The Nature, a topmost science journal in the world has published a breakthrough research paper of Indian scienists recently, “A chickpea genetic variation map based on the sequencing of 3,366 genomes, led by Prof Rajeev Varshney, Research Program Director at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) on November 10, 2021. Since then, this research is making rounds in social media, newspapers, magazines, blogs, etc. Biotech Express has undertaken in-depth analysis of this research and interviewed Prof Varshney to know background, achievements and future plan of this work. To the best of our knowledge, in recent decades, this is the first time, that an agricultural biotechnology research led by an Indian scientist has found its place in Nature. Not only from India perspective, but this is also the largest genome sequencing study for any crop that reports whole genome sequencing of 3,366 genotypes on an average of 12X coverage.
Prof Varshney, a JC Bose National Fellow, is a recipient of the most coveted Shanti Swarup Bhatnagar Prize (honored by Hon’ble Prime Minister Narendra Modi), and ICAR-India’s highest and most prestigious Rafi Ahmed Kidwai Award- 2019 from the Government of India. He is an elected fellow of all four national science and agriculture academies of India (INSA, NASI, IASc and NAAS) as well as of several foreign science academies including the German National Science Academy, The World Academy of Sciences, America Association for Advancement of Science, Crop Science Society of America, and American Society of Agronomy. He is a recipient of several prestigious awards including Professor Jayashankar Life Time Achievement Award, GD Birla Award for Scientific Research, Professor Lalji Singh Achievement Award, Career360 Outstanding Faculty Research Award- 2018, China’s Qilu Friendship Award-2015, Illumina Agricultural Greater Good Initiative Award etc. It is also important to mention that the “Tropical legumes Project” led by Prof Varshney recently got Africa Food Prize for ICRISAT.
Prof Rajeev Varshney, an Indian scientist, popularly known as “genomics guru”, after completing his post-doctoral tenure at Leibniz Institute of Plant Genetics & Crops Plant Research (IPK), Gatersleben, Germany and joining ICRISAT in 2005 took it as a challenge for bringing genomics revolution. In 2007, after establishing the Centre of Excellence in Genomics (now called Centre of Excellence in Genomics & Systems Biology) at ICRISAT, and working with a range of partners across the world, Prof Varshney has been engaged in developing genomic resources and translating these genome information for crop improvement in tropical crops such as chickpea, pigeonpea, groundnut and pearl millet.
Interview Questions
Brief background of the group leader
Leader of this study, Prof. Rajeev Varshney is an agricultural research scientist specializing in genomics and molecular breeding with 20+ years of service in developing countries in sub-Saharan Africa and Asia. He is currently serving as Research Program Director- Accelerated Crop Improvement; and Director, Center of Excellence in Genomics & Systems Biology at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). He is an Honorary and/or Adjunct Professor in 10 universities/institutes in Australia, China, Ghana and India including Murdoch University, The University of Western Australia and The University of Queensland, Australia. He is a globally recognized leader for his work on genome sequencing, genomics-assisted breeding and translational genomics in legume and cereal crops and capacity building in developing countries.
Prof. Varshney has made centrally important contributions to improving food security in India and Africa by creating genomic resources of ten major “orphan” tropical crops including pigeonpea, chickpea, groundnut and pearl millet. He has developed and deployed DNA marker technologies for the identification of useful genetic variation in these key crops. He has used these resources to identify genetic loci and candidate genes for drought and pest tolerance in key staple crops for sub-Saharan Africa and India. He has initiated and led major international programmes that are creating and already delivering 11 superior crop varieties through genomics-assisted breeding to some of the world’s poorest farmers.
Prof. Varshney, a highly prolific author and Highly Cited Researcher for 8 consecutive years (2014-2021) in a row has published >500 papers in high impact factor journals including 19 papers in Nature journals. Based on his publications, he has h-Index of 108 with >46,000 citations. He is the youngest and the only Indian agricultural/plant scientist and the 4th Indian to achieve an h-index of 100 as per Google Scholar. He is editor of 17 books from Springer, CRC Publishers, etc.
Prof. Varshney is an elected fellow to about 10 science and agriculture academies/ societies in India, Germany, USA, etc. and recipient of several noted awards including the most coveted science award, Shanti Swarup Bhatnagar Prize, and the most prestigious agricultural science award, Rafi Ahmed Kidwai Award from Government of India. Recently ICRISAT won the 2021- Africa Food Prize for the outputs and impact of Tropical Legume projects, led by Prof Varshney as Principal Investigator for 7 years.
