Extensive Genetic Diversity and Low Linkage Disequilibrium within the COMT Locus in Germplasm Enhancement of Maize Populations

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 COMT locus between populations sampled within the Germplasm Enhancement of Maize (GEM) Project and 70 elite lines. In total, we investigated 55 exotic alleles from the GEM Project at the COMT locus, and discovered more than 400 polymorphisms in a 2.2 kb region. The pairwise nucleotide diversity (π) for the exotic alleles of COMT gene was 0.0172, and much higher than the reported pairwise nucleotide diversity of various genes in elite inbred lines (π=0.0047 to 0.0067).  At this locus, the average number of nucleotide differences between any two randomly selected alleles was 27.7 for exotic populations, much higher than 18.0 for elite lines. The ratio of non-synonymous to synonymous SNPs was 3:1 in exotic populations, and significantly higher than the 1:1 ratio for elite lines. Selection tests detected selection signature in this gene in both pools. But different evolution patterns from progenitor to landraces and from landrace to inbred lines were suggested by significant negative and positive neutral test statistics. The linkage disequilibrium decay in exotic populations was at least four times more rapid than for elite 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 elite background. Moreover, the low linkage disequilibrium makes this material suitable for high resolution association analyses.