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United States Department of Agriculture

Agricultural Research Service

Title: Identifying Genes of Agronomic Importance in Maize by Screening Microsatellites for Evidence of Selection During Domestication

Authors
item Vigouroux, Y - UNIV OF WISCONSIN
item McMullen, Michael
item Hittinger, C - UNIV OF WISCONSIN
item Guill, Katherine
item Schulz, L - UNIV OF MISSOURI
item Kresovich, S - CORNELL UNIVERSITY
item Matsuoka, Y - UNIV OF WISCONSIN
item Doebley, J - UNIV OF WISCONSIN

Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 29, 2002
Publication Date: July 23, 2002
Citation: VIGOUROUX, Y., MCMULLEN, M.D., HITTINGER, C.T., HOUCHINS, K.E., SCHULZ, L., KRESOVICH, S., MATSUOKA, Y., DOEBLEY, J. IDENTIFYING GENES OF AGRONOMIC IMPORTANCE IN MAIZE BY SCREENING MICROSATELLITES FOR EVIDENCE OF SELECTION DURING DOMESTICATION. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES. 2002. v. 99. p. 9650-9655.

Interpretive Summary: One of the limiting factors in crop improvement is the identification of genes that control agronomic traits. We have developed a novel approach that looks at the reduction in genetic diversity in corn landraces compared to the wild teosinte races to identify genes that underwent selection upon crop domestication. These genes become candidates for traits that differ between corn and its ancestor. We used simple sequence repeat markers to test 500 genes with no prior restriction of gene identity. We found 15 genes with a signature of selection that are now candidates for agronomic traits. By the extension of this approach to sequence data, any gene can be tested for selection. While tests of individual genes as "domestication genes" have been conducted in the past, this manuscript is significant to agronomists and basic scientists in that it documents a global, genomic approach to finding genes of agronomic importance.

Technical Abstract: Crop species experienced strong selective pressure directed at genes controlling traits of agronomic importance during their domestication and subsequent episodes of selective breeding. Consequently, these genes are expected to exhibit the signature of selection. We screened 501 maize genes for the signature of selection using microsatellites or simple sequence repeats (SSRs). We applied the Ewens-Watterson test, which can reveal deviations from a neutral-equilibrium model, as well as two non-equilibrium tests that incorporate the domestication bottleneck. We investigated two classes of SSRs: those known to be polymorphic in maize (Class I) and those previously classified as monomorphic in maize (Class II). Fifteen SSRs exhibited some evidence for selection in maize and 10 showed evidence under stringent criteria. The genes containing non-neutral SSRs are candidates for agronomically important genes. Since demographic factors can bias our tests, further independent tests of these candidates are necessary. We applied such an additional test to one candidate, which encodes a MADS box transcriptional regulator, and confirmed that this gene experienced a selective sweep during maize domestication. Genomic scans for the signature of selection offer a means of identifying new genes of agronomic importance even when gene function and the phenotype of interest are unknown.

Last Modified: 9/20/2014
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