QTL mapping and candidate gene identification for corn leaf aphid resistance (Rhopalosiphum maidis F.) in maize (Zea mays L.) using SLAF-seq

The corn leaf aphid (Rhopalosiphum maidis F.) is one of the most destructive pests that frequently threaten seed yield in maize (Zea mays L.). Understanding the genetic mechanisms of resistance to aphid is crucial for aphid-resistant maize breeding. Here, a panel of 234 F₂ individuals derived from two parents, Huangzaosi (HZS, susceptible) and X224M (resistant), were genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) method. 6, 186 SNP markers were obtained and used to construct a high-density genetic map with a total length of 1, 667.36 centimorgan (cM). QTL mapping identified a novel major-effect dominant QTL, qRta3.1, on chromosome 3, accounting for 21.7% of the phenotypic variation. While 76 genes were initially annotated within the primary QTL region, subsequent recombination analysis refined the QTL to a 1.72 Mb physical interval, thereby narrowing the candidate genes to only three candidate genes. To further investigate the candidate genes exhibiting aphid resistance in X224M, the expression analysis of three candidate genes was performed at different time points using qRT-PCR. The results indicated that one aphid resistance candidate gene (Zm00001d043311), associated with jasmonic acid (JA) signaling pathway, was significantly down-regulated after aphid infestation, whereas two genes, including cell wall biosynthesis and acid phosphatase activity, exhibited no significant difference in expression. Therefore, the gene Zm00001d043311, encoding probable a transcription factor LBD20, is considered a key candidate gene in maize in response to aphid infestation. This study provides a theoretical basis and valuable germplasm resource for increasing maize aphid resistance.