| Summary: | Grain shape is a key factor for yield and quality in rice. To investigate the genetic basis of grain shape in the high-yielding hybrid rice variety Nei2You No.6, a set of recombinant inbred sister lines (RISLs) were used to map quantitative trait loci (QTLs) determining grain length (GL), grain width (GW), and length-width ratio (LWR) in four environments. A total of 91 medium/minor-effect QTL were detected using a high-density genetic map consisting of 3203 Bin markers composed of single nucleotide polymorphisms, among which 64 QTL formed 15 clusters. Twelve of 15 clusters co-localized with QTL previously reported for grain shape/weight. Three new QTL were detected: <i>qGL-7a</i>, <i>qGL-8</i>, and <i>qGL-11a</i>. A QTL cluster, <i>qLWR-12c/qGW-12</i>, was detected across all four environments with phenotypic variation explained (PVE) ranging from 3.67% to 11.93%, which was subsequently validated in paired lines of F<sub>17</sub> progeny and tightly linked marker assay in F<sub>10</sub> generation. Subsequently, 17 candidate genes for <i>qLWR-12c/qGW-12</i> were detected in the 431 Kb interval utilizing bulk segregant analysis (BSA). Among these, <i>OsR498G1222170400</i>, <i>OsR498G1222171900</i>, <i>OsR498G1222185100</i>, <i>OsR498G1222173400</i>, and <i>OsR498G1222170500</i> were the best candidates, which lays the foundation for further cloning and will facilitate high-yield breeding in rice.
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