A comparative genomics approach to characterize variation within maize lethal necrosis-associated QTL to identify new sources of resistance

Maize lethal necrosis (MLN) remains a significant threat to maize production in Sub-Saharan Africa (SSA). MLN results from the synergistic infection of maize chlorotic mottle virus (MCMV) and any potyvirus, generally sugarcane mosaic virus (SCMV). The rapid evolution of viruses highlights the need for continued research to identify novel and durable resistance mechanisms. In this study, we utilized previously mapped MLN QTL regions to explore new genetic diversity by focusing on genetic variants known to significantly affect gene function and phenotypic traits. We used whole-genome pairwise alignments to compare three SSA inbred lines (CKL05004, CKL05022, and CML536) and one resistant non-SSA line (KS23-6) against the moderately resistant CML543. QTL within chromosomes 1, 3, 5, 6, and 9, were selected based on the strength of the QTL signal and the presence of CML543 in the mapping panels. Variations, including single nucleotide polymorphisms (SNPs), insertions-deletions (InDels), and structural variations (SVs), within these QTL regions were quantified and visualized. We identified several candidate genes with potential roles in virus resistance or susceptibility. These included RNA helicases, RNA-binding proteins, WRKY transcription factors, methyltransferases, and SNARE-associated proteins of the Golgi apparatus. Transcriptomic validation further helped identify two genes, a plasmodesmata-associated movement protein (PDLP5) and a methyltransferase implicated in RNA silencing, that were downregulated in the susceptible genotype, suggesting viral manipulation of cell-to-cell movement and suppression of host RNA silencing mechanisms. The diversity of candidate genes within key QTL regions includes genes that may be directly involved in viral replication or suppression, offering promising targets for future breeding or gene-editing efforts to develop MCMV/SCMV resistance. This comparative genomics analysis validated known resistant QTL and revealed potential candidate genes, providing valuable resources for MLN resistance breeding in SSA maize improvement programs.