Genome-Wide Variations in Indian Rice Landraces Revealed by Whole Genome Sequencing

Rice (Oryza sativa L. ssp. indica) is a major food crop cultivated in India, which occupies first and second position with respect to area and production, respectively. It is estimated that only 15 % of rice genetic diversity is utilized so far in rice improvement. Unutilized valuable genetic variations of economically significant traits can be explored through novel genomics tools such as next generation sequencing. We evaluated 230 landraces of rice in two locations of South India (Mandya and Ponnampet) for rice blast disease. We selected eight extremely resistant and seven susceptible rice landraces and sequenced using illumina HiSeq. The high quality sequence reads were assembled and annotated. The total genome size of all 15 landraces was in the rage of 266 Mb to 342 Mb. We compared all 22 cloned blast resistant (R) genes across 15 genomes to identify mutation in the landraces. We identified 1.1 Million variants comprise of both SNPs and InDels by comparing with indica (HR12) and japonica (Nipponbare) subspecies of Oryza. Overall we obtained one variant per 320 nts in the indica rice genomes. The genome sequence and annotation of 15 landraces will hasten the process of disease resistance breeding for rice blast in India.