A global team of scientists, including from India, has unlocked the genetic diversity of chickpea (Cicer arietinum), world’s second most widely grown legume, pinpointing crucial genes for heat and drought tolerance.

The results could lead to the potential development of newer varieties of chickpea with higher yields, which are disease-and-pest-resistant and better able to withstand unpredictable weather.

A significant reduction in diversity was observed from wild genotypes to landraces and breeding lines suggesting that about 80 percent of genetic diversity captured in the study has been lost during chickpea domestication.

The global study also confirms that chickpea came to India from the Fertile Crescent/ Mediterranean via Afghanistan and may have been introduced back to the primary centres of origin after 200 years.

A global team of scientists, including from India, has unlocked the genetic diversity of chickpea (Cicer arietinum), world’s second most widely grown legume, pinpointing crucial genes for heat and drought tolerance.

The team successfully completed the genome sequencing of 429 lines of chickpeas, including 176 from India, opening the door for the potential development of newer varieties of chickpea with higher yields, which are disease-and-pest-resistant, and better able to withstand unpredictable weather.

The effort led by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in close collaboration with the BGI-Shenzhen, China saw 39 scientists from 21 research institutes across 45 countries tapping into next-generation sequencing (NGS) technology to better understand the genetic background of chickpea.

They harnessed the germplasm wealth available in genebanks in a three-year long effort that spawned the largest exercise of whole-genome resequencing (WGRS) of chickpea.

The research provides insights into naturally occurring genetic variation, population structure, domestication and selection in 429 chickpea genotypes including the diversity of cultivated chickpea, a cool season legume hit hard by drought and rising temperatures globally.

The study also confirms that chickpea came to India from Fertile Crescent/ Mediterranean via Afghanistan and may have been introduced back to the primary centres of origin after 200 years.

“These 429 lines that we have examined come from 45 countries and may have been subject to harsh environmental conditions. So the question is why these lines were able to cope with drought and heat over time? This resilience may not be present in the varieties grown by farmers,” Rajeev Varshney, the project leader and Research Program Director, Genetic Gains, ICRISAT, told Mongabay-India.

India, as the biggest consumer of pulses in the world, faces an increasing production gap. Despite contributing more than 70 percent to the global chickpea area and production, India remains a net importer of chickpea due to high national demand. Although significant yield increases have been reported under experimental research conditions, farm-level increases have been more modest.

In order to ensure self-sufficiency, the pulse requirement in the country is projected at 39 million tonnes by the year 2050 which necessitates an annual growth rate of 2.2 percent, states the ‘Vision 2050′ document crafted by ICAR-Indian Institute of Pulses Research.

This new research could take India closer towards attaining self-sufficiency in pulse production, the study authors believe.

The genome-wide association studies identified several candidate genes for 13 agronomic traits.

“For example, we could identify genes (e.g. REN1, beta-1, 3-glucanase, REF6) which can help the crop tolerate temperatures up to 38 degree Celsius and provide higher productivity,” said Varshney.

A candidate gene is a gene whose chromosomal location is associated with a particular disease or other observable characteristics (phenotype) such as agronomic ones in this case.

The team analysed 2.57 terabase pairs (Tbp) of raw data comprising 28.36 billion reads. “This is equivalent to approximately 1187 GB of digital data which is pretty huge,” said co-author and ICRISAT senior manager Annapurna Chitikineni, adding three important drought tolerant genes were identified during the course of the research.

The next step in shoring up genetic gains would involve the application of modern (molecular) breeding approaches to develop high-yield varieties with heat and drought tolerance faster.

“Some of these lines that we have studied have the genes for heat and drought tolerance but they may not have genes for high yield. The varieties developed by breeders have genes for high yield but they may lack genes for heat and drought tolerance. So what we can do now is we can use the genes identified in our study for drought and heat tolerance and make the varieties currently cultivated across the world drought and heat tolerant,” said Varshney.

Lauding the effort, professor Andreas Graner, Managing Director and Head of the Department Genebank at Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), said the research blazes the trail for a knowledge-based utilisation of genetic resources of chickpea to develop improved cultivars.

“To understand the genetic alterations that were brought about by man during domestication of chickpea will provide a major key for the targeted management of the genetic diversity held in ex situ genebanks. At the same time, it will provide researchers and plant breeders a golden thread to explore regions of the genome that will hold promise for the improvement of agronomic traits,” Graner told Mongabay-India.

Loss in genetic diversity

With its capacity for biological nitrogen fixation, chickpea replenishes soil fertility, diminishes the need for added nitrogen fertilisers and is a source of high quality dietary vegetarian protein.

Originating in southeast Turkey and Syria, chickpea is known as one of the founder crops of modern agriculture. It is grown mostly in south Asia and sub-Saharan Africa, which accounts for more than 75 percent of the world’s chickpea area.

The highly nutritious, drought-tolerant chickpea contributes to income generation and improved livelihoods of smallholder farmers in African countries like Ethiopia, Tanzania and Kenya, and is crucial to the food security in India (being the largest producer, consumer and importer of the crop).

Chickpea is also an important component of the pulse industry in Australia, Canada and the United States.

There are two main types of chickpeas: small-seeded desi and larger-seeded kabuli. Consumption of desi is restricted primarily to some parts of Asia, whereas kabuli is a popular and valuable global commodity, the researchers said.

As with most annual crops, in chickpea too, crop domestication, post-domestication diversification and recent breeding efforts have selected traits to meet human needs, resulting in narrow genetic diversity in cultivated gene pools.

Crop diversity is key to how crops adapt in varying environments. Loss of crop diversity threatens food security.

A significant reduction in diversity was observed from wild genotypes to landraces (locally adapted and domesticated traditional variety of a species) and breeding lines suggesting that about 80 percent of genetic diversity captured in the study has been lost during chickpea domestication, which means it doesn’t have a lot of resistance and tolerance to diseases.

The sequencing threw up other interesting nuggets of information.

Among the cultivated chickpeas, Pusa 1103 [(Pusa 256×Cicer reticulatum)×Pusa 362], an elite variety developed at Indian Agricultural Research Institute (IARI), New Delhi, India, (tolerant to drought and diseases) and ICC 9636 (landrace originating from Afghanistan) grouped away from the other cultivated genotypes.

“While we expected cultivated genotypes to club together, our study revealed that Pusa 1103 grouped away from the other cultivated genotypes because it may still have parental blood of the wild species. This can be seen from the fact that Cicer reticulatum, the wild progenitor of chickpea, is one its parental sources,” Varshney told Mongabay-India.

The study was done in close collaboration with partners from the national agricultural research system, including the Indian Council of Agricultural Research (ICAR), other central research institutes, and national research centres set up by ICAR.

The genome sequence of chickpea was decoded in 2013. In 2018, the chickpea (Cicer arietinum) got its own genetic atlas following a five-year long effort by ICRISAT researchers.

The Cicer arietinum gene expression atlas (CaGEA) is a comprehensive catalogue that provides data on when (timing) and where (site) a particular gene on the genome will be expressed during chickpea plant growth.

As for the origin and mapping the migration route of the chickpea, scientists confirm the chickpea came to India via Afghanistan and may have been introduced back to the primary source of origin 200 years later.

“Our study indicates Ethiopia as a secondary centre of diversity and also maps a migration route from Mediterranean/ Fertile Crescent to Central Asia, and in parallel from Central Asia to East Africa (Ethiopia) and south Asia (India),” Varshney added.

CITATION

Rajeev K. Varshney et al. (2019).Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. Nature Genetics. https://www.nature.com/articles/s41588-019-0401-3.