An international team of researchers has studied the genome of 3,366 chickpea varieties from different parts of the world. Their work provided a clearer picture of the chickpea’s evolutionary history and the effects of domestication on the genome, while also highlighting interesting genetic variations that could be used to develop varieties with a higher yield and better suited to climate conditions of the future.
In Nepal, India, and many countries in South Asia, the chickpea is called chana. In South America, it is known as garbanzo. In the Arab world, it is called hummus. And in France? Le pois chiche. Yet the diversity of this legume is not limited to its name: in 2019, an international team of researchers revealed the incredible genetic diversity of these seeds. This year, the same team, now composed of 57 researchers from 41 research institutes (India, Australia, China, France, USA, Russia, Canada, Egypt and Morocco) focused on the genetic variations of this pulse that is grown in various arid regions around the world. Their mission: create the world’s first map of the chickpea’s pangenome, the entire set of genes within this species. .
Seed banks
“The green revolutionAgricultural development policy aimed at food security through innovation has favoured the emergence of improved varieties at the expense of those considered less valuable,” says Yves Vigouroux, Director of the Diversity, Adaptation, and Development (DIADE) plant research unit at IRD. “In response, efforts to conserve this endangered biodiversity led to the creation of international conservation centres between 1950 et 1970. This was the case for the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), based in India and specialised in chickpeas and other tropical crops, which led this multi-partner study.”
The genome of 3,366 chickpea accessions was sequenced to a great depth.
© Rajeev K. Varshney
These seed “banks” have collected no less than 80,000 accessions, each of which is distinct and representative of the global diversity of chickpeas grown as crops as well as their wild relatives. “From this vast collection, ICRISAT chose to study 3,171 chickpea species grown as crops and 195 wild varieties, focusing on varieties that were representative of different geographical areas, elite varieties from an agronomic perspective, as well as wild varieties,” the researcher explains.
The chickpea differs depending on its area of origin: the chana grown in South Asia, which scientists call the desi type, is much smaller and less mealy than French chickpeas (kabuli type), whereas the ceci neri, from Italy is distinguished by its black seeds. This phenotypic diversityall the observable characteristics of an individual is not limited to physical appearance. It also pertains to the agricultural properties of the different varieties, such as their yield and ability to withstand drought. The goal behind this new research was to characterise the underlying genetic differences in the phenotypic differences between chickpea varieties in order to gain a better understanding of each one’s strengths and weaknesses.
Domestication and selection pressure
In order to characterize the chickpea pangenome, researchers searched for genetic variations in data from the full sequencing of the chickpea genome, tracking the presence or lack of whole genes and SNPs (single nucleotide polymorphisms), which are single base-pair differences that exist between two individuals of the same species. The identification of various SNPs, and their presence or absence in a given variety, allowed researchers to identify when the Cicer arietinum, the chickpea, and Cicer reticulatum, the species most closely related to it, diverged, 12,600 years ago. The scientists also highlighted the “genetic bottleneck” that occurred in chickpeas 10,000 years ago, following its domestication, which affected the diversity of the newly created domestic species.
Repeated selection led to a loss of diversity in the domestic chickpea (pods pictured above).
© Rajeev K. Varshney
“Following this domestication, certain chromosomal areas show much lower genetic variation. This is due to the fact that when chickpeas were grown as crops, the genes involved in the expression of interesting characteristics, such as the size of the seed, were subjected to selection pressure. In this specific example, only the allelesvariable version of the same gene. A gene generally exists in several forms or alleles, which define the variability of the genome. of genes promoting large seeds were selected and passed on to subsequent generations. The other alleles were lost in the domesticated species. However, the genes directly involved in traits of interest are not the only ones affected: all around them, along the chromosomes, the adjacent genetic sequences are also indirectly selected through the process of genetic hitchhiking, and they also show less diversity,” says Anne-Céline Thuillet, an expert on the evolution and adaptation of plants grown as crops at DIADE who worked on these aspects with her colleagues Yves Vigouroux and Philippe Cubry. “This method is used to identify which genetic areas were important in the plants’ adaptation to their environment and to humans, and which areas could be significant in future adaptations.” Based on this phenotypic and sequencing data, the scientists identified superior haplotypes, which are specific combinations of genes that can be used to develop better varieties. The authors also proposed different approaches to genomic prediction and optimum contribution selection, techniques which can also be used to develop high-yield varieties.
A legume of the future
India, the world’s largest producer of chickpeas, has increased its production by expanding crops in hot, tropical regions, where chickpeas are now grown in winter.
© Rajeev K. Varshney
“Included in the diets of over 50 countries, chickpeas will need to respond to the challenges of population growth and an increased demand for vegetable protein in order to make protein production more environmentally friendly and reduce dependence on meat. Chickpeas are very nutritious and rich in protein when consumed whole. The legumes also fix nitrogen in the soil, which reduces the need for nitrogen fertilizers. In developing countries, this represents valuable savings for small-scale farmers and reduces ammonia and nitrous oxide emissions, both greenhouse gases,” says Rajeev K. Varshney, Director of the Accelerated Crop Improvement research programme at ICRISAT, in India. Agriculture’s contribution to global emissions is now well-known and the transition to environmentally friendly agriculture is being encouraged worldwide. “In this context, we hope that the development of political thought will also include a transition from agriculture focused on yield to agriculture focused on nutrition. In other words, not merely seeking to produce enough food, but to produce nutritious food. Chickpeas perfectly meet this requirement and studies like the ones we have just conducted play a key role in supporting this transition,” says the expert.
