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.
