Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in Japonica Rice

Abstract

Seed germination is a key contributing factor to the yield of direct seeding cultivation in rice. Unraveling the genetic architecture underlying rice seed germination is pivotal for breeding elite direct-seeded rice varieties. However, only a limited number of genes regulating seed germination have been characterized in rice. In this study, we implemented a genome-wide association study (GWAS) to dissect the genetic structure of seed germination by using 131 Japonica rice accessions. We identified six stable loci (qGR1.1, qGR2.1, qGR3.1, qGR7.1, qGR8.1 and qGR9) associated with seed germination in two consecutive years, all of which were co-localized with previously reported quantitative trait loci (QTLs). OsGA2ox5, encoding a gibberellin 2-oxidase, was identified as the most plausible candidate gene of the major locus qGR7.1. Knockout of OsGA2ox5 led to delayed seed germination and retarded seedling growth. A non-synonymous variant (Chr7-218,245) within the coding region of OsGA2ox5 might be closely associated with variation in seed germination among Japonica accessions. Low nucleotide diversity at the OsGA2ox5 locus in Japonica could be a result of selection during rice improvement. Taken together, our results provide an important foundation for elucidating the molecular mechanism underlying seed germination and genetic improvement of rice seed vigor in the future.