Designing and Development of 62K Genic SNP Chip of Pigeonpea (Cajanus cajan (L.) Millsp.)

Pigeonpea (Cajanus cajan), also known as red gram, gandule bean, tropical green pea, congo pea, etc. is a member of the family fabaceae. Its center of origin is in the eastern part of peninsular India, where it was domesticated along with rice and other legumes. More than eighty-five percent of the world pigeonpea is produced and consumed in India. Till date available genetic map of pigeonpea is consist of only few hundred markers, due to which the trait associated QTLs identification and analysis is very tough and time consuming job. In plant genome Single Nucleotide Polymorphism (SNP) is the most abundant DNA sequence variation which governs several traits expression in genome. Under the Indo-Swiss Collaboration In Biotechnology (ISCB) program we generated ~ 235 Gbp of sequence data using Illumina sequencing technology for the development of genic chip, which is used for the development of high density genetic map of pigeonpea genome. We have predicted and identified total of 17,125 single-copy (SC) gene set from unpublished pigeonpea draft genome (655 Mbp). Using bioinformatics approach we identified 654,642 high quality SNPs from the gene set. After filtration according to the Affymetrix customized chip parameter’s and on the basis of p-convert score (>.6) we are finally left with 62,053 SNPs which were used for fabrication of 62K pigeonpea chip by Affymetix. The designed chip is highly useful in generation of high density genetic map, association studies, in genetic diversity and phylogenetic studies in pigenopea. This will contribute to pigenopea variety improvement.