Dissecting the Genetic Basis of Preharvest Sprouting in Rice Using a Genome-Wide Association Study

Preharvest sprouting (PHS) is an unfavorable trait in cereal crops that significantly reduces grain yield and quality. However, the regulatory mechanisms underlying this complex trait are still largely unknown. Here, 276 rice accessions from the 3000 Rice Genomes Project were used to perform a genome-wide association study. In total, seven PHS-associated quantitative trait loci (QTLs) were identified, including two novel QTLs and five previously reported QTLs. Among them, four QTLs were identified in 2020 and 2021, and rice accessions carrying at least two favorable alleles exhibited significantly improved PHS resistance. Within these four stable QTLs, five candidate genes were identified based on haplotype and gene expression analyses, including two genes in qPhs-1.1, one gene in qPhs-3, one gene in qPhs-6, and one gene in qPhs-7. Notably, the novel QTL qPhs-6 was found to contain the candidate gene Pi starvation-induced transcription factor 1 (OsPTF1). We discovered that OsPTF1 plays a novel role in negatively regulating PHS in rice and identified two elite haplotypes of OsPTF1 associated with low PHS. Our results provide future insight into the genetic basis of PHS and will prove useful in the future studies on the role of OsPTF1 in PHS in rice.