White and green chickpeas. Photo: Sanjay Acharya/Wikimedia Commons, CC BY-SA 3.0
- A recent international collaboration, including several Indian scientists, studied 3,366 chickpea genomes.
- The study found that in both chickpea and common beans, an important reproductive trait resulted from a mutation of the same gene.
- The sequencing effort also identified groups of genes inherited from one parent associated with particular crop performance traits.
Chole bhature, onion pakoda, besan laddoo, Mysore pak – rare is the Indian who doesn’t relish these treats. The main ingredient is the chickpea seed (Cicer arietinum), or its flour, besan.
A recent international collaboration, including several Indian scientists, from the International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, studied 3,366 chickpea genomes. This effort, and its findings, are both rendered notable by its great scale.
The chickpea genome comprises eight DNA molecules. Together, they contain 593 million nucleotide-base pairs. Each DNA molecule is the backbone of one of the eight chromosomes in the cells of the chickpea plant.
Most cells have two copies of each chromosome, one inherited from the mother and the other from the father. The maternally and paternally derived chromosome pairs are said to be homologous. Homologous chromosomes have DNA of pretty much the same length and the same sequence. But they are not identical. They differ wherever one or the other DNA suffered a mutation in the chromosome’s ancestry.
Mutations are changes in the DNA’s sequence of nucleotide base pairs, and occur randomly over time. Having two copies of each DNA molecule ensures that even if one copy has a mutationally inactivated gene, the intact gene on the other copy provides normal function.
Special cells such as pollen (paternal gametes) and ovules (maternal gametes) contain only one copy of each chromosome. But the pairs are restored in the progeny embryo that forms when an ovule is fertilised by a pollen. The embryo is encased in the seed, which is encased in a pod, and the pod develops from the fertilised flower. In Cicer reticulatum – the chickpea’s wild ancestor – the pods shatter to disseminate the seeds. The ability to shatter was naturally selected to disperse the progeny.
However, human domestication selected for plants with “shatterproof” pods. Humans surely found that pods that retain seeds are more convenient to pluck than to search for seeds shed on the ground. Domestication also selected for other traits, such as larger seeds. In this way, a subset of wild C. reticulatum populations became the cultivated C. arietinum crop.
Other crops, such as peas and common beans also underwent domestication-associated selection, for shatterproof pods.
The genome-sequencing study found that in both chickpea and common beans, the ‘shatterproof’ trait resulted from a mutation of the same gene. Chickpea was domesticated 11,000 years ago in the “fertile crescent” of present-day Syria, Turkey and Iraq – while the common bean was domesticated 8,000 years ago in present-day northern Mexico.
The study found that chickpea migrated along with humans to the rest of the world by two routes. One took it to South Asia and to East Africa, and the other took it to the Mediterranean region and to the Black Sea and Central Asia, up to Afghanistan.
The common bean was also independently domesticated in what are today Colombia, Ecuador and Peru. Another group of scientists has already found that the ‘shatterproof’ trait in the South American domesticates resulted from mutations in a different gene.
Cultivated chickpea varieties contain much less DNA sequence diversity than wild varieties. The sequencing effort identified groups of genes inherited from one parent – or haplotypes – associated with particular crop performance traits. One aim of genetic studies is to identify haplotypes associated with particular traits – and the progeny that have inherited them.
The study identified 56 promising lines for crop improvement through wild-to-cultivated and cultivated-to-cultivated breeding programmes. For example, one might increase resistance to pests and pathogens by the targeted transfer of a superior haplotype from a wild strain.
Alternatively, the seeds of cultivated varieties can be purged of haplotypes that lower crop performance. The plant may have unwittingly picked up the deleterious genes in the course of being selected for domestication traits (e.g. ‘shatterproof’).
Given the study’s unprecedented scale, and any forthcoming demonstration of crop improvement based on its findings, scientists may be able to justify the application of this approach to other crops as well.
D.P. Kasbekar is a retired scientist.