title: Extensive genetic diversity and low linkage disequilibrium within the COMT locus in maize exotic populations.
abstract: The caffeic acid 3-O-methytransferase (COMT) gene is a prime candidate for cell wall digestibility improvement based on the characterization of brown midrib-3 mutants. We compared the genetic diversity and linkage disequilibrium at this locus between exotic populations sampled within the Germplasm Enhancement of Maize (GEM) project and 70 inbred lines. In total, we investigated 55 exotic COMT alleles and discovered more than 400 polymorphisms in a 2.2 kb region with pairwise nucleotide diversity (π) up to 0.017, much higher than reported π values of various genes in inbred lines. The ratio of non-synonymous to synonymous SNPs was 3:1 in exotic populations, and significantly higher than the 1:1 ratio for inbred lines. Selection tests detected selection signature in this gene in both pools, but with different evolution patterns. The linkage disequilibrium decay in exotic populations was at least four times more rapid than for inbred lines with r²>0.1 persisting only up to 100 bp. In conclusion, the alleles sampled in the GEM Project offer a valuable genetic resource to broaden genetic variation for the COMT gene, and likely other genes, in inbred background. Moreover, the low linkage disequilibrium makes this material suitable for high resolution association analyses.
authors.affiliation: Department of Agronomy, Iowa State University, Ames, IA 50011, USA; Interdepartmental Genetics Program, Iowa State University, Ames, IA 50011, USA.
authors.forename: Yongsheng
authors.initials: Y
authors.lastname: Chen
authors.affiliation: USDA-ARS, Plant Introduction Research Unit, Ames, IA 50011, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Blanco
authors.affiliation: Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
authors.forename: Qing
authors.initials: Q
authors.lastname: Ji
authors.affiliation: Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
authors.forename: Ursula Karoline
authors.initials: UK
authors.lastname: Frei
authors.affiliation: Department of Agronomy, Iowa State University, Ames, IA 50011, USA. Electronic address: thomasl@iastate.edu.
authors.forename: Thomas
authors.initials: T
authors.lastname: Lübberstedt
mesh_terms: D014644:Genetic Variation; D015810:Linkage Disequilibrium; D008780:Methyltransferases / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D003313:Zea mays / Q000235:genetics* / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D008780:Methyltransferases; C019608:caffeate O-methyltransferase
keywords: Caffeic acid 3-O-methytransferase; Genetic diversity; Germplasm Enhancement of Maize; Linkage disequilibrium