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.