Genomics: Behind the science of making India’s ‘super chana’

A career-defining moment for Rajeev Varshney arrived in 2003 while attending a conference in Italy titled ‘From Green Revolution to Gene revolution’. The American agronomist Norman Borlaug, a Nobel Peace Prize winner and one of the architects of India’s Green Revolution of the early 1970s, ended his lecture with a challenge for the young scientists in attendance.

He asked them to put to use the advances in biological and genetic sciences to tackle the problem of global hunger.

At the time, Varshney, now 47, was working at the prestigious Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany. His research involved improving the malting quality of barley that was of considerable interest to the brewing industry.

Borlaug’s words buzzing in his ears, Varshney wondered why barley and Germany. As a teetotaller, he wasn’t particularly keen on making beer taste better. In 2005, he headed back to India and since then Varshney has been part of an elite group of Indian scientists distributed across several public research institutions that has revolutionised India’s chickpea or chana farming.

Record yield

In December 2020, using a cutting edge technique known as genomics assisted breeding, Varshney, Research Programme Director – Genetic Gains at the Hyderabad-headquartered International Crop Research Institute for the Semi Arid Tropics (ICRISAT), a publicly-funded global organisation working alongside 49-year-old Chellapilla Bharadwaj, Principal Scientist at Indian Agriculture Research Institute’s (IARI) Chickpea and Molecular breeding programme released a new variety of chickpea called Pusa Manav in double quick time that can not only double the farmer’s yield to nearly 2,400 kg per hectare but is also resistant a fungal disease called fusarium wilt that eats away more than 15 per cent of the output in the major growing regions of central and southern India.

Known as Bengal gram, black chana or simply chana, it is a veritable superfood. Dietary fibres that help in digestion, high in vitamin C and B6, folates, improves the heart’s functioning and controls blood sugar levels.

India produces nearly 12 million tonnes of chana annually and accounts for 80 per cent of the global output. The country’s most important pulse crop is a vital part of India’s nutrition security and is grown by some of the poorest and marginal farmers in un-irrigated drylands.

The legume can grow on soil with just 20 per cent moisture content and low organic content. Despite its importance, average yields in India have stagnated at around 975-1,000 kg/ha, significantly lower than other growing regions in the world. “Higher yields will not only help increase smallholder farmer income but also free up land to grow other more profitable crops,” says Bharadwaj.

Changing chana

Genomics assisted breeding can cut the time from lab R&D to largescale commercial farm use of new varieties by more than 50 per cent. What takes 12-15 years with traditional breeding, genomics assisted breeding can help scientists achieve in 7-8 years.

For thousands of years farmers have produced new varieties by crossing two plants of the same species to produce an offspring that shares the best traits of the parents.

Unlike genetic modification that involves transferring individual genes from one organism into another of unrelated species, genomics assisted breeding allows scientists to precisely select genes associated with specific traits such as resistance to a certain disease or high yields and cross them with another of the same species.

For instance, the genetically modified “Golden Rice” was created by adding to the rice genome a gene from the daffodil plant to increase 20-fold beta-carotene levels in rice.

Gene editing and genetic modification require regulatory approvals while genomics assisted breeding is simply ultra-fast-tracked conventional breeding.

A genome is the complete set of genetic information in an organism. It provides all of the information the organism requires to function. All living things have a unique genome and it is made of DNA or in the case of some viruses, RNA. A gene is segments of the DNA and the basic physical unit of inheritance.

Genes are passed from parents to offspring and contain the information needed to specify traits. IARI’s Bharadwaj developed the Pusa Manav chickpea by adding a gene from a variety called WR 315 that was responsible for giving it the trait of resistance to fusarium wilt to another called Pusa 391.

Decoding the gene

The key to successful genomics assisted breeding however is access to as wide a bank of varieties of a particular plant and enormous genetic information on them.

Only then can parents with specific genetic traits can be chosen. “When I joined ICRISAT in 2005, chickpea was considered an orphan crop. It means, unlike well researched crops like wheat, rice or maize, there was very little genomic information about the plant and a collection of limited number of chickpea varieties. Now ICRISAT has the world’s largest gene bank for chickpea with more than 20,000 land races, and wild varieties from around the world,” explains Varshney.

The chickpea genome has 28,000 genes. Whole genome sequencing allows scientists to associate each of chickpea’s 28,000 genes with a different trait. Once the relationship is established, a breeder can select the better variety or the one with a specific attribute they may be searching (say, resistance to high or low temperature).

“You don’t have to send the crossed variety to the field to study it. The selection and analysis can be done inside a lab,” says Bharadwaj.

Pusa Manav, the new chickpea variety

The Pusa Manav “super” chickpea is not a flash in the pan. In the last five years, collaboration among Indian research organisations have led to several new varieties of the legume with quantum leaps in productivity and resistance to region specific biotic (diseases, pest, insect and weed attacks) and abiotic (flood, drought and poor soil) stress. India’s gains in genomics assisted chickpea is considered one of the best public breeding programmes in the world.

It is estimated that seed related R&D accounts for nearly 70 per cent of the worldwide gain in yields. According to IHS Markit, the three biggest seed sellers Bayer, Corteva and Syngenta, now owned by the Chinese government, spent more than $2.8 billion in R&D. To put that in perspective, ICAR’s annual budget is ₹8,000 crore of which ₹6,000 crore are spent on salaries.

Despite the lack of financial resources, public recognition or attention, and in the face of bureaucratic bungles that choke up the innovations from reaching the farmers, India’s public sector agriculture scientists command a great deal of respect from international peers. Bharadwaj for instance has ten new chickpea varieties to his credit. Breeding a new line of a crop takes about 15 years from the lab to market.

In November this year, Stanford Public Library of Science journal run by scientists at Stanford University ranked Varshney 123rd in the field of plant biology and botany among 1,00,000 global scientists it tracks.

Norman Borlaug would certainly be happy with Varshney’s progress on his hunger challenge.

COMMENT NOW