Pilot scale genome wide association mapping identified novel loci for grain yield traits in rice

Success of crop improvement program depends on systematic exploitation of genetic diversity. Improved understanding on the genetic basis of traits contributing to yield and stress tolerance is necessary to accelerate development of resilient crop varieties. In this study, a subset of 102 diverse rice accessions was assembled after analysing population structure (K = 8) and removal of admixtures from a larger set of IRRI 3 K panel. The constructed subset showed adequate diversity in yield related traits. Genome wide association analysis using the genome wide SNP markers identified a total of 42 SNPs showing significant association with major yield traits. Out of the identified SNPs, 20 SNPs were found to be present in QTL or genes reported previously for yield traits. Remaining 22 loci were found to be novel and needs validation. Elite genetic stocks with increased yield potential will permit us to dissect out the physiological and molecular basis of spikelet number per panicle in rice and thereby accelerate yield enhancement in rice through haplotype based breeding.