ARS | Publication request: Using Association Mapping in Teosinte (Zea Mays ssp Parviglumis) to Investigate the Function of Selection-Candidate Genes

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 16, 2009
Publication Date: December 9, 2009
Citation: Weber, A.L., Zhao, Q., McMullen, M.D., Doebley, J. 2009. Using Association Mapping in Teosinte (Zea Mays ssp Parviglumis) to Investigate the Function of Selection-Candidate Genes. PLoS One. 4:e8227.

Interpretive Summary: Previous experiments have demonstrated that about 1-2% of corn genes have been selected for reduced genetic variability during domestication or corn improvement. These genes are candidates for controlling important agronomic traits, however, the limited remaining genetic diversity makes it difficult to determine in modern corn what traits individual selected genes may control. As a step toward defining the traits controlled by these genes, we conducted a genetic test called association analysis between polymorphisms in 32 selected genes and 32 traits in teosinte, the wild immediate progenitor of domesticated corn. Although we observed a few potentially interesting associations, surprisingly the selection-candidate genes were no more likely to associate with trait variation in teosinte than genes chosen at random from the genome. Among the significant associations were genes controlling maturity and seed number. These results are important to corn breeders in identifying candidate genes for possible use in modifying the traits of flowering time and kernel number.

Technical Abstract: Large-scale screens of the maize genome identified 48 genes that show the putative signature of artificial selection during maize domestication or improvement. These selection-candidate genes may act as quantitative trait loci (QTL) that control the phenotypic differences between maize and its progenitor, teosinte. The selection-candidate genes appear to be located closer in the genome to domestication QTL than expected by chance. As a step toward defining the traits controlled by these genes, we performed phenotype-genotype association mapping for 32 of the 48 published, plus three other selection-candidate genes. Our analyses assayed 32 phenotypic traits, many of which were altered during maize domestication or improvement. We observed relatively few significant associations between SNPs in the selection-candidate genes and trait variation in teosinte. The utility of selection scans for identifying genes underlying maize domestication may be improved by using more rigorous tests of selection.