Genome-wide association in quality protein maize: identifying key loci for yield enhancement

Grain yield in maize (Zea mays L.) is a complex quantitative trait influenced by multiple component traits. Achieving sustainable yield improvement in nutritionally enhanced Quality Protein Maize (QPM) lines under growing population pressure and changing climate requires enhanced genetic gain. This study aimed to dissect the genetic basis of key yield components in 149 QPM inbred lines using five genome-wide association study (GWAS) models. Multi-environment phenotypic evaluation revealed moderate to high heritability and significant genotypic and environmental effects for most traits. GWAS identified a total of 27 stable marker-trait associations (MTAs) distributed across all chromosomes except chromosome 6, including nine pleiotropic loci. Novel genomic bins 3.03-3.04 and 5.01 were associated with kernel length. Functional annotation of potential candidate genes revealed enrichment for processes related to cell elongation, seed development, and sugar transport, with predominant expression in reproductive tissues during early kernel development. The gene Zm00001d039637 encoding GLK14 exhibited pleiotropic effects on kernel length and cob diameter, whereas MADS-box and AP2/EREBP transcription factors were linked to kernel number. Collectively, these results refine the current understanding of kernel development and identify promising genomic regions and functional candidates for deployment in genomics-assisted breeding for yield improvement in maize.