L-R: ICRISAT’s Dr Rachit Saxena, Senior Scientist (Pigeonpea Genomics) with Director General Dr David Bergvinson, Research Program Director and Project Director Dr Rajeev K Varshney and Dr Sameer Kumar, Principal Scientist (Pigeonpea Breeding). Photo: S Sharma, ICRISAT

Genome Re-sequencing to Accelerate Genetic Gains of Pigeonpea

L-R: Dr Rachit Saxena, Senior Scientist (Pigeonpea Genomics), Dr David Bergvinson, Director General ICRISAT, Dr Rajeev K Varshney,Research Program Director (Genetic Gains) and Dr Sameer Kumar, Principal Scientist (Pigeonpea Breeding). Photo: ICRISAT

L-R: Dr Rachit Saxena, Senior Scientist (Pigeonpea Genomics), Dr David Bergvinson, Director General, ICRISAT, Dr Rajeev K Varshney,Research Program Director (Genetic Gains) and Dr Sameer Kumar, Principal Scientist (Pigeonpea Breeding). Photo: S Sharma, ICRISAT

The genome of 292 pigeonpea lines from 23 countries has been re-sequenced by a global team of 19 scientists. The re-sequencing has led to the discovery of new traits such as resistance to fusarium wilt and sterility mosaic disease for developing superior varieties and hybrids. In addition, a specific gene ‘efl3’ has been identified for making pigeonpea photo-period insensitive (the duration of daylight hours required for reaching maturity) so that it can be cultivated more widely.  This breakthrough will lead to the development of pigeonpea varieties which can enable higher production, higher profits for smallholder farmers and better market value.

These findings offer a better understanding of patterns of genome-wide variations and the genetic basis of agronomic traits specific to pigeonpea.

“The study used re-sequencing data to identify genomic regions impacted by domestication and breeding that have contributed to narrowing the genetic base. The study also identified the genetic origin of the crop for the first time at a DNA level and identified genes with agronomically useful traits that will help to accelerate pigeonpea breeding and reduce the time to develop superior varieties from 8-10 years to 5 years,” said Dr Rajeev K Varshney, Research Program Director-Genetic Gains, ICRISAT, and the project director.

Dr Rachit Saxena, Senior Scientist (Pigeonpea Genomics), ICRISAT, added “The research also mapped similarities and dissimilarities between modern cultivars, landraces and wild species to arrive at the source and subsequent movement of pigeonpea from South Asia to sub-Saharan Africa and finally to Central and South America.”

ICRISAT’s Director General, Dr David Bergvinson, emphasizing the importance of the study, said, “Pigeonpea is a very important commercial crop for smallholder farmers in Africa and Asia as it has a huge export potential. This breakthrough will help us better understand the grain quality traits and unlock the huge potential of this crop and allow farmers access to high value markets.”

Dr Robert Bertram, Chief Scientist, USAID, said, “This USAID supported research is an important milestone in pigeonpea genetics and genomics. Pigeonpeas are vital to the livelihoods of millions of farmers across Asia and sub-Saharan Africa. The findings in this study will help pigeonpea farmers boost their productivity and expand food and nutritional security across Asia and sub-Saharan Africa.”

Mr SK Pattanayak, Secretary, Ministry of Agriculture, Cooperation and Farmers Welfare, Government of India, put this discovery in the context of doubling farmers’ incomes in India. “India needs such critical discoveries that are not just adding scientific knowledge but also contributing to enhance production by delivering photo-insensitive lines and enhance productivity by delivering high yielding varieties.”

“These genomic advances provide an effective means to harness the genetic diversity present in pigeonpea germplasm collections in genebanks for bigger yields and enhancing disease resistance.
This will help to provide more produce to farmers,” said Dr Trilochan Mohapatra, Director General, Indian Council of Agricultural Research.

This research will allow for comparative studies against other legumes, contributing valuable resources to accelerate genetic gains to benefit pigeonpea farmers.

Research findings have been published by the prestigious journal, Nature Genetics, ‘Whole-genome resequencing of 292 pigeonpea accessions identifies genomic regions associated with domestication and agronomic traits’

The nine collaborating institutes are the School of Agriculture and Environment and Institute of Agriculture, The University of Western Australia, Australia; Shenzhen Millennium Genomics Inc., China; Macrogen Inc., Republic of Korea; Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), India; Agricultural Research Station–Gulbarga, University of Agricultural Sciences (UAS), India; Department of Plant Sciences at University of California, Davis, USA; Biological Sciences and International Center for Tropical Botany, Florida International University, USA; Visva-Bharati, India and led by ICRISAT, India.

The study was made possible with the financial support from the United States Agency for International Development (USAID) and the Government of India. It has been undertaken as part of the CGIAR Research Program on Grain Legumes.

For more information about chickpeas see ICRISAT scientific portal 

This work contributes to UN Sustainable Development Goal

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