Genome-wide association analysis identifies natural allelic variants associated with leaf rolling in rice (Oryza sativa L.)

Abstract Background and Aims Leaf rolling in rice affects plant architecture, light interception and photosynthetic efficiency. This study aims to identify the genetic basis of adaxial leaf rolling using a genome-wide association study (GWAS) in a diverse panel of rice accessions. Methods A GWAS was performed using 1.5 million single nucleotide polymorphisms (SNPs) across 113 rice accessions. The analysis included population structure, linkage disequilibrium, haplotype patterns and expression correlation. To validate the identified association, an additional panel of japonica inbred lines was analyzed, supporting the link between the SNP and adaxial leaf rolling. Key Results A japonica-specific quantitative trait locus, qALR1, was identified on chromosome 1. A putative causal SNP was located within a shared cis-regulatory motif (RAV1-B) upstream of two candidate genes, LOC_Os01g72370 and LOC_Os01g72380. Previous studies suggest that variation in this motif can influence gene expression, supporting the hypothesis that regulatory divergence in these genes may underlie variation in leaf rolling. Validation with an expanded panel of japonica inbred lines revealed its enrichment in breeding germplasm, indicating possible historical selection. Conclusions This study identifies a subspecies-specific regulatory mechanism underlying adaxial leaf rolling in rice. The putative causal SNP may affect transcription factor binding and gene regulation, ultimately influencing leaf morphology. These findings offer valuable targets for optimizing canopy architecture and enhancing photosynthetic performance through molecular breeding.