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

doi:10.1073/pnas.112324299

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

^*Laboratory of Genetics, University of Wisconsin, Madison, WI 53706; ^†United States Department of Agriculture–Agricultural Research Service, Plant Genetics Research Unit and Plant Sciences Unit, University of Missouri, Columbia, MS 65211; ^‡Maize Mapping Project, University of Missouri, Columbia, MS 65211; and ^§Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853

Communicated by Steven D. Tanksley, Cornell University, Ithaca, NY (received for review April 3, 2002)

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.

Footnotes

↵ ¶ Present address: Fukui Prefectural University, Matsuoka-cho, Yoshida-gun, Fukui 910-1195, Japan.
↵ ‖ To whom reprint requests should be addressed. E-mail: jdoebley{at}facstaff.wisc.edu.
Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. AY089919-AY089950).
Abbreviations:

SSR,

simple sequence repeat;

H,

heterozygosity;

MW,

Mann–Whitney U test;

IAM,

infinite allele model;

SMM,

stepwise mutation model;

EST,

expressed sequence tag;

QTL,

quantitative trait locus;

N,

number of alleles;

ΔGD,

relative loss in genetic diversity;

Δ Allele,

relative loss in the number of alleles