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Genome-Wide Association Study Reveals Loci and New Candidate Gene Controlling Seed Germination in Rice

Author

Listed:
  • Shaona Chen

    (Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China)

  • Guanlong Chen

    (Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China)

  • Zepeng Peng

    (Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China)

  • Jiping Liu

    (Seed Industry Innovation Research Institute, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China)

  • Yixiong Zheng

    (Seed Industry Innovation Research Institute, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China)

  • Bin Yang

    (Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China)

Abstract

Improving seed germination and seedling development can potentially increase crop yield and improve quality in direct-seeded rice. This study aimed to detect loci or genes associated with rice seed germination. We reported the phenotypic analysis of seed germination in 103 rice accessions across two years, and a genome-wide association study (GWAS) was conducted to identify loci underlying the genetic regulation of seed germination. A total of seven genetic loci were found to be associated with seed germination, including five loci that overlapped with the previously reported loci/genes, and two novel loci. Of these, two loci ( qGP2 and qGP4.1 ) were stable across different environments. GP4 ( Germination percentage 4 ), encoding a 9-cis-epoxycarotenoid dioxygenase, was identified as the candidate gene of the major locus qGP4.1 . A sequence analysis of GP4 revealed that four functional polymorphic sites in the coding region were significantly associated with germination percentage. The disruption of GP4 by gene editing resulted in faster seed germination and seedling establishment. Taken together, we have identified GP4 as a novel gene involved in rice seed germination, and we provide a potential target gene for improving rice seed vigor via gene editing or molecular breeding.

Suggested Citation

  • Shaona Chen & Guanlong Chen & Zepeng Peng & Jiping Liu & Yixiong Zheng & Bin Yang, 2024. "Genome-Wide Association Study Reveals Loci and New Candidate Gene Controlling Seed Germination in Rice," Agriculture, MDPI, vol. 14(9), pages 1-11, September.
    • Handle: RePEc:gam:jagris:v:14:y:2024:i:9:p:1613-:d:1478380
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    Keywords

    rice; GWAS; seed germination; loci;
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