栽培稻芽期耐低温全基因组关联分析

doi:10.3864/j.issn.0578-1752.2022.21.001

Abstract

Abstract:

【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.

Key words: Oryza sativa L., seed germinability, cold tolerance, germination rate, GWAS

PANG HongBo, CHENG Lu, YU MingLan, CHEN Qiang, LI YueYing, WU LongKun, WANG Ze, PAN XiaoWu, ZHENG XiaoMing. Genome-Wide Association Study of Cold Tolerance at the Germination Stage of Rice[J].Scientia Agricultura Sinica, 2022, 55(21): 4091-4103.

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Figures/Tables 7

Fig. 1

Fig. 2

Fig. 3

Fig. 4

Table 1

Gene annotation of 24 candidate genes"

染色体 Chr.	基因号 Gene ID	基因注释 Annotation
Chr.4	LOC_Os04g24830	含锌指、CCHC型结构域的蛋白质 Zinc finger, CCHC-type domain containing protein
Chr.4	LOC_Os04g24840	糖基转移酶，推测，表达Glycosyltransferase, putative, expressed
Chr.4	LOC_Os04g24850	细胞分裂素-O-葡糖基转移酶2，假定的，表达Cytokinin-O-glucosyltransferase 2, putative, expressed
Chr.4	LOC_Os04g24860	逆转录酶子蛋白，推定，未分类，表达Retrotransposon protein, putative, unclassified, expressed
Chr.4	LOC_Os04g24870	逆转录酶子蛋白，推定，未分类Retrotransposon protein, putative, unclassified
Chr.4	LOC_Os04g24880	逆转录酶子蛋白，推定，未分类，表达Retrotransposon protein, putative, unclassified, expressed
Chr.4	LOC_Os04g24900	表达蛋白Expressed protein
Chr.4	LOC_Os04g24910	表达蛋白Expressed protein
Chr.4	LOC_Os04g24920	转座子蛋白，推定，CACTA，En/Spm亚类，表达 Transposon protein, putative, CACTA, En/Spm sub-class, expressed
Chr.4	LOC_Os04g24930	表达蛋白Expressed protein
Chr.4	LOC_Os04g24940	表达蛋白Expressed protein
Chr.4	LOC_Os04g24950	假定的蛋白质Hypothetical protein
Chr.4	LOC_Os04g24960	转座子蛋白，推定，CACTA，En/Spm亚类，表达 Transposon protein, putative, CACTA, En/Spm sub-class, expressed
Chr.4	LOC_Os04g25100	转座子蛋白，推定，未分类，表达Transposon protein, putative, unclassified, expressed
Chr.4	LOC_Os04g25110	Ulp1蛋白酶家族，含有C端催化域的蛋白，表达式ulp1; Ulp1 protease family, C-terminal catalytic domain containing protein, expressedulp1
Chr.4	LOC_Os04g25120	表达蛋白Expressed protein
Chr.4	LOC_Os04g25130	逆转录子蛋白，推定，LINE亚类，表达Retrotransposon protein, putative, LINE subclass, expressed
Chr.4	LOC_Os04g25140	OsFBDUF20-含有F-box和DUF结构域的蛋白，已表达; OsFBDUF20- F-box and DUF domain containing protein, expressed
Chr.4	LOC_Os04g25150	花粉过敏原，推定，表达Pollen allergen, putative, expressed
Chr.4	LOC_Os04g25160	花粉过敏原，推定，表达Pollen allergen, putative, expressed
Chr.4	LOC_Os04g25170	逆转录酶原蛋白，推定，未分类，表达Retrotransposon protein, putative, unclassified, expressed
Chr.4	LOC_Os04g25180	假定的蛋白质Hypothetical protein
Chr.4	LOC_Os04g25190	花粉过敏原，推定，表达Pollen allergen, putative, expressed
Chr.4	LOC_Os04g25210	转座子蛋白，推定，未分类，表达Transposon protein, putative, unclassified, expressed

Table 1

Fig. 5

Fig. 6

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