Historically, association tests have been used extensively in medical genetics1,2, but have had virtually no application in plant genetics. One obstacle to their application is the structured populations often found in crop plants3, which may lead to nonfunctional, spurious associations4. In this study, statistical methods to account for population structure5 were extended for use with quantitative variation and applied to our evaluation of maize flowering time. Mutagenesis and quantitative trait locus (QTL) studies suggested that the maize gene Dwarf8 might affect the quantitative variation of maize flowering time and plant height6,7,8. The wheat orthologs of this gene contributed to the increased yields seen in the 'Green Revolution' varieties6. We used association approaches to evaluate Dwarf8 sequence polymorphisms from 92 maize inbred lines. Population structure was estimated using a Bayesian analysis4 of 141 simple sequence repeat (SSR) loci. Our results indicate that a suite of polymorphisms associate with differences in flowering time, which include a deletion that may alter a key domain in the coding region. The distribution of nonsynonymous polymorphisms suggests that Dwarf8 has been a target of selection.
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We would like to thank T. Helentjaris for his input on this project, and N. Harberd and Plant Bioscience Ltd. for providing genomic sequence. D. Remington provided the tb1 sequence alignments and contributed helpful discussions. We would like to thank anonymous reviewers for their thoughtful comments regarding this manuscript. All sequencing was performed at the North Carolina State University Genome Research Laboratory. This work was supported by NSF (DBI-9872631) and USDA-ARS.
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