Locating QTL associated with spike traits of Dongxiang wild rice (Oryza rufipogon Griff.)

Improvements in the spike of rice play an essential role in modern super-rice breeding projects. In this study, two sets of population, including 230 F 2 plants and 150 F 2:3 lines derived from a cross of Dongxiang wild rice (DXWR) and 93–11, were developed to identify quantitative trait loci (QTLs) for spike traits. A total of 38 QTLs affecting 20 spike traits and 37 epistatic QTL pairs with more than one interaction were detected in the two populations, explaining the wide phenotypic variation of QTLs ranging from 10.17 to 47.79% and from 27.07 to 78.60%, respectively. Among these QTLs, eight genomic regions containing clustered QTLs affecting two or more traits were detected on chromosome 3, 6, 7, 8, and 12 in the two populations, and two co-localized QTLs were located at intervals of RM3724–RM5745 and RM3484–RM6776 on chromosome 6 and 7, with pleiotropic effects on the MPW, NPB, GSD, NFG, and Ppb IV IL. The additive-dominant-epistatic QTLs played an essential role in controlling the genetic expression of panicle traits in DXWR. Overall, these results can serve as a foundation for facilitating future cloning and molecular breeding in crop science.