Towards Cataloguing Genome Wide Sequence Diversity in Pigeonpea

Pigeonpea (Cajanus cajan L.), the sixth most important legume food crop globally, is grown in marginal environments and exposed to a range of biotic and abiotic stresses. As a result, crop productivity is heavily challenged and remained stagnant (750 kg/ha) for the last six decades. Although a large number of varieties have been developed in past, only a limited genetic diversity from germplasm collection has been used and therefore existing varieties have a narrow genetic base. Nevertheless, ICRISAT genebank has 13,632 pigeonpea accessions from 74 countries. With an objective of enhancing the use of germplasm diversity in breeding programmes, a reference set comprising of 300 most diverse accessions has been developed after genotyping of 1000 accessions with 20 simple sequence repeat (SSR) markers. This set includes 165 traditional varieties, 113 breeding lines, 4 advanced cultivars and 18 wild species accessions. The reference set represents 95% of SSR alleles present in the composite collection as well as several traits of interests to the breeders. Therefore, to utilize the available genomic tools (mainly genome sequence) for harnessing the genetic diversity present in the genebanks, we conducted whole genome re-sequencing (WRGS) of 285 accessions from the reference set. WGRS yielded 2.15 Tb of sequence data with the coverage ranging from 5X to 10X. Genome-wide diversity features across the reference set will be presented. In summary, the availability of this rich genetic diversity at sequence level combined with the phenotyping data on the reference set should provide candidate genomic regions to accelerate pigeonpea improvement.