Genome-wide association and genomic selection analysis of the number of leaves above the ear in maize

The number of leaves on the ear is an important trait influencing maize plant architecture. Genetic mapping approaches can identify single nucleotide polymorphisms (SNPs) significantly associated with this trait and facilitate the discovery of candidate genes, thereby laying a foundation for targeted breeding of ideal maize plant architecture and efficient enhancement of grain yield. In this study, a natural population of 291 maize inbred lines was evaluated across multiple environments. Genotyping was performed using sequencing technologies, and both genome-wide association studies (GWAS) and genomic selection (GS) were conducted for the leaf number above the ear (LNAE). LNAE was significantly affected by genotype (G), environment (E), and the genotype-by-environment interaction (G × E) (<italic>P</italic> &lt; 0.001), with a broad-sense heritability of 81.23%. Using the MLMM model, 15 SNPs significantly associated with LNAE were identified, each explaining 1.12% to 22.43% of the phenotypic variation. The FarmCPU model identified 37 significant SNPs, with individual contributions ranging from 0.02% to 18.23%. A total of 11 co-located loci were detected on chromosomes 2, 4, 5, 6, 7, and 9 were detected by two different models. Among them, SNP 5_93495559 on chromosome 5 was identified as both an environmentally stable and model co-located locus. Compared with previous reports, this SNP represents a novel genetic locus. By integrating association mapping, co-location analysis, and candidate gene expression profiling, three genes—<italic>Zm00001eb315650</italic>, <italic>Zm00001eb315660</italic>, and <italic>Zm00001eb089980</italic>—were found to exhibit high expression during key leaf development stages and were identified as likely candidates underlying LNAE. Genomic selection analysis indicated that using 70% of the population as a training set and 3000 SNPs could achieve high prediction accuracy. This parameter can be utilized for molecular breeding selection of the number of leaves above the ear.