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.
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
Recommended Citation
Chen, Yongsheng; Blanco, Michael; Ji, Qing; Frei, Ursula Karoline; and Lubberstedt, Thomas, "Extensive genetic diversity and low linkage disequilibrium within the COMT locus in maize exotic populations" (2014). Agronomy Publications. 287.
https://lib.dr.iastate.edu/agron_pubs/287
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.