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International Team Reports on Findings from Chickpea Genome

NEW YORK (GenomeWeb News) – Members of an international consortium have sequenced a draft version of the chickpea genome, making chickpea, or Cicer arietinum, the third crop legume plant to have its genome unraveled and published so far.

The India, China, and US-led team used whole-genome shotgun sequencing to tackle the nearly 740 million base pair genome of a kabuli chickpea variety. The group also re-sequenced and/or genotyped dozens more cultivated and wild chickpea accessions for the study, which appeared online this week in Nature Biotechnology — data that's helping researchers understand the genetic diversity present within chickpea and its relationship to chickpea traits of interest.

"Combined with knowledge of germplasm diversity and candidate gene regions, the analyses … should accelerate future breeding of elite cultivars," first author Rajeev Varshney, with the International Crops Research Institute for the Semi-Arid Tropics, and co-authors wrote.

"This will eventually move us closer to the goal of improving the livelihood and productivity of chickpea farmers worldwide," they added, with particular emphasis on the resource-poor, marginal environments of sub-Saharan Africa and Southeast Asia."

The chickpea plant is believed to have originated in the area that is now southeast Turkey and Syria some 7,400 years ago. It has since become one of the most commonly cultivated legume crop plants, authors of the new study noted, serving as a source of dietary protein and providing nitrogen fixation benefits for the soil it's grown in.

Kabuli is the most widely grown chickpea type, though the smaller-seeded desi chickpeas are still grown for food in parts of the Middle East and Southeast Asia.

But the varieties of chickpea that exist in various parts of the world belie the limited genetic diversity detected in cultivated versions of the plant, researchers explained. And that has slowed some efforts to improve the crop and bump up the crop's yield in certain parts of the world.

In an effort to get a better handle on the chickpea's genetic and genomic diversity, members of the team started by sequencing a kabuli chickpea variety from Canada called CDC Frontier.

"The sequencing of the chickpea provides genetic information that will help plant breeders develop highly productive chickpea varieties that can better tolerate drought and resist disease — traits that are particularly important in light of the threat of global climate change," University of California at Davis plant pathology researcher Douglas Cook, a co-corresponding author on the study, said in a statement.

Cook, Varshney, and their colleagues generated an initial Illumina-based assembly that spanned almost 545 million bases of the chickpea genome. By adding in paired-end BAC sequences, they further improved on that assembly, developing a 532.3 million base sequence that was largely anchored across eight linkage groups using existing genetic markers.

The team's analyses uncovered an estimated 28,269 gene models and hundreds more transfer RNA, ribosomal RNA, microRNA, or small nuclear RNA coding sequences in the chickpea genome.

It also offered new insights into the plant's genome organization, evolution, and synteny with other sequenced legume and non-legume plants. Along with simple sequence repeats in the kabuli assembly itself, for instance, the group used comparisons with several genotyped desi chickpeas to find more than 76,000 chickpea SNPs.

They also performed Roche 454 transcriptome sequencing on the same line used to generate the draft assembly, as well as whole-genome resequencing on a dozen more kabuli chickpea lines and on 17 desi lines to a depth of 9.5-fold coverage, on average.

That data, coupled with genotyping-by-sequencing information on 61 wild, improved, or landrace lines, offered a better look at the genetic diversity present across the Cicer genus.

As expected, the genetic diversity was generally lower in cultivated chickpea plants. For example, researchers saw signs of genetic sweeps and balancing selection associated with historical chickpea breeding and domestication events.

But the work also provided new clues about the genetic differences that underlie some of the trait differences found in desi and kabuli — information that the study authors said may ultimately prove useful for improving chickpea crops.

"These data comprise a resource for chickpea improvement through molecular breeding," they explained, "and provide insights into both genome diversity and domestication."