Genome-Wide Association Study Reveals Loci and New Candidate Gene Controlling Seed Germination in Rice
2024
Shaona Chen | Guanlong Chen | Zepeng Peng | Jiping Liu | Yixiong Zheng | Bin Yang
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 (<i>qGP2</i> and <i>qGP4.1</i>) were stable across different environments. <i>GP4</i> (<i>Germination percentage 4</i>), encoding a 9-cis-epoxycarotenoid dioxygenase, was identified as the candidate gene of the major locus <i>qGP4.1</i>. A sequence analysis of <i>GP4</i> revealed that four functional polymorphic sites in the coding region were significantly associated with germination percentage. The disruption of <i>GP4</i> by gene editing resulted in faster seed germination and seedling establishment. Taken together, we have identified <i>GP4</i> 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.
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