Characterization of Genetic Diversity and Linkage Disequilibrium of <em>ZmLOX4</em> and <em>ZmLOX5</em> Loci in Maize

<div><p>Maize (<em>Zea mays</em> L.) lipoxygenases (<em>ZmLOXs</em>) are well recognized as important players in plant defense against pathogens, especially in cross kingdom lipid communication with pathogenic fungi. This study is among the first to investigate genetic diversity at important gene paralogs <em>ZmLOX4</em> and <em>ZmLOX5</em>. Sequencing of these genes in 400 diverse maize lines showed little genetic diversity and low linkage disequilibrium in the two genes. Importantly, we identified one inbred line in which <em>ZmLOX5</em> has a disrupted open reading frame, a line missing <em>ZmLOX5</em>, and five lines with a duplication of <em>ZmLOX5</em>. Tajima's D test suggests that both <em>ZmLOX4</em> and <em>ZmLOX5</em> have been under neutral selection. Further investigation of haplotype data revealed that within the <em>ZmLOX</em> family members only <em>ZmLOX12</em>, a monocot specific <em>ZmLOX</em>, showed strong linkage disequilibrium that extends further than expected in maize. Linkage disequilibrium patterns at these loci of interest are crucial for future candidate gene association mapping studies. <em>ZmLOX4</em> and <em>ZmLOX5</em> mutations and copy number variants are under further investigation for crop improvement.</p>