IDEAS home Printed from https://ideas.repec.org/a/gam/jagris/v11y2021i4p318-d530201.html
   My bibliography  Save this article

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

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: https://www.mdpi.com/2077-0472/11/4/318/pdf
    Download Restriction: no

    File URL: https://www.mdpi.com/2077-0472/11/4/318/
    Download Restriction: no
    ---><---

    References listed on IDEAS

    as
    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Alejandro del Pozo & Nidia Brunel-Saldias & Alejandra Engler & Samuel Ortega-Farias & Cesar Acevedo-Opazo & Gustavo A. Lobos & Roberto Jara-Rojas & Marco A. Molina-Montenegro, 2019. "Climate Change Impacts and Adaptation Strategies of Agriculture in Mediterranean-Climate Regions (MCRs)," Sustainability, MDPI, vol. 11(10), pages 1-16, May.
    2. San Mar Lar & Jeonghwan Seo & Seong-Gyu Jang & Hongjia Zhang & Ah-Rim Lee & Fang-Yuan Cao & Ja-Hong Lee & Na-Eun Kim & Yoonjung Lee & Yong-Jin Park & Joohyun Lee & Soon-Wook Kwon, 2021. "Genome-Wide Association Study for Detecting Salt-Tolerance Loci and Candidate Genes in Rice," Agriculture, MDPI, vol. 11(11), pages 1-17, November.
    3. Xiaohang Ma & Yongze Wu & Jingfang Shen & Lingfeng Duan & Ying Liu, 2021. "ML-LME: A Plant Growth Situation Analysis Model Using the Hierarchical Effect of Fractal Dimension," Mathematics, MDPI, vol. 9(12), pages 1-17, June.
    4. Wei Wang & Xue Gao & Yukun Cheng & Yi Ren & Zhihui Zhang & Rui Wang & Junmei Cao & Hongwei Geng, 2022. "QTL Mapping of Leaf Area Index and Chlorophyll Content Based on UAV Remote Sensing in Wheat," Agriculture, MDPI, vol. 12(5), pages 1-19, April.
    5. Yongqi He & Shan Sun & Jia Zhao & Zhibo Huang & Liling Peng & Chengwei Huang & Zhengbin Tang & Qianqian Huang & Zhoufei Wang, 2023. "UDP-glucosyltransferase OsUGT75A promotes submergence tolerance during rice seed germination," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

    More about this item

    Keywords

    GWAS; cold tolerance; seedling; rice;
    All these keywords.

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:gam:jagris:v:11:y:2021:i:4:p:318-:d:530201. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: MDPI Indexing Manager (email available below). General contact details of provider: https://www.mdpi.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.