Who are other prominent members in the group
This is one of the largest study of its kind involving 57 researchers from 41 organizations across 10 countries. From ICRISAT, members from the team included Dr Manish Roorkiwal, Mr Prasad Bajaj, Ms Anu Chitikineni, Dr Mahendar Thudi, Dr Hari D Upadhyaya, Dr Aamir W. Khan, Dr Vanika Garg, Mr Vinod Kumar Valluri, Dr Pallavi Sinha, Dr Vikas K. Singh, Dr Abhishek Rathore, Dr Muneendra K. Singh & Dr Himabindu Kudapa. For contributions of each member, please refer the nature paper:https://www.nature.com/articles/s41586-021-04066-1#author-information.
Why Chickpea only, why it is found important for this study?
Chickpea is one of the important legume crops, cultivated in more than 50 countries and is a rich source of protein. With high nutritional values, chickpea is a key crop towards nutritional security, especially in developing countries of Asia and sub-Saharan Africa. Having chickpea in its basket of mandate crops, ICRISAT embarked on this ambitious initiative of the “3000 chickpea genome sequencing” project in 2014.
When and how did you come up with the idea of this study?
An international team of researchers led by me published the first chickpea genome in Nature Biotechnology in 2013. After we published the chickpea reference genome, we were encouraged by the then Secretary, Department of Agriculture and Cooperation, Shri Ashish Bahuguna, and the then Deputy Director General of ICAR, Dr Swapan Datta, and the then Director General of ICRISAT, Dr William Dar to develop a road map for genomics- assisted breeding in chickpea. Subsequently, we worked with the then Director, ICAR- IIPR, Dr NP Singh and chickpea breeders and researchers from ICRISAT, ICAR-IIPR, International Centre for Agricultural Research in Dryland Areas, and state agricultural universities in Madhya Pradesh, Rajasthan, Gujarat, West Bengal, New Delhi. With the initial funding support from DAC, Ministry of Agriculture, and encouragement from the then Management of ICRISAT, “The 3000 Chickpea Genome-Sequencing Initiative” was launched in 2014
Any preliminary studies by your group or lab?
Yes, our group together with partners from across the globe have undertaken several projects on chickpea crop. The key selected ones that played significant role in transforming chickpea crop breeding programs for development and delivery of improved varieties includes:
– Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement – Nature Biotechnology 2013(https://www.nature.com/articles/nbt.2491)
– Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.)- Scientific Reports 2016(https://www.nature.com/articles/srep38636)
Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits- Nature Genetics 2019(https://www.nature.com/articles/s41588-019-0401-3)
– A chickpea genetic variation map based on the sequencing of 3,366 genomes- Nature, 2021 (https://www.nature.com/articles/s41586-021-04066-1)
From where you get the fund for this project?
The project launched with initial funding from Ministry of Agriculture, Government of India. However, over the years several partners alongwith their donors and funding agencies contributed in this study. Some key funders include Department of Biotechnology, Ministry of Science and Technology under the Indo- Australian Biotechnology Fund, Government of India and the Bill & Melinda Gates Foundation.
How many different types of novel genes are uncovered through this project?
This study identified 29,870 genes that includes 1,582 previously unreported novel genes. Furthermore, the study identified blocks of genes in landraces (domesticated varieties developed by farmers) that can significantly enhance performance of the crop by improving traits like yield, climate resilience and seed characteristics. Called haplotypes, these blocks of genes are what crop breeders strive to bring into cultivars. Using historical data of all chickpea varieties released between 1948 and 2012, the research sheds light on the deployment of these haplotypes in the varieties. We examined 129 varieties released in the past. Though a few superior haplotypes were detected in some of these varieties, we found that most varieties lacked many beneficial haplotypes. We have arrived at 56 promising lines that can bring these haplotypes into breeding programs to develop enhanced varieties.
What various accessions are included in the study?
In this study, we have sequenced 3,366 chickpea germplasm accessions including 3,171 cultivated and 195 wild types.
What other crops you think are important for such kind of studies and why?
Most of the crops, including legumes, grown in the dryland regions of the world are important from this point of view. As roughly 2.5 billion people – 30 percent of the world’s population – live in the dry areas, which cover more than 40 percent of the world’s land surface. Scarce natural resources, land degradation and frequent droughts severely challenge food production in these areas. Productivity in dryland regions face a multitude of challenges – persistent water scarcity, frequent droughts, high climatic variability, various forms of land degradation, including desertification, and loss of biodiversity.
What are future implications of this study on hunger index and/or to combat world hunger?
