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Rice is frequently affected by cold weather at high altitudes in temperate and subtropical regions. With the popularity of direct seeding, a better understanding of the genetic mechanisms regulating cold tolerance will enable breeders to develop varieties with strong low temperature germinability (LTG). In this study, six indices including low temperature germination percentage (LTGP), relative germination percentage (RGP), relative plumule length (RPL), plumule length after 6-day recovery (PLR), plumule length recovery rate (PLRR) and recovery ability of plumule length after cold stress (RAPL) were measured to assess LTG, and carried out a genome-wide association study (GWAS) to identify QTL and candidate genes related to LTG by using a natural population comprising 211 rice accessions. A total of 18 QTL including two for LTGP, three for RGP, five for PLR, four for PLRR, two for RPL and two for RAPL were uncovered on 12 chromosome regions located in chromosome 1, 2, 4, 5, 6, 9, 10 and 12. On chromosome 2, qLTGP2 and qRGP2 were co-localized at 3.3 Mb, and qPLR2 and qPLRR2 were co-localized at 5.5 Mb; qLTGP5, qPLR5 and qPLR5 were co-localized at 27.8 Mb on chromosome 5; qPLR6 and qPLRR6 were co-localized at 5.7 Mb on chromosome 6; and qPLR12 and qPLRR12 were co-localized at 23.5 Mb on chromosome 12. These results indicated that some LTG-related traits may share the same genetic pathway. For the 18 LTG-related QTL, seven QTL (qLTGP2, qRGP2, qPLR2, qPLRR2, qLTGP5, qPLR5 and qPLR5) were reported for the first time. According to candidate gene analysis, fourteen genes from five QTL (qLTGP2, qPLR2, qLTGP5, qRAPL10 and qPLR12) were considered as candidate genes and will be further functionally validated in subsequent experiments. QTL with superior candidate genes identified in this study will be useful in improving cold tolerance in rice cultivars. The rice varieties with strong LTG identified in this study will enrich the resources of rice cultivation project. [ABSTRACT FROM AUTHOR]

The application of heterosis during plant breeding increases rice grain yield. However, there have been limited studies on heterosis during rice grain development during the grain-filling stage; therefore, the genetic basis of heterosis for grain development during the grain-filling stage should be highly valued. In this study, a hybrid combination with the super hybrid rice WFYT025 was used to perform a transcriptomic dynamic analysis in grains at the beginning and middle grain-filling stages. A total of 1556 and 1507 transcripts that were differentially expressed between WFYT025 and its parents (DGHP) were identified at 1-day post-anthesis (DPA) and at 10 DPA, respectively. The analysis of the genetic effects of heterosis showed that the over-dominant effect (66.90% and 55.87%) was the main mode of action during grain development. The KEGG pathway and GO analysis of the DGHP indicated that the gibberellin biosynthetic, starch metabolic, and diterpenoid biosynthetic signaling pathways may be associated with heterosis during grain development. To further explore the candidate genes for grain development heterosis, a recombinant inbred line (RILs) population with a high-density genetic map of 2578 bin markers was constructed by crossing the parents of WFYT025, and nine stable QTLs for grain weight-related traits were identified. By comparing the DGHP with 20 QTLs, LOC_Os02g28820, LOC_Os02g32580, LOC_Os04g25440, and LOC_Os12g04980 were identified as grain development heterosis-related candidate genes. These findings provide resources for the study of heterosis during the grain development of super hybrid rice and provide valuable theoretical references for the cloning and functional analysis of heterosis-related genes. [ABSTRACT FROM AUTHOR]