Mining Genetic Variations Reveals the Differentiation of Gene Alternative Polyadenylation Involving in Rice Panicle Architecture Regulation

ABSTRACT Panicle architecture is a critical determinant of rice yield and resilience, yet the genetic and environmental factors shaping this trait remain incompletely understood. Here, we applied an integrative genomic approach combining multi‐locus association mapping, transcriptome analysis and population genomics to dissect the genetic basis of key panicle traits in rice. We identified robust genetic loci underlying the number of primary branches, panicle length and spikelets per panicle, with many showing sensitivity to temperature, underscoring the importance of gene–environment interactions for yield stability. Notably, we discovered that variation in alternative polyadenylation (APA) of specific transcripts is associated with panicle trait diversity at the population level, suggesting that regulatory mechanisms such as APA are significant contributors to phenotypic plasticity and adaptation. These findings deliver both novel candidate genes in panicle development and mechanistic insights to support the breeding of rice varieties with enhanced productivity and climate resilience.