Genome-wide association study identifies stable loci for heading date, culm length, and panicle length in early-maturing japonica rice

Climate change-induced instability in cultivation environments poses a major threat to rice productivity, highlighting the need to develop climate-adaptive rice cultivars. The identification of favorable alleles from diverse genetic resources is therefore essential for broadening the genetic basis of breeding materials and improving agronomic performance under variable environments. In this study, 147 rice accessions derived from the International Rice Research Institute’s 3 K Rice Genomes Project, consisting primarily of japonica accessions showing relatively early heading under temperate field conditions, were evaluated for days to heading (DTH), culm length (CL), and panicle length (PL) across three environments. A genome-wide association study (GWAS) was performed using the FarmCPU model with 926,373 single nucleotide polymorphisms (SNPs). Three stable QTLs, qDTH3 , qCL9 , and qPL11 , were identified for DTH, CL, and PL, respectively, and their lead SNPs showed significant phenotypic differences between allelic groups. Haplotype analyses further suggested Os03g0401200 (LHD3) and Os09g0422500 (BC6) as promising candidate genes underlying qDTH3 and qCL9 , respectively. Specifically, qDTH3 may facilitate the adjustment of heading date with limited effects on culm and panicle development, whereas qCL9 suggests a potential link between culm length variation and cell wall biosynthesis. These findings provide useful genetic resources and molecular breeding targets for the development of climate-resilient rice cultivars.