Extensive genetic diversity and low linkage disequilibrium within the COMT locus in maize exotic populations

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2014-05-01
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Chen, Yongsheng
Blanco, Michael
Lubberstedt, Thomas
Ji, Qing
Frei, Ursula
Lubberstedt, Thomas
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Agronomy
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AgronomyGenetics and Genomics
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.

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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.

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