Genetic architecture of node-specific leaf length and candidate gene identification in maize revealed by a temperate–tropical multiparental population

Abstract

Optimizing leaf morphology is essential for improving maize plant architecture, plant density tolerance, and yield. Leaf length is a key agronomic trait controlled by complex genetic mechanisms. In this study, upper leaf length (ULL), ear leaf length (ELL) and lower leaf length (DLL) were evaluated across two environments using a multiparent RIL population derived from crosses between the temperate inbred line Ye107 and three tropical inbred lines. Combined with high-density GBS markers, genome-wide association study (GWAS) and QTL mapping were integrated to dissect the genetic basis of leaf length. Leaf length traits exhibited high heritability (54.85%–76.85%). A total of 133 significant SNPs were identified by GWAS, and 13 candidate regions were detected by QTL localization, among which ql1-17 explained 12.10% of the phenotypic variation. Joint analysis revealed multiple colocalized regions on chromosomes 1, 6 and 8, resulting in the identification of three key candidate genes ZmHUA2 (Zm00001d029223) , ZmCAMTA5 (Zm00001d025235) , and ZmPAT16 (Zm00001d038367) . Haplotype and qRT-PCR analyses showed that favorable haplotypes from tropical parents significantly increased leaf length, and these genes exhibited high expression specificity in the leaf elongation region. This study elucidates the complex genetic architecture of leaf length in temperate × tropical hybrid populations. Through integrated analyses, we identified key genomic loci and prioritized three candidate genes, particularly ZmHUA2 (Zm00001d029223) and ZmCAMTA5 (Zm00001d025235) . These findings provide valuable genomic resources and favorable alleles for marker-assisted selection, establishing a robust theoretical and practical foundation for maize ideotype breeding aimed at optimizing leaf morphology to enhance yield potential under high-density planting conditions.