Mining Elite Alleles of Growth Duration and Productive Panicle Number per Plant by Association Mapping with Conditional Phenotypic Value in Japonica Rice

To provide genetic information and materials for breeding hybrid japonica rice with wide adaptability and strong competitive advantage of yield, elite alleles and their carrier varieties of growth duration (GD) and productive panicle number per plant (PN) were detected. A natural population composed of 94 japonica varieties was phenotyped for the GD, PN and plant height (PH) in two environments. The conditional phenotypic data were transferred by the linear model method in software QGAStation 1.0, and association mapping based on the unconditional and conditional phenotype values of GD and PN was analyzed by using general linear model in software TASSEL. A total of 34 simple sequence repeat (SSR) marker loci associated with GD and PN were detected in the two environments. Among them, 15 were associated with GD, and 19 were associated with PN. Four elite alleles of RM8095-120bp, RM7102-176bp, RM72-170bp and RM72-178bp were associated with GD, and their carrier varieties were Hongmangshajing, Nipponbare, Hongmangshajing and Nannongjing 62401, respectively. These elite alleles from the carrier varieties can shorten GD by 2.03-9.93 d when they were introduced into improved materials. RM72-182bp associated with PN was an elite allele, and its carrier variety was Xiaoqingzhong. It can increase PN by three when introduced into improved materials. Moreover, these elite alleles can be used to improve target traits without influencing another two traits.