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Maize ( Zea mays  L.) lipoxygenases ( ZmLOXs ) 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  ZmLOX4  and  ZmLOX5 . 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  ZmLOX5  has a disrupted open reading frame, a line missing  ZmLOX5 , and five lines with a duplication of  ZmLOX5 . Tajima's D test suggests that both  ZmLOX4  and  ZmLOX5  have been under neutral selection. Further investigation of haplotype data revealed that within the  ZmLOX  family members only  ZmLOX12 , a monocot specific  ZmLOX , 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.  ZmLOX4  and  ZmLOX5  mutations and copy number variants are under further investigation for crop improvement.

Characterization of Genetic Diversity and Linkage Disequilibrium of ZmLOX4 and ZmLOX5 Loci in Maize