Detection of QTLs for outcrossing-related traits in rice (Oryza sativa L.) by association mapping and the RSTEP-LRT method

The outcrossing traits in rice affect the yield of hybrid rice seed production. In this study, 30 quantitative trait loci (QTLs) were detected in a natural population composed of 522 accessions by using a mixed linear model for the four outcrossing-related traits in 2017 and 2018. We detected 3, 4, 9 and 14 QTLs for flag leaf length (FLL), flag leaf width (FLW), flag leaf angle (FLA) and panicle neck length (PNL), respectively, among which 26 QTLs were novel. The favorable alleles and their carrier varieties were noticed with the largest phenotypic effect value. For FLL, marker allele RM6997-105 bp on chromosome 4 carried by Yue96 cultivar showed the highest phenotypic effect value (PEV), allele RM562-280 bp on chromosome 1 carried by Wanzhongqiu genotype for FLW, allele RM152-375 bp on chromosome 8 in typical carrier variety Zhongzuo93 for FLA and allele RM134-150 bp on chromosome 7 carried by Yue34 cultivar for PNL showed the highest PEVs. Additionally, nine QTLs were detected for the 4 traits with percentage of phenotypic variance explained (PVE) ranging from 16.24% (RM21) to 28.75% (RM5479) using a chromosome segment substitution line (CSSL) population. Among these detected QTLs, qFLL-12 and qFLW-12 showed 19.85% and 19.57% PVE, respectively. Four QTLs ( qFLA-10 , qFLA-11 , qFLA-12.1 , qFLA-12.2 ) detected for FLA showed PVEs ranging from 16.24% to 28.75%. For PNL, qPNL-7 , qPNL-12.1 , qPNL-12.2 were observed with PVEs of 20.14%, 17.39% and 28.36%, respectively. The favorable allele RM125-145 bp on chromosome 7 for PNL was detected in both the natural population and CSSL population and was carried by Yue38 accession and parent Xiushui79. The detected favorable alleles could be used to improve target traits.