Campus Units

Agronomy, Genetics and Genomics

Document Type

Article

Publication Date

5-2014

Journal or Book Title

Plant Science

Volume

221

First Page

69

Last Page

80

DOI

10.1016/j.plantsci.2014.02.004

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.

Comments

This article is published as Chen, Yongsheng, Michael Blanco, Qing Ji, Ursula Karoline Frei, and Thomas Lübberstedt. "Extensive genetic diversity and low linkage disequilibrium within the COMT locus in maize exotic populations." Plant Science 221 (2014): 69-80. 10.1016/j.plantsci.2014.02.004. Posted with permission.

Rights

Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.

Language

en

File Format

application/pdf

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