科研之友
微信
新浪微博
Facebook
分享链接
摘要
【Objective】Rice is an important food crop, and its growth and development are most vulnerable at the germination stage. Under cold stress, direct-seeded rice exhibited significantly reduced germination rates (GRs) and yield compared with normally grown plants. Thus, a better understanding of genetic mechanisms regulating cold tolerance will enable to develop rice varieties with improved tolerance during germination. 【Method】238 representative rice germplasm resources from 14 countries worldwide were tested in phenotypic identification in Shenyang in 2021 and 2022; the low-temperature germination rate and relative low-temperature germination rate (LTGR and relative LTGR; 1-10 days under 15℃) were evaluated in an artificial climate incubator, and a 5-10 day LTGR histogram was constructed using R. The day suitable for GWAS was determined by phenotypic variation (Hill) and a mixed linear model combining LTGR and relative LTGR phenotype data with resequencing data.【Result】LTGR histogram and phenotypic variation showed optimal GR on day 8 (Hill=0.84), i.e., it was higher than on other days (Hill=0.48-0.83), which could be used for GWAS. The principal component analysis results divided all germplasms into five groups-indica, aus, temperate japonica, tropical japonica, and aromatic. GWAS analysis of two indicators detected three identical significant single nucleotide polymorphisms (SNPs) related to cold tolerance in rice at the germination stage. These were located on chromosome 4, which could explain 11.9%-25.4% of the phenotype. In addition, 24 candidate genes were screened in the 50-kb region upstream and downstream of these three SNPs. Further linkage disequilibrium analysis and haplotype analysis were carried out and highly significant differences were found between different haplotypes of the LOC_Os04g24840 and LOC_Os04g25140 genes for cold tolerance. LOC_Os04g24840 was divided into five haplotypes by the coding region SNP, and Hap_3 was significantly more cold tolerant than Hap_1; LOC_Os04g25140 was divided into 18 haplotypes by the coding region SNP and the amino acid variation (S＞L) at 77 bp was different in japonica and indica rice. These results showed that the genes encoding glycosyltransferases (LOC_Os04g24840) and F-box protein (LOC_Os04g25140) might be closely related to cold tolerance in rice.【Conclusion】 A total of three SNP loci were detected in 238 rice germplasm resources, and two candidate genes were screened for their association with cold tolerance during germination in rice.
-
单位中国农业科学院
