Quantitative trait loci (QTLs) and HQTL (heterosis QTLs) for grain shape are two major genetic factors of grain yield and quality in rice (Oryza sativa L.). Although many QTLs for grain shape have been reported, only a few are applied in production. In this study, 54 QTLs for grain shape were detected on 10 chromosomes using 33 SSSLs (single-segment substitution lines) and methods of statistical genetics. Among these, 23 exhibited significant positive additive genetic effects, including some novel QTLs, among which qTGW4-(1,2), qTGW10-2, and qTGW10-3 were three QTLs newly found in this study and should be paid more attention. Moreover, 26 HQTLs for grain shape were probed. Eighteen of these exhibited significant positive dominant genetic effects. Thirty-three QTLs for grain shape were further mapped using linkage analysis. Most of the QTLs for grain shape produced pleiotropic effects, which simultaneously controlled multiple appearance traits of grain shape. Linkage mapping of the F₂ population derived from sub-single-segment substitution lines further narrowed the interval harbouring qTGW10-3 to 75.124 kb between PSM169 and RM25753. The candidate gene was identified and could be applied to breeding applications by molecular marker-assisted selection. These identified QTLs for grain shape will offer additional insights for improving grain yield and quality in rice breeding.

Panicle length (PL) is one of the most important agronomic traits of rice; it determines panicle architecture and strongly affects grain yield and quality. Although several genes related to PL quantitative trait loci have been identified, PL has not been well characterized genetically, and its contribution to breeding and genetic improvement is unknown. Herein, we identified a novel quantitative trait locus for PL, i.e., qPL6.2, from single fragment substitution line P50, and mapped it to a region of 232.29-kb. The mapped region harbored 28 candidate genes, 7 of which were expressed more in young panicles than in other tissues. Further analysis of gene-knockout plants revealed LOC_Os06g06490 as a putative candidate gene of qPL6.2, and that the encoded protein was localized in the cell membrane. Sequence analysis of 102 modern Chinese rice varieties indicated that 3 variations at the LOC_Os06g06490 locus, among which C189G was proposed as a marker for indica-japonica differentiation, and A3259T which was specific to P50 might be as a functional variant. We hypothesize that mutations in the LOC_Os06g06490 locus affect the accumulation of indoleacetic acid, which regulates the length of young panicle. Therefore, the A3259T mutation may facilitate the breeding of better-quality high-yield japonica rice with moderate PL.

QTL and HQTL (heterosis QTL) of grain shape are two important components for grain yield and influence the end-use rice quality. However, limited QTLs of grain shape were detected, with only a few applied in production. In this study, 54 QTLs of grain shape were detected on 10 chromosomes over 2 years,twenty-three of which showing positive additive genetic effects, including some QTLs that were newly found and with large positive effect such as qHGW4-1,qHGW4-2 and qHGW10-2. 26 HQTLs of grain shape were probed, with eighteen of which providing positive dominance genetic effects. 33 QTLs of grain shape were mapped by linkage analysis. Most of grain shape QTLs have pleiotropic effects which control simultaneously the multiple appearance traits of the grain shape, for instance GL, GW, LWR, GS, GC, GR and TGW. Linkage mapping by F₂ population deriving from sub-SSSLs further narrowed the interval containing qTGW10-3 down to about 75.124 kb between markers PSM169 and RM25753, where eight candidate genes were predicted. In this study, the finding of grain shape QTL will provide us greater insight into improving rice quality and grain yield in rice breeding.