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Identification of Candidate Genes for Salt Tolerance at the Germination Stage in Japonica Rice by Genome-Wide Association Analysis

Author

Listed:
  • Yuxuan Duan

    (Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
    These authors contributed equally to this work.)

  • Hongliang Zheng

    (Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
    These authors contributed equally to this work.)

  • Haoran Wen

    (Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
    These authors contributed equally to this work.)

  • Di Qu

    (Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China)

  • Jingnan Cui

    (Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China)

  • Chong Li

    (Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China)

  • Jingguo Wang

    (Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China)

  • Hualong Liu

    (Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China)

  • Luomiao Yang

    (Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China)

  • Yan Jia

    (Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China)

  • Wei Xin

    (Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China)

  • Shuangshuang Li

    (Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China)

  • Detang Zou

    (Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin 150030, China)

Abstract

Rice salt tolerance at the germination stage directly affects the germination rate and seedling establishment of rice directly seeded in saline soils, which in turn affects yield. In this study, we determined the relative germination potential (RGP) and relative germination index (RGI) under 200 mM salt stress and control conditions using 295 japonica rice accessions. Statistical analysis showed extensive phenotypic variations under salt stress conditions. Twenty-one varieties with an RGP ≥ 80% and an RGI ≥ 80% were screened. Based on genotypic data including, 788,396 single-nucleotide polymorphisms (SNPs), 40 quantitative trait loci (QTL) were localized on rice chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12, which were shown to be significantly associated with rice salt tolerance at the germination stage, including 20 for RGP and 20 for RGI, using genome-wide association analysis. Six QTL with ≥ 3 consecutive significant SNP loci and localized in the same LD interval were selected for further analysis. Four rice genes ( LOC_Os01g04920 , LOC_Os10g38350 , LOC_Os10g38470 , and LOC_Os10g38489 ) were selected as important candidates for salt tolerance based on haplotype analysis and functional annotation. The findings could facilitate the development of valuable rice varieties for direct seeding in salinized soil and improve japonica rice salt tolerance at the germination stage through molecular breeding.

Suggested Citation

  • Yuxuan Duan & Hongliang Zheng & Haoran Wen & Di Qu & Jingnan Cui & Chong Li & Jingguo Wang & Hualong Liu & Luomiao Yang & Yan Jia & Wei Xin & Shuangshuang Li & Detang Zou, 2022. "Identification of Candidate Genes for Salt Tolerance at the Germination Stage in Japonica Rice by Genome-Wide Association Analysis," Agriculture, MDPI, vol. 12(10), pages 1-15, October.
  • Handle: RePEc:gam:jagris:v:12:y:2022:i:10:p:1588-:d:931451
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    References listed on IDEAS

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    1. Nanyan Deng & Patricio Grassini & Haishun Yang & Jianliang Huang & Kenneth G. Cassman & Shaobing Peng, 2019. "Closing yield gaps for rice self-sufficiency in China," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
    2. Susanna Atwell & Yu S. Huang & Bjarni J. Vilhjálmsson & Glenda Willems & Matthew Horton & Yan Li & Dazhe Meng & Alexander Platt & Aaron M. Tarone & Tina T. Hu & Rong Jiang & N. Wayan Muliyati & Xu Zha, 2010. "Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines," Nature, Nature, vol. 465(7298), pages 627-631, June.
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