Identification of QTLs and genes regulating panicle number through genome-wide association studies in Oryza sativa L

Background Panicle number is a key determinant of grain yield and plant architecture in rice. Here, we investigated quantitative trait loci (QTLs) and genetic factors associated with panicle number using genome-wide association studies. Methods We used 3.3 million high-quality single nucleotide polymorphisms and phenotypic data from the Micro Core Collection and Expanded Micro Core Collection, evaluated under two photoperiods across three agroecological zones in China (12 datasets). Results We identified 138 QTLs associated with panicle number. Several previously cloned genes, including OsJAG , OsTB1 , OsAP2-39 , and D53 , were located within these intervals. QTL effect analysis showed that panicle number increased with favorable allele accumulation and decreased with unfavorable alleles, consistent with quantitative genetic principles. Allelic distribution analysis in landraces and improved varieties revealed a higher frequency of loss alleles than gain alleles. Environmentally stable QTLs with small effects were more suitable for breeding than environmentally sensitive QTL or environmentally stabilizing QTL with larger effects (over three spikes). An integrated approach, including haplotype analysis, pathway analysis, Ho-index unified linkage and association mapping, expression profiling, and T-DNA mutant validation, was used to identify candidate genes within key QTLs. Two cloned genes, OsARF25 ( qPN12-1 ) and ETR3 ( qPN2-2 ), were preliminarily identified as regulators of panicle number. In qPN7-2 , a gibberellin receptor ( GR ) was identified within the fine-mapped region. Initial functional analysis indicated that GR regulates multiple agronomic traits, including panicle number, plant height, panicle length, and secondary branch number. Its expression pattern in Nipponbare roots (RiceXPro database) was similar to that of D10 , a well-characterized regulator of tiller number. Conclusion The identified QTLs and candidate genes provide valuable resources for regulating panicle number in rice through marker-assisted selection, supporting future rice breeding efforts.