Dissecting the Molecular Basis for Genetic Improvement of Rice

Abstract Rice quality is one of the important indicators of rice breeding, including milling quality, appearance, cooking and eating quality and nutritional quality. Guangxi is one of the origins of cultivated rice, and great progress has been made in the genetic improvement of rice quality by utilizing abundant rice germplasm resources. In this study, 1570 rice varieties approved in Guangxi from 1983 to 2021 were used to analyze the changes of 16 traits. We found that the appearance quality and cooking and eating quality of Guangxi rice were significantly improved, especially the hybrid rice varieties. By conducting genome-wide association analysis and variant allele frequency analysis from 38 representative varieties, we found that ALK, BG2, GL3.1, GL7/GW7, GPA3, GS3, OsMKKK10, Wx, An-1, BG1, CLG1, GS5, GW8 and RGG2 may be closely related to the genetic improvement of rice quality traits in Guangxi, among which 11 genes are related to rice grain shape. The functional variation sites of seven important quality genes, including ALK, Wx, and GS3, were analyzed by the penta-primer amplification refractory mutation system (PARMS). The data showed that Gui569, Gui117, Gui721, Gui726, RYousi, RSimiao, and RBasi exhibited multiple elite alleles. In this study, we analyzed the phenotypic changes and molecular basis of varieties in Guangxi over the past 40 years. These results will provide theoretical guidance for the genetic improvement of rice quality and the cultivation of new varieties, which is of great significance for improving rice quality.