Identification of a genetic marker locus (GML) associated with a trait locus (TL) from a crop species, comprises: (a) creating a genotypic survey for a crop species using germplasm of multiple ancestry, the survey created using genetic markers, where individual entries of the germplasm survey are not members of a segregating population created for the purposes of the analysis; (b) comparing the genotypic survey to phenotypic data collected on the same entries used to create the genotypic survey or their progeny; (c) estimating the association between GML and TL, and (d) identifying a GML that is associated with the TL. The genetic markers are selected from RFLPs, SSRs, RAPDs, AFLPs nd allozymes. The trait locus contributes to an observable characteristic selected from yield, lodging, height, maturity, disease resistance, pest resistance, nutrient deficiency and grain composition.
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