|DE LA FUENTE, GERALD - Texas A&M University|
|MURRAY, SETH - Texas A&M University|
|ISAKEIT, THOMAS - Texas A&M University|
|PARK, YONG-SOON - Texas A&M University|
|YAN, YUAXIN - Texas A&M University|
|KOLOMIETS, MICHAEL - Texas A&M University|
Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/1/2012
Publication Date: 1/1/2013
Citation: De La Fuente, G.N., Murray, S., Isakeit, T., Park, Y., Yan, Y., Warburton, M.L., Kolomiets, M.V. 2013. Characterization of genetic diversity and linkage disequilibrium of ZmLOX4 and ZmLOX5 loci in maize. PLoS One. 8(1):e53973. doi:10.1371/journal.pone.0053973.
Interpretive Summary: Pathogenic fungi that attack crop plants can cause severe economic damage, and occasionally human and animal health damage. Many classes of plant proteins can provide a defense against fungal attack. One family of defense proteins is the maize lipoxygenase family. This study analyzes the genetic sequence of several gene members of this family. Two of these genes, ZmLOX4 and ZmLOX5, are very similar among all higher plants and animals, and here we show that the sequences of these genes do not vary among all the maize plants investigated. Only ZmLOX12, the only gene found only in grasses (including maize) and no other plant or animal species, has many differences in the gene sequence, and these differences may have been acted on by natural or human selection for fungal resistance. Knowing the diversity present in gene sequences is useful first step towards further studies which will allow them to be exploited in crop improvement.
Technical Abstract: Maize 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 believed to be highly conserved among all Eukaryotes. We show very little genetic diversity and very low linkage disequilibrium in these genes, but also identified one natural variant line with frame shift insertion in ZmLOX5, a variant line missing ZmLOX5, and five line variants 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, the only 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 ZmLOX5mutations and copy number variants are under further investigation for crop improvement.