Originally published as Genetics Published Articles Ahead of Print on October 18, 2007.

Genetics, Vol. 177, 2349-2359, December 2007, Copyright © 2007
doi:10.1534/genetics.107.080424

Major Regulatory Genes in Maize Contribute to Standing Variation in Teosinte (Zea mays ssp. parviglumis)

Allison Weber*,1, Richard M. Clark*,2, Laura Vaughn*, José de Jesús Sánchez-Gonzalez{dagger}, Jianming Yu{ddagger}, Brian S. Yandell§, Peter Bradbury** and John Doebley*

* Laboratory of Genetics and § Department of Statistics, University of Wisconsin, Madison, Wisconsin 53706, {dagger} Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Jalisco, Mexico CP45110, {ddagger} Department of Agronomy, Kansas State University, Manhattan, Kansas 66506 and ** United States Department of Agriculture–Agricultural Research Service, Washington, District of Columbia 20250

1 Corresponding author: Laboratory of Genetics, University of Wisconsin, 425 Henry Mall, Madison, WI 53706.
E-mail: allisonweber{at}wisc.edu.

In plants, many major regulatory genes that control plant growth and development have been identified and characterized. Despite a detailed knowledge of the function of these genes little is known about how they contribute to the natural variation for complex traits. To determine whether major regulatory genes of maize contribute to standing variation in Balsas teosinte we conducted association mapping in 584 Balsas teosinte individuals. We tested 48 markers from nine candidate regulatory genes against 13 traits for plant and inflorescence architecture. We identified significant associations using a mixed linear model that controls for multiple levels of relatedness. Ten associations involving five candidate genes were significant after correction for multiple testing, and two survive the conservative Bonferroni correction. zfl2, the maize homolog of FLORICAULA of Antirrhinum, was associated with plant height. zap1, the maize homolog of APETALA1 of Arabidopsis, was associated with inflorescence branching. Five SNPs in the maize domestication gene, teosinte branched1, were significantly associated with either plant or inflorescence architecture. Our data suggest that major regulatory genes in maize do play a role in the natural variation for complex traits in teosinte and that some of the minor variants we identified may have been targets of selection during domestication.