Multi-model GWAS reveals key loci for leaf angle in maize inbred lines from southeast China

Maize is a vital grain and forage crop with continuously increasing yield demands, making the improvement of plant architecture for high-density planting particularly significant. Among architectural traits, leaf angle (LA) is a key factor influencing light interception and canopy architecture. To dissect the genetic basis of LA in maize, a genome-wide association study was conducted.

A panel of 212 maize inbred lines from breeding programs in Southeast China was genotyped using the Maize6H-60 K SNP array. Employing five GWAS models (GLM, MLM, SUPER, FarmCPU, and BLINK), we identified 14 significant SNPs (p < 8.55 × 10⁻⁷) and 342 candidate genes within the 200 kb flanking regions, 134 of which were functionally annotated. Multi-model cross-validation revealed six stably associated SNPs, including four novel loci (AX-107936049, AX-108102817, AX-107953621, and AX-108061477). AX-86,305,869 was located within 2 Mb of a previously reported significant SNP, while AX-107,994,145 fell within a known QTL interval. Within these six stable loci, 11 high-confidence candidate genes are putatively associated with LA variation, potentially acting via hormone signaling, leaf morphogenesis, and midvein development. Notably, GRMZM2G036905 (homologous to Arabidopsis ELF1) may play a role in regulating upright leaf architecture, and GRMZM2G003565 may contribute to leaf rolling as previously suggested. Based on these stable SNPs, KASP markers were developed and validated in 52 varieties/lines (including Zhengdan 958, MY73, and Anke 985) and 20 inbred lines, confirming the association between these SNPs and LA variation.

Our study identified six stable SNPs and 11 candidate genes for maize LA through multi-model GWAS in 212 inbred lines. Four novel loci were discovered, and KASP markers were developed for three stable SNPs, providing genetic resources and tools for breeding maize varieties tolerant to high planting density.