Originally published as Genetics Published Articles Ahead of Print on September 14, 2008.

Genetics, Vol. 180, 1221-1232, October 2008, Copyright © 2008
doi:10.1534/genetics.108.090134

The Genetic Architecture of Complex Traits in Teosinte (Zea mays ssp. parviglumis): New Evidence From Association Mapping

Allison L. Weber^*,1, William H. Briggs^*,2, Jesse Rucker^*, Baltazar M. Baltazar^,3, José de Jesús Sánchez-Gonzalez, Ping Feng, Edward S. Buckler^**, and John Doebley^*

^* Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, Pioneer Hi-Bred International, Tapachula, Nayarit, Mexico CP63733, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Jalisco, Mexico CP45110, Monsanto Company, Ankeny, Iowa 50021, Department of Plant Breeding and Genetics and Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853 and ^** United States Department of Agriculture–Agricultural Research Service, Ithaca, New York 14853

¹ Corresponding author: Department of Genetics, North Carolina State University, Gardiner Hall 3510, Box 7614, NCSU Campus, Raleigh, NC 27695.
E-mail: alweber{at}ncsu.edu

Previous association analyses showed that variation at major regulatory genes contributes to standing variation for complex traits in Balsas teosinte, the progenitor of maize. This study expands our previous association mapping effort in teosinte by testing 123 markers in 52 candidate genes for association with 31 traits in a population of 817 individuals. Thirty-three significant associations for markers from 15 candidate genes and 10 traits survive correction for multiple testing. Our analyses suggest several new putative causative relationships between specific genes and trait variation in teosinte. For example, two ramosa genes (ra1 and ra2) associate with ear structure, and the MADS-box gene, zagl1, associates with ear shattering. Since zagl1 was previously shown to be a target of selection during maize domestication, we suggest that this gene was under selection for its effect on the loss of ear shattering, a key domestication trait. All observed effects were relatively small in terms of the percentage of phenotypic variation explained (<10%). We also detected several epistatic interactions between markers in the same gene that associate with the same trait. Candidate-gene-based association mapping appears to be a promising method for investigating the inheritance of complex traits in teosinte.

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