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PMID: 12105270 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 99 ·No. 15 ·2002-07-23 ·Pages 9650-5

Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J

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 nonequilibrium 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 nonneutral SSRs are candidates for agronomically important genes. Because 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.

MeSH Terms
Agriculture/methods Alleles Base Sequence DNA Primers Genes, Plant Genetic Variation Microsatellite Repeats Molecular Sequence Data Selection, Genetic Zea mays/genetics
Chemicals
DNA Primers
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Vigouroux Y
Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA.
McMullen M
Hittinger C T
Houchins K
Schulz L
Kresovich S
Matsuoka Y
Doebley J
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.112324299
Published
2002-07-23
Epub
2002-00-08
Pages
9650-5
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC124964
Subset
IM
Grants
NIGMS NIH HHS · R01 GM058816 · United States
NIGMS NIH HHS · GM-58816 · United States
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GENBANK
AY089919, AY089920, AY089921, AY089922, AY089923, AY089924, AY089925, AY089926, AY089927, AY089928, AY089929, AY089930, AY089931, AY089932, AY089933, AY089934, AY089935, AY089936, AY089937, AY089938, AY089939, AY089940, AY089941, AY089942, AY089943, AY089944, AY089945, AY089946, AY089947, AY089948, AY089949, AY089950
External Links
PubMed source DOI: 10.1073/pnas.112324299 PMC Full Text View journal details
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