Genome-Wide Association Analysis of Gibberellin Sensitivity for Panicle Exsertion Length in Rice and Candidate Gene Identification

Insufficient panicle exsertion length (PEL) in hybrid rice production requires heavy gibberellin (GA3) application, increasing costs and pollution. This study explored genetic resources regulating GA3 sensitivity to enable low-GA3-dependent breeding. A panel of 173 rice accessions was treated with GA3 (0.1 mg/plant) over two years. The GA3 sensitivity index (PELGSI) was calculated as (PELGA3 − PELn)/PELn. A genome-wide association study identified seven QTLs controlling PELGSI, with qPELGSI3.2 on chromosome 3 being the major locus. Through linkage disequilibrium analysis, non-synonymous mutation screening, and qRT-PCR, LOC_Os03g15770 (encoding a receptor-like cytoplasmic kinase) was identified as a promising candidate gene. Haplotype analysis showed that Hap 1 is the elite allele, conferring significantly higher PELGSI (2.69%) than Hap 2 (1.41%). This study reports the genetic locus and candidate gene regulating exogenous GA3 sensitivity in rice, providing new resources for marker-assisted breeding of low-GA3-dependent hybrid rice parents.