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Home > Archive>Volume 25, Issue 10, 2024 >1748-1755. DOI:10.13430/j.cnki.jpgr.20240103001
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Nucleotide Diversity and Haplotype Analysis of qCTS-9 Gene Related to Cold Tolerance in Rice
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Affiliation:

1.Longping Branch， College of Biology， Hunan University， Changsha 410125;2.Rice Research Institute， Hunan Academy of Agricultural Sciences， Changsha 410125;3.Institute of Crop Sciences， Chinese Academy of Agricultural Sciences， Beijing 100081;4.Sanya National Research Institute of Breeding in Hainan， Chinese Academy of Agricultural Sciences， Sanya 571700， Hainan;5.College of Life Science， Shenyang Normal University， Shenyang 110034

Fund Project:

Foundation projects： Hunan Provincial Science and Technology Innovation Program （2023NK1010，2021NK1011）； National Natural Science Foundation of China （32341026）

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    Abstract:

    qCTS-9 is reported to be a rice cold-tolerant gene， which functions stably under a wide range of low temperature conditions at seedling stage. Detailed knowledge of the haplotype and adaptive evolution pattern of qCTS-9 will provide support for breeding cold-tolerant rice varieties. In this study， 116 accessions of cultivated rice （Oryza sativa L.） and 37 accessions of wild rice （Oryza rufipogon Griff.） were used to analyze the nucleotide diversity and haplotypes of qCTS-9. There are a total of 14 SNPs in the coding region of qCTS-9， and these SNPs comprised eight haplotypes. Four non-synonymous SNPs constituted three functional haplotypes， which showed significant differences in cold tolerance. The SNP at the 1535 bp in the coding region was hypothesized to be the key mutation site of qCTS-9. The analysis of cis-acting elements in the promoter region of qCTS-9 showed that a SNP （G→A） at -1107 bp resulted in the deletion of a MYB recognition site in the cold-sensitive haplotype Hap4， which may lead to a decrease in cold tolerance in indica rice. Wild rice contains most of the variations of qCTS-9 gene in cultivated rice， but it does not have any unique variant sites within the coding region and promoter cis-acting elements. During the differentiation from wild rice to indica and japonica rice， cold-tolerant related alleles or mutations were fixed and expanded， which in turn enhanced its regional adaptability.

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History
  • Received:January 03,2024
  • Online: October 09,2024
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