Year: 2025
Type: article
Abstract: 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 Wx a allele of the Waxy gene ( OsGBSSI ) and none possessed low-AC alleles: wx , Wx mq or Wx op . 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 alk j allele of the OsSSII_a/SSII_3 ( Alk ) gene and most aromatic varieties had alk i . 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.
Source: Cereal Research Communications
Institutions: Bangor University, University of Karachi, Hamdard University
Language: English
Subfield: Genetics
Domain: Life Sciences
SDG: Zero hunger
Open Access status: hybrid
Estimated APC paid: $3,090
Award: G7018760889
OpenAlex ID: W4411430743