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Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage

Author

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  • Tae-Ho Ham

    (Department of Crop Science, Konkuk University, Seoul 05029, Korea)

  • Yebin Kwon

    (Department of Crop Science, Konkuk University, Seoul 05029, Korea)

  • Yoonjung Lee

    (Department of Crop Science, Konkuk University, Seoul 05029, Korea)

  • Jisu Choi

    (Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50434, Korea)

  • Joohyun Lee

    (Department of Crop Science, Konkuk University, Seoul 05029, Korea)

Abstract

We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

Suggested Citation

  • Tae-Ho Ham & Yebin Kwon & Yoonjung Lee & Jisu Choi & Joohyun Lee, 2021. "Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage," Agriculture, MDPI, vol. 11(4), pages 1-13, April.
  • Handle: RePEc:gam:jagris:v:11:y:2021:i:4:p:318-:d:530201
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    References listed on IDEAS

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    1. Wanneng Yang & Zilong Guo & Chenglong Huang & Lingfeng Duan & Guoxing Chen & Ni Jiang & Wei Fang & Hui Feng & Weibo Xie & Xingming Lian & Gongwei Wang & Qingming Luo & Qifa Zhang & Qian Liu & Lizhong , 2014. "Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice," Nature Communications, Nature, vol. 5(1), pages 1-9, December.
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    Keywords

    GWAS; cold tolerance; seedling; rice;
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