Genome-wide association studies for agronomical traits in winter rice accessions of Assam.

Abstract The 297 winter rice accessions of Assam were genotyped by sequencing (GBS), after filtering, 50,985 high-quality SNPs were assigned to 12 chromosomes. The population genetic structure analysis revealed three major subgroups SG1, SG2 and SG3 which contained 23, 82 and 69 accessions respectively. The remaining 123 accessions were grouped as admixtures. The phenotypic data recorded for 13 agronomical traits was used for GWAS. A total of 60 significant marker-trait associations were identified for 11 agronomical traits and explained 0 to 15% of phenotypic variance (PV). Clustering of four QTLs for panicle length and plant height was observed on chromosome 6 and 10 respectively. A QTL ‘hot spot’ was identified on chromosome 6 consisted of highest number of 10 QTLs associated with various yield traits. The identified QTLs will be validated in future and also utilized in marker-assisted breeding of yield in lowland rice cultivars of Assam and North Eastern Regions.