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.

Rice, a cold-sensitive crop, is a staple food for more than 50% of the world’s population. Low temperature severely compromises the growth of rice and challenges China’s food safety. Dongxiang wild rice (DXWR) is the most northerly common wild rice in China and has strong cold tolerance, but the genetic basis of its cold tolerance is still unclear. Here, we report quantitative trait loci (QTLs) analysis for seedling cold tolerance (SCT) using a high-density single nucleotide polymorphism linkage map in the backcross recombinant inbred lines that were derived from a cross of DXWR, and an indica cultivar, GZX49. A total of 10 putative QTLs were identified for SCT under 4 °C cold treatment, each explaining 2.0–6.8% of the phenotypic variation in this population. Furthermore, transcriptome sequencing of DXWR seedlings before and after cold treatment was performed, and 898 and 3413 differentially expressed genes (DEGs) relative to 0 h in cold-tolerant for 4 h and 12 h were identified, respectively. Gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) analysis were performed on these DEGs. Using transcriptome data and genetic linkage analysis, combined with qRT-PCR, sequence comparison, and bioinformatics, LOC_Os08g04840 was putatively identified as a candidate gene for the major effect locus qSCT8. These findings provided insights into the genetic basis of SCT for the improvement of cold stress potential in rice breeding programs.

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.