Unlocking the genetic secret to future ready chickpea

The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad

About author

Prof. Rajeev Varshney is an agricultural scientist specializing in genomics, crop breeding, seeds system and capacity building 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 with ICRISAT, and International Chair in Agriculture & Food Security (Honorary) with Murdoch University (Australia).

Prof. Varshney has made centrally important contributions towards improving food and nutrition security in India and Africa by assembling genomes of ten major “orphan” tropical crops and additional genomic resources in pigeonpea, chickpea, groundnut and pearl millet. He has developed and integrated genomic technologies in crop improvement programs that have already delivered 11 superior crop varieties to some of the world’s poorest farmers. For his seminal contributions, Prof Varshney has received awards, fellowships and recognitions from several countries. Prof Varshney led the Tropical Legumes project, amongst others, as Principal Investigator for 7 years, implemented in 15 countries in Africa and Asia and won the 2021 Africa Food Prize to ICRISAT.

Research Program Director- Accelerated Crop Improvement, The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad. (https://cegsb.icrisat.org/ and https://www.icrisat.org/).

Professor, Murdoch University, Perth, Australia.

Interview

How would you explain your research outcomes to the non-scientific community?

A genome is the complete set of genetic information or the set of DNAs present is any organism. It provides all of the information the organism requires to function. In living organisms, the genome is stored in long molecules of DNA called chromosomes. There are 23 pairs of chromosomes in the human genome. The process of figuring out the order of DNA nucleotides, or bases, in a genome—the order of As, Cs, Gs, and Ts that make up an organism’s DNA is called Genome sequencing. In more simple terms, genome sequencing is the process of decoding the genetic information of any organism to have a better understanding of its genome architecture and its genes.

In this first of its kind largest genome sequencing effort on chickpea crop, we, an international team of 57 researchers from 41 organizations across 10 countries sequenced the genomes of 3,366 chickpea lines from 60 countries. In this research study, we identified 29,870 genes including 1,582 previously unreported novel genes, which provided us a deeper understanding of chickpea’s genome architecture. More importantly, this study gave a complete picture of the genetic variations within chickpea crops available from global composite collections (representing possible chickpea varieties available across the globe), which will be a game changer towards development of improved chickpea varieties. In addition, the knowledge generated from this study can be very helpful for other crop improvement programs.

How do these findings contribute to your research area?

By utilizing the genomic resource and knowledge generated from earlier studies on chickpea crop, where only few genes with trait of interest were identified, we together with our collaborators and national partners in India and sub-Saharan Africa were able to develop and deliver around seven high yielding and improved varieties of chickpea with better resistance to drought and fusarium wilt. Some of these being the first chickpea varieties developed using marker assisted backcrossing. Now, with the help of our findings from this new study, where we have identified around 29,870 genes including 1,582 previously unreported novel genes, we believe, this information can be harnessed to introgress in cultivable elite varieties and further develop new improved varieties with better yield, nutrition, and higher resistance to several biotic and abiotic factors. This study opens new avenues for accelerating chickpea crop improvement efforts for the global scientific community and delivers better varieties in the hands of smallholder farmers.

“This study opens new avenues for accelerating chickpea crop improvement efforts for the global scientific community and delivers better varieties in the hands of smallholder farmers.”

What was the exciting moment during your research?

The whole study itself was an exciting one, as this was first of its kind across any crop involving such a huge team of researchers from across the globe. It was a long journey, which started in 2014, just after we published the first reference genome of chickpea in Nature Biotechnology 2013. Since 2014, it took about 3 years for us to generate all data at ICRISAT (India), and then about 3-4 years for data analysis and interpretation 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, which is getting global attention- what can be more exciting for a scientist!

What do you hope to do next?

Well, I wish to continue such research studies that may be of importance for the global scientific community and can contribute towards improving the state of food and nutrition security across the world, specifically in developing countries.

Where do you seek scientific inspiration from?

I would like to mention the motivation first, which goes long back to my tenure in IPK-Gatersleben, Germany, where I attended a conference “From Green Revolution to Gene Revolution”, in Bologna- Italy. This conference was a defining moment in my scientific career, where I met and listened to Dr. Norman Borlaug, the father of Green Revolution, who in his talk challenged the next-generation scientists to embrace new tools and technologies and work to address food security in the developing world. This motivated me to work in the area of translational research that can be utilized toward addressing food and nutrition security across the globe. The fact that the scientific research we conduct together with our partners, especially on genomics-assisted breeding is delivering significant results that matters in the context of the global agricultural landscape, is what keeps me inspired to continue this scientific journey.

How do you intend to help Indian science improve?

During the course of my scientific journey, together with colleagues, collaborators and partners I have delivered several novel scientific concepts like Genomics-Assisted Breeding (GAB), GAB 2.0, 5Gs for crop genetic improvement, Super-Pangenome, and most recently published “Fast-forward breeding for a food-secure world” and “Rapid Delivery Systems for Future Food Security”. In these articles, we have highlighted a roadmap for advancing and accelerating the crop improvement efforts. These advanced genomic concepts, approaches and tools if deployed in national crop breeding programs can help to improve Indian science. Of course, support of the government with enabling policies and working environment will be key enablers for this.

Reference

Varshney, R.K., Roorkiwal, M., Sun, S. et al. A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature (2021). https://doi.org/10.1038/s41586-021-04066-1

Edited by: Anjali Mahilkar