Identification of genes associated with early growth and quick development in rice by genome-wide association studies.

Main conclusion: GWAS identified key genetic loci on chromosome 8 associated with early growth vigor in direct-seeded rice, with four candidate genes (including a zinc-finger protein gene) implicated in regulating seed germination and leaf growth. Direct seeding rice, recognized for its water-efficient and resource-conserving attributes, has seen a steady expansion in cultivation area. However, this method demands enhanced early growth vigor and rapid developmental traits in seeds. To unravel the genetic basis of these characteristics, we performed genome-wide association studies (GWASs) on 196 rice accessions. Whole-genome resequencing of the panel was integrated with population structure analysis to identify loci governing early growth dynamics. Subsequent high-density genotyping pinpointed significant associations on chromosome 8, where single nucleotide polymorphisms (SNPs) correlated strongly with target traits. In proximity to the GWAS signals, four genes were highlighted as potential candidate genes. The identified candidate genes encode zinc-finger proteins involved in regulating seed germination and leaf growth. This finding provides a basis for further functional validation of these candidate genes through the development of multiple mutant lines.