Effectiveness of KASP-SNP markers in selecting for grain quality traits in rice

Asante, M.D., Ofosu, K.A., Frimpong, F., Alphonso, D.K., Nartey, E., Obeng, A.E., Bam, R.K., Gamenyah, D.D., Ribeiro, P.F. and Manilal, W. 2025. Effectiveness of KASP-SNP markers in selecting for grain quality traits in rice. Plant Gene 43:100503.

Grain quality is a crucial factor for rice consumers, and as such, it is a major focus for breeders. Phenotyping for grain quality traits can be a laborious and costly process. In this study, we evaluated the effectiveness of KASP-SNP markers in selecting for grain quality traits, including aroma, gelatinization temperature, grain length, grain width, and grain length: width ratio. We phenotyped 300 diverse rice genotypes for these four traits and genotyped them using their respective KASP-SNP markers. A regression analysis of the phenotype on the genotype was performed. The markers associated with the fgr-1 and GS3 genes explained 97 % and 94 % of the phenotypic variation for aroma and grain length, respectively. Two SNP markers (snpOS00440 and snpOS00441) associated with the GW5/SW5 gene each explained 82 % of the phenotypic variation for grain width, which increased marginally to 85 % when combined. However, two markers, snpOS00036 and snpOS00450, for gelatinization temperature explained only 2 % and 25 % of the phenotypic variation, respectively, indicating that these markers were not efficient in predicting this trait. Our findings suggest that the markers associated with aroma (fgr-1), grain length (GS3), and grain width (GW5/SW5) are highly efficient and reliable for marker-assisted selection.