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

Author
item CHEN, YONGSHENG - Iowa State University
item Blanco, Michael
item JI, QING - Iowa State University
item FREI, URSULA - Iowa State University
item LUBBERSTEDT, THOMAS - Iowa State University

Submitted to: Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/18/2014
Publication Date: 2/25/2014
Citation: Chen, Y., Blanco, M.H., Ji, Q., Frei, U., Lubberstedt, T. 2014. Extensive genetic diversity and low linkage disequilibrium within the COMT locus in maize exotic populations. Plant Science. 221-222:69-80.

Interpretive Summary: Maize has been widely used for silage with approximately four million hectares grown in the U.S. annually. In addition to high yield, an important trait for silage is high cell wall digestibility to enhance intake and nutritional value for livestock. While significant progress has been made for yield, there has been very limited progress made for cell wall digestibility. One reason for limited progress is lack of sufficient genetic variability in maize breeding material, or germplasm. An important gene identified for cell wall digestibility is the brown midrib gene, bmr3, which reduces the level of the indigestible component called lignin. Gene variation was studied by isolating DNA from leaf tissue and analyzing sequence variation of 55 exotic alleles of the bmr3 gene (an allele is an alternate state of a gene). The exotic alleles were studied from 41 maize populations representing 37 races from 10 countries, and comparisons were made to 70 adapted elite lines. The results indicated that GEM exotic populations were more diverse, or "polymorphic" at the bmr3 gene than the 70 elite line sources. In addition, higher variation at the bmr3 gene would be expected to result in changes at the protein level which may influence lignin content, cell wall digestibility, and agronomic performance. Future studies are in progress to determine if this molecular diversity translates into improved cell wall digestibility and effects on agronomic performance. The impact of this research may potentially provide breeders with new sources of germplasm for improving silage digestibility.

Technical 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 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 (p) for the exotic alleles of COMT gene was 0.0172, much higher than the reported pairwise nucleotide diversity of various genes in elite inbred lines (p=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, significantly higher than the 1:1 ratio for elite lines. Signature of selection was detected for this gene in both pools, but different evolutionary 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 for other genes, in elite backgrounds. Moreover, the low linkage disequilibrium makes this material suitable for high resolution association analyses.