Development and utilization of functional KASP markers to improve rice eating and cooking quality through MAS breeding

There is a steady demand for high-quality rice varieties though consumers’ preference for high-quality rice varies from regions. The improvement of the quality of rice, especially its eating and cooking quality (ECQ), is an important breeding target as rice is mainly consumed in cooked form. The development and utilization of breeder-friendly and high-throughput marker systems play a pivotal role in marker-assisted breeding of rice cultivars, with pyramids of valuable genes affecting rice ECQ. In this study, we developed functional markers based on the Kompetitive Allele-Specific PCR (KASP) method for three principal genes, Wx, BADH2 and ALK, affecting ECQ in rice. The accuracy of all KASP markers was verified and confirmed with Sanger sequencing. A diverse rice panel consisting of 38 indica cultivars, 9 japonica cultivars and 1 Javanica cultivar were used to assess the validity of these markers for genotyping. The results showed that the functional KASP markers of Wx, ALK and BADH2 could effectively distinguish the different alleles. The genotyping results highly coincided with the phenotypic traits of rice eating and cooking quality. Eight rice entries harboring 3 favorable alleles were identified and superior rice restorers with improved ECQ were bred via functional marker genotyping. Breeders can develop rice cultivars that have desirable ECQ, customized to meet the market requirements in target regions. Hence, the development of these 3 applicable KASP functional markers based on allelic variation would be valuable for improving rice eating and cooking quality through maker-assisted selection to carter various consumer preferences especially in Asian areas.