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Background  The spread of maize cultivation to the highlands of central Mexico was accompanied by substantial introgression from the endemic wild teosinte  Zea mays  ssp.  mexicana , prompting the hypothesis that the transfer of beneficial variation facilitated local adaptation.    Methods  We used whole-genome sequence data to map regions of  Zea mays  ssp.  mexicana  introgression in three Mexican highland maize individuals. We generated a genetic linkage map and performed Quantitative Trait Locