, Dave Hoisington, Said Silim, Cynthia Bantilan, PM Gaur and KB Saxena (ICRISAT); Boukar Ousman and Hesham Agrama (IITA); Steve Beebe and JC Rubyogo (CIAT); Dr Jeff Ehlers, Senior Program Officer, Gates Foundation; and regional Principal Investigators from ICRISAT, CIAT and IITA. Jim Pollock from aWhere consultancy participated as an observer.

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Farmers’ field day on combine harvester for chickpea held in Gulbarga

Dignitaries addressing farmers during the field day.

Nearly one hundred farmers from three villages (Martur, Nelogi, and Etiga) in Gulbarga district of Karnataka participated in a field day to demonstrate the use combine harvester for chickpea. The event was organized on 18 January by Agricultural Research Station (ARS), Gulbarga of the University of Agricultural Sciences (UAS), Raichur.

In Gulbarga, labor shortage in agricultural operations such as chickpea harvesting has become a constraint in crop production. Hence, the use of combine harvester has become necessary. Combine harvesting of the chickpea variety JG 11 grown on nearly 2 hectares showed <1% harvest loss. Farmers, however, prefer to use the machine in spite of the loss considering the time and economics involved.

Farmers in the villages had been provided with two chickpea varieties – MNK1 and JG11 – for large-scale testing.  Both varieties performed well during this season in spite of severe drought.  During the field day, farmers and researchers had the opportunity to share their views on the chickpea varieties supplied in the village, and the potential management technologies needed, including mechanical harvesting.

Dr CLL Gowda, Director, Research Program -  Grain Legumes was the Chief Guest during the event. It was attended by staff of ARS Gulbarga (Drs Dharnaraj, Mannur, Patil, Kantharaju); KP Viswanatha (Director of Extension UAS, Raichur); Dr DM Mannuur, chickpea breeder at ARS; staff from the Department of Agriculture; and students from Agricultural College, Gulbarga.

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