Reports suggest that global efforts to end world hunger and malnutrition in all its forms by 2030 are not on track, due to several drivers including the recent COVID-19 pandemic. In fact, the latest FAO report estimates that between 720 and 811 million people in the world faced hunger in 2020 – as many as 161 million more than in 2019. The world needs to realize this urgency and put together all possible efforts to address global hunger and malnutrition, in best possible manner. Such kind of advanced genomic research has the potential to revitalize the agricultural landscape by advancing and accelerating the crop breeding efforts. It has the potential to provide a complete picture of genetic variation within any crop with a validated roadmap for using the knowledge and genomic resources for crop improvement programs.
We have already suggested some novel approaches such as haplotype based breeding, genomic prediction, optimal contributions selection for redefining the chickpea breeding etc. These approaches are expected to deliver high-yielding, climate resilient and nutrition rich crop varieties to provide food and nutrition.
Chickpea (Cicer arientinum L.), commonly called “chana” or “bengal gram” is one of the oldest grain legume crops that is grown over 50 countries worldwide. Due to its rich protein and nutrient content, chickpea provides an affordable dietary resource to meet the nutrition security demands of growing population, particularly in India and several other countries of Asia and sub-Saharan Africa. Although crop improvement programmes in India and elsewhere have delivered superior varieties in past, it is imperative to use biotechnology approaches for bringing revolution in crop improvement in chickpea. Genomics- assisted breeding approach is a key approach in this direction. However until 2005, there were very limited genomic resources available in the crop. Therefore, the crop often used to be called ‘orphan crop’ and genomics- assisted breeding was like a dream in this crop. The timeline of sequencing projects conducted under the leadership of Prof Varshney is provided in Figure 1.
With an objective to bring genomic revolution, the first chickpea genome sequence was reported in Nature Biotechnology in 2013 (https://www.nature.com/articles/nbt.2491) by an international team led by Prof Rajeev K Varshney. This scientific breakthrough provided for the first time a much-required gene repertoire for chickpea. This genome sequence was used to understand the genetic base by sequencing of 100 elite varieties of chickpea released in 14 countries under the leadership of Prof Varshney. This study was published in 2016 in Scientific Reports (https://www.nature.com/articles/srep38636). Subsequently, Prof. Varshney’s team embarked on the scientific journey to sequence 429 chickpea lines from 45 countries and the results of this study were published in Nature Genetics (https://www.nature.com/articles/s41588-019-0401-3). This study involving scientists from 21 research institutes globally identified genes for tolerance to drought and heat. This effort also provided key insights into the crop’s genetic diversity, domestication and molecular basis of agronomic traits for chickpea improvement.
The new breakthrough study published in Nature on Nov 10, 2021, however, provided a deeper understanding of chickpea’s genome based on the development of a detailed genetic variation map from 3,171 cultivated and 195 accessions of wild species of chickpea. Involving 57 researchers from 41 organizations across 10 countries, this study assembled chickpea’s pan-genome based on genome sequencing data of 3,366 chickpea lines from 60 countries. This article provides: (a) genome variation map (pangenome) of chickpea, (b) origin and migration routes of chickpea to various parts of the world, (c) chickpea species divergence, (d) genetic load/burden responsible for lowering crop performance, (e) superior haplotypes for agronomic traits for undertaking haplotype-based breeding, (f) foundation for genomic prediction and optimal selection for developing superior varieties.
“By employing whole-genome sequencing, we have been able to affirm the history of chickpea’s origin in the Fertile Crescent and identify two paths of diffusion or migration of chickpea to the rest of the world. One path indicates diffusion to South Asia and East Africa, and the other suggests diffusion to the Mediterranean region (probably through Turkey) as well as to the Black Sea and Central Asia (up to Afghanistan),” said Prof Varshney. He added, “The team, by developing pangenome, identified 29,870 genes that includes 1,582 previously unreported novel genes and by employing whole genome sequencing”. A pangenome highlighting genome diversity in chickpea is given in Figure 2.
In an interview with Mr K P Singh, Professor Varshney told, “Our Nature paper added knowledge on both fronts- basic biology, and agriculture related applications. While the study provides insights on genetic diversity, species divergence, domestication, migration routes, the study also identifies “good” genes and “bad” genes in chickpea genome. We propose not only accumulating good genes to develop better varieties, but also purge bad genes during breeding so that we have high performing crop varieties”.
While recollecting the history of the project, Prof Varshney mentioned that after we published the chickpea reference genome, we were encouraged by the then Secretary, Department of of Agriculture and Cooperation, Shri Ashish Bahuguna, and the then Deputy Director General of ICAR, Dr Swapan Datta, and the then Director General of ICRISAT, Dr William Dar to develop a road map for genomics- assisted breeding in chickpea.
Subsequently, we worked with the then Director, ICAR- IIPR, Dr NP Singh and chickpea breeders and researchers from ICRISAT, ICAR-IIPR, International Centre for Agricultural Research in Dryland Areas, and state agricultural universities in Madhya Pradesh, Rajasthan, Gujarat, West Bengal, New Delhi. With the initial funding support from DAC, Ministry of Agriculture, “The 3000 Chickpea Genome-Sequencing Initiative” was launched in 2014 (Figure 3). Subsequently several partners, funding agencies joined the project and we enhanced the scope of the project.
Large-scale sequencing data were generated on HiSeq 2500 sequencing machine at ICRISAT (India) following “Make In India” initiative of Government of India.
It took about 3 years to generate all data at ICRISAT and partners in India, and then about 3-4 years for data analysis and interpretation together with partners around the world and about one and half years with the manuscript preparation, submission, revision and acceptance. “In summary, though it has been a long journey with many ups and downs (excitements and disappointments), we have successfully completed this project and published its outputs in Nature, the world’s topmost science journal”, said Prof Varshney.
Translating genome information for developing better varieties
Based on genome information from earlier studies, ICRISAT together with its national partners in Asia and sub-Saharan Africa, mapped around 30-50 agronomic traits. Notably a genomic region (referred as “QTL-hotspot”) containing genes for drought tolerance traits was identified by Prof Varshney and his team. He together with researchers from ICRISAT and other institutes from India and other countries introgressed this “QTL-hotspot” for drought tolerance, and also genes for Fusarium wilt (a serious disease responsible for yield reduction) in several elite varieties. As a result, several improved varieties were developed together with national partner Indian Council of Agricultural Research (ICAR) – Indian Agricultural Research Institute (IARI), Indian Institute of Pulses Research (IIPR), University of Agricultural Sciences, Raichur (UAS-R) and others in last 3 years. These varieties include three drought tolerant varieties: ‘Pusa 10216’ (with ICAR- IARI, Figure 5), ‘Pusa Chickpea 4005’ or ‘BG 4005’ (with ICAR- IARI) and ‘IPCL4-14’ (with ICAR- IIPR), and three Fusarium wilt resistant varieties: ‘MABC-WR-SA-1’ alias ‘Super Annigeri-1’ (with UAS-R), ‘Pusa Chickpea 20211’ alias ‘Pusa Chickpea Manav’ and ‘IPCMB 19-3’. Drought tolerant Pusa Chickpea 4005 and IPCMB 19-3 were among 35 crop varieties dedicated by Hon’ble PM Narendra Modi to the nation on 28 September2021.
Taking improved varieties to small-holder farmers
While crop improvement teams around the world has been delivering improved varieties, in many countries they don’t reach to farmers in real time. Secondly, even if the varieties reach to farmers, without availability of information and practicing proper agronomy, farmers are not able to harness the full potential of genetics. To overcome the above mentioned issues, Prof Varshney highlighted two examples- one on Tropical Legumes project funded by Bill & Melinda Gates Foundation, and the other one on delivering more produce and income to small-holder farmers funded by Ministry of Agriculture & Farmers Welfare, that were led by him as Principal Investigator. He said, “Tropical Legumes projects through collaborative efforts of ICRISAT, IITA, CIAT and national programmes in 13 countries in Africa and two countries (India and Bangladesh) in Asia, facilitated release of 266varieties, production of 498,034 tons seeds, adoption of improved varieties of legumes under in 5 million ha area and creation of 52 next generation scientists (Figure 4). By assuming 0.2 ha land per farmer, the Tropical Legume projects is benefitting 25 million lives in 15 countries of SSA and Asia”. For this outstanding work and positive impact on livelihood of small-holder farmers in 13 African countries through TL projects led by Varshney, ICRISAT has been awarded Africa Food Prize-2021 on 8th Sept 2021.
Regarding delivering more produce and income to small-holder farmers project, Prof Varshney mentioned, “In collaboration with scientists from ICRISAT, ICAR-IIPR and 7 agricultural research stations/ state agricultural universities in 6 states (Madhya Pradesh, Maharashtra, Andhra Pradesh, Telangana, Karnataka and Uttar Pradesh), we had an outreach of 32 varieties/hybrids of pulse crops to about 1,822 farmers from 158 villages of 25 districts from above mentioned 6 states. Farmers- preferred varieties and hybrids are being promoted for production at large scale in these states.
