KASP™ based markers reveal a population sub-structure in temperate rice (Oryza sativa L.) germplasm and local landraces grown in the Kashmir valley, north-western Himalayas

The conservation and utilization of germplasm is contingent on its proper characterization at morphological or molecular levels. The present study aimed to elucidate the population sub-structure of 470 temperate rice germplasm collections of the Kashmir Valley. Analysis was carried out using KASP (Kompetitive Allele Specific PCR) assay on 213 genomic loci. Of these, a restricted set of 114 KASP loci were selected by the elimination of redundant, i.e. tightly linked markers based on map positions. STRUCTURE grouping was carried out to reveal three distinct sub-populations, K1, K2 and K3 comprising of 209, 156 and 105 germplasm accessions, respectively. Population FST values for K1, K2 and K3 were at 0.60, 0.24, 0.69, respectively, with highest pair-wise FST obtained between K2 and K3 (0.53). Analysis using the restricted set of 114 markers gave a better inferred membership with a low average admixture of 15.1% compared with 22.6% based on the whole marker set. An improved agreement between STRUCTURE grouping and principal coordinate analysis was reached using the restricted marker set. ΦST values calculated based on nucleotide diversity also suggested three sub-populations: K2, mostly indica germplasm; K1 mostly exotic temperate japonica; and K3, local japonica varieties and landraces. Polymorphic SNPs and haplotypes were discovered which discriminated the three sub-populations. Fifteen KASP markers were most important in discriminating K2 from K1 and K3 and included SNPs associated with domestication within the Wx, Ghd7 and Ghd8 genes. KASP markers are cheaper than SSR markers. Some of the KASP markers were highly discriminatory, using both model and distance based approaches, and so can be used as a cost-effective tool for efficient maintenance and use of rice genetic resources.