Association of KASP with starch‑trait diversity in modern rice grown in Pakistan

The eating and cooking quality of rice varieties should not compromised during breeding for future growing conditions in all rice growing countries. As a case study, KASP markers for genes related to starch and aroma traits were tested for their association with amylose content (AC) and alkaline spreading value (ASV) in thirty-two rice varieties from Pakistan representing diversity in both traits. Seventeen KASP revealed variants among Pakistani varieties: SNPs in six starch-related genes and an InDel in the fragrance gene BADH2. All Pakistani varieties had the Wxa allele of the Waxy gene (OsGBSSI) and none possessed low-AC alleles: wx, Wxmq or Wxop. Population structure analysis of marker data indicated four ancestorial subgroups among the Pakistani genotypes: Japonica, Basmati, low-ASV Indica and high-ASV indica. Varieties with alleles for ‘low’ and intermediate’ AC tended to have alleles for ‘lower’ ASV. Fragrance and AC were correlated (r = 0.608) with non-aromatic varieties having 25.4% mean AC and aromatic varieties having 21.9% mean AC. Most non-aromatic varieties had the alkj allele of the OsSSII_a/SSII_3 (Alk) gene and most aromatic varieties had alki. Functional SNPs in Alk, BADH2, and PPR genes were associated with ASV, and a functional SNP in OsSSII_b was associated with AC and ASV. Three exonic Waxy loci were correlated with both AC and ASV while four non-functional KASP were in linkage disequilibrium with these alleles. These findings indicate that KASP could inform selection of eating and cooking quality in appropriate crosses.