Mapping Quantitative Trait Loci for Cold Tolerance in Rice under Germination Stage by Whole Genome Resequencing and Analysis of Candidate Genes

Abstract

Low-temperature stress significantly affects rice growth and causes serious loss of yield in temperate and high-altitude areas of the world. Rice lacks cold tolerance (CT) at germination stage, which reduces seedling vigor, hinders crop establishment and crop growth, and even affect direct-seeded rice. A chromosome segment substitution line (CSSL) population, including 271 lines, was derived from cold-tolerant donor wild rice Y11 (Oryza rufipogon Griff.) crossed with cold-sensitive rice variety GH998 to explore new genetic resource with CT and further investigate quantitative trait loci (QTLs) responsible for germination properties under low temperature. The germination rates of Y11 and GH998 were 95% and 73.33%, respectively, under cold stress. The range of variance of the germination rate in the CSSLs was between 0% and 98.33%. In addition, the CSSLs and parents were sequenced via whole genome resequencing. Results showed 33.46, 33.36, and 475.65 Gbp of clean data of GH998, Y11, and CSSLs, respectively. In 12 linkage groups, the general map distance was 941.49 cM, while the average map distance was 0.63 cM. On thebasis of 1484 bins, a high-density linkage map of the CSSLs was developed. The average distance of the linkage map ranged from 0.42 cM to 1.39 cM. The phenotype of CSSLs under low temperature and 615,466 single nucleotide polymorphisms (SNPs) between Y11 and GH998 were used for QTL analysis. Two QTLs, namely, low-temperature germination 8 (qLTG8) and qLTG11, were responsible for the germination ability under low temperature in rice. qLTG8 was mapped on chromosome 8, and it explained 14.55% of the total phenotypic variation explained (PVE) during the germination stage. qLTG8 was in 195.5 kb, and 32 genes were predicted based on the Rice Genome Annotation Project. qLTG11 was located on chromosome 11, and it explained 14.31% of the total PVE during the germination stage. qLTG11 was mapped at a narrow distance in 78.83 kb, and only 12 genes fall within this range according to the Rice Genome Annotation Project. The expression patterns of these 32 genes in the qLTG8 region demonstrated that LOC_Os08g01120, LOC_Os08g01140, LOC_Os08g01390, LOC_Os08g01170, and LOC_Os08g01380 were highly induced by cold stress in Y11 compared with GH998. The expression patterns of 12 genes in the qLTG11 region suggested that LOC_Os11g32880 and LOC_Os11g32940 were highly induced by cold stress in Y11 compared with GH998. This study provides an effective method, i.e., constructing CSSLs of wild rice, to explore excellent genes of wild rice and create new genetic resources. The results also provide a basis for identifying the genes underlying qLTG8 and qLTG11, indicating that QTL could be used for genetic improvement of CT in cultivar rice.