Testimonials to Prof Varshney by Stalwarts of Agribiotechnology
GurdevKhush, World Food Prize Laureate, University of California- Davis, USA
“Congratulations Rajeev and your team for this outstanding achievement. I am so proud that this breakthrough research has been published in the high impact journal Nature. I am sure this paper will be read and appreciated by agricultural scientists world over.”
Rajendra S Paroda, Padama Bhushan Awardee & President, Trust for Advancing of Agricultural Sciences, India
“I am extremely happy to see this chickpea genomics paper published in Nature, which is not easy yet you have done it Rajeev. Let me congratulate you and all the co-authors for this. I am sure the findings of this study will help in accelerating pre-breeding and genomics-assisted breeding for needed genetic improvement in chickpea.”
Partha P Majumder, National Science Chair, Government of India
“This is awesome work! Very elegant and deep, with significant translational implications. I am very proud of you, Rajeev. Especially because you are making these contributions from India”.
Shobha Sivasankar, Section Head- Plant Breeding and Genetics, International Atomic Energy Agency, Austria
“Congratulations, Rajeev, on this excellent work!!! Great to see your leadership for this massive effort, and a wonderful achievement and contribution to the chickpea community! Well done!!”
Arvind Kumar, Deputy Director General- Research, ICRISAT, India
“Rajeev and Team, Heartiest congratulations to you all. A proud moment for all of us. The outputs from this article are expected to help chickpea improvement programmes around the world and will contribute to enhance crop productivity, resilience and nutrition. Great work and keep it up”.
David Morrison, Deputy Vice Chancellor, Murdoch University, Australia
“It is wonderful to see this international collaboration delivering impact oriented outputs to improve international agriculture. Congratulations, Rajeev and thanks for working with us at Murdoch University.”
Yemi Akinbamijo, Executive Director, Forum for Agricultural Research in Africa, Ghana
Congratulations, to you Rajeev and your team for this outstanding feat. It is great to see so-called orphan crops like chickpea joining the elite group of crops- thanks to your leadership and contributions. I am sure that the outputs of this article will be contributing to enhance crop productivity and deliver higher produce to small-holder farmers in Asia and sub-Saharan Africa and further help to raise livelihoods.”.
Andreas Graner, Executive Director & Head of Genebank, IPK-Gatersleben, Germany
“Many many congratulations to Rajeev and team for this landmark paper in crop genomics published in Nature. This is indeed a largest plant genome sequencing study at the whole genome level. Pan genome, species divergence, and domestication and migration routes are providing insights in the area of basic plant science. At the same, superior haplotypes, genomic prediction approach and genetic load reported in this article will turbocharge chickpea improvement. Further, the outputs of this article will also help in germplasm management. Great work, indeed, Rajeev!”
Peter Davies, Pro-Vice Chancellor and Director, Food Futures Institute, Murdoch University, Australia
“Here at Murdoch, we’re working hard in pursuit of the UN’s Sustainable Development Goals of eliminating hunger and poverty and promoting sustainable production. Rajeev’s research is important in this pursuit and we’re really pleased to be collaborating with him on a global scale.”
Chike Mba, Team Leader, Seeds and Plant Genetic Resources, Plant Production and Protection Division, Food and Agriculture Organization of the United Nations, Italy.
“I have read with keen interest the recent publication on the chickpea genome variation in the esteemed scientific journal, Nature. The seminal article, which chronicles a massive amount of work on whole genome sequencing of chickpea at a large scale, is a most timely contribution to the efforts to understand and exploit the heredity of the crop’s traits. In particular, the information contained in the paper will be extremely important for enhancing use of genomics-assisted breeding in the genetic improvement of this food security crop. I look forward therefore to a greater ease in breeding more productive and nutritious varieties of chickpea that are also climate resilient in support of the low input production systems of small-holder farmers in developing countries. My sincere congratulations and appreciation to you, Rajeev, for establishing and leading this international consortium and for the successful completion of this herculean task! Well done, Rajeev and team!”
Prof Rajeev Varshney Once again appears among the Top 1% of the Highly Cited Researcher in world
Last but not the least, Prof. Varshney has been included (again) 8th time in a row in #HighlyCitedResearchers list for 2021 https://bit.ly/3cdpgyq. This list recognizes the true pioneers in their fields over the last decade, demonstrated by the production of multiple highly-cited papers that rank in the top 1% by citations for field and year in the Web of Science™. Of the world’s scientists and social scientists, Highly Cited Researchers truly are one in 1,000.
As per one study at Stanford University (USA) published in PLoS Biology on 16 Oct 2021, Prof. Varshney was included again in Top 2% World’s Scientists. He is ranked at 2nd in Plant Biology & Botany section among Indian scientists.
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