QTL mapping for plant architecture in rice based on chromosome segment substitution lines

: Plant architecture is a compound trait integrated with multiple morphological and physiological traits, and it is closely related to rice yield. Deciphering excellent plant architecture alleles or QTLs is of great significance for high-yield rice breeding. In this study, we constructed a set of Changhui 121/Koshihikari chromosome segment substitution lines (CSSLs) with the size of 208 in our laboratory. QTLs controlling plant height, flag leaf morphology, and tiller numbers were detected under three environments. A total of 35 QTLs for rice architecture were identified on 11 chromosomes except chromosome 9, and the range of the phenotypic variation explaining was 2.00%–22.86%. It was worth noting that qPH-1-1 , qFLW-6 , and qFLA-3 could be detected in three environments, among which qFLW-6 was a newly identified QTL of the flag leaf width. Phenotypic identification verified that the additive effects and environmental stability of the two locus alleles by the replacement lines carrying qPH-1-1 and sites. The results of this study laid the foundation for further fine mapping and cloning of QTLs for rice plant architecture and the molecular marker-assisted selection (MAS) in rice breeding.