Breakthrough: Pigeonpea genome re-sequencing will lead to superior varieties and make the pulse more affordable

Dr Rajeev K Varshney Research Program Director and Senior Scientist Dr Rachit Saxena inspect pigeonpea accessions for agronomically important traits and disease resistance. Photo: S Sharma, ICRISAT

Hyderabad, India (22 May 2017) ― In a significant breakthrough, a global team of 19 scientists from 9 institutes have re-sequenced the genome or DNA of 292 pigeonpea varieties (Cajanus cajan – commonly called arhar or tur dal in India) and discovered new traits such as resistance to various diseases that affect the crop and its insensitivity to photo-period (the duration of daylight hours required for reaching maturity). The research also traces the likely origin of the domesticated pigeonpea to Madhya Pradesh in central India. These discoveries have been published in the prestigious journal Nature Genetics (doi:10.1038/ng.3872) today.

This breakthrough will lead to the development of superior varieties of this important pulse crop which can enable higher production and profits for smallholder farmers, better market value and bring it within an affordable price range for the consumer, especially the poor. Pigeonpea is a major source of protein, fiber, minerals, vitamins and resistant starch. It is important for ensuring nutritional security for millions in the developing world. However, the crop yield has remained stagnant over the last six decades, with limited genetic diversity and genome information, which is required for the development of superior varieties.

The 9 collaborating institutes are the School of Agriculture and Environment and Institute of Agriculture, The University of Western Australia; Shenzhen Millennium Genomics Inc., China; Macrogen Inc., Seoul, Republic of Korea; Institute of Biotechnology at Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, India; Agricultural Research Station–Gulbarga at University of Agricultural Sciences (UAS), Karnataka, India; the Department of Plant Sciences at University of California–Davis, USA; Biological Sciences and International Center for Tropical Botany, Florida International University, Miami, USA; Visva-Bharati, Shantiniketan, India and led by the India-based International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad.

Grown on more than 5 million hectares (ha), primarily by smallholder farmers, pigeonpea is the sixth most important food crop in the world. It is central to the Indian Prime Minister Narendra Modi’s goal of attaining self-sufficiency in pulse production, and an important source of protein to ensure nutritional security for mothers and children. Pigeonpea imports were close to 300,000 tons in 2012-13 [1] and the prices of pulses have put them out of reach for a majority of the Indian population.

“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 at a DNA level for the first time and identified genes with agronomically useful traits such as resistance to sterility mosaic disease and fusarium wilt, and insensitivity to photoperiod 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, ICRISAT, and the project director.

This is one of the biggest breakthroughs in pigeonpea research since the decoding of its DNA sequence (published in Nature Biotechnology) in 2011 by an ICRISAT-led global research team, and allows for a better understanding of patterns of genome-wide variations and the genetic basis of agronomic traits.

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, highlighting 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’s quality traits and unlock the huge potential of this crop and allow farmers access to high value markets. Understanding the photoperiod sensitivity is an example as this will allow the crop to be established in many regions where it is currently not grown.”

Dr Robert Bertram, Chief Scientist, USAID, the main sponsor of the study said, “This USAID supported research is an important milestone in pigeonpea genetics and genomics. Pigeonpea is 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.”

Dr S. K. Pattanayak, Secretary, Ministry of Agriculture and Farmers Welfare, Government of India, that co-sponsored the research, puts this discovery in the context of doubling of farmers’ incomes in India.  “India needs such critical discoveries that do not just add to scientific knowledge but also enhance production by delivering photo-insensitive lines and increase 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 also allow for comparative studies against other legumes, contributing valuable resources to accelerate genetic gains to benefit pigeonpea farmers and ensure profitability and a food-secure future through effective risk management.


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: ICRISAT


  • Study published in Nature Genetics – a top-ranking genetics journal globally
  • Unlocked the potential of germplasm by re-sequencing 292 pigeonpea lines from 23 countries
  • Traced the origin of cultivated pigeonpea to central India and migration path from Asia to sub-Saharan Africa
  • Identified superior genes of agronomic traits g. resistance to Fusarium wilt and sterility mosaic disease for developing superior varieties/hybrids faster
  • Identified one gene “efl3” for making pigeonpea “photo-period” insensitive so that it can be cultivated more widely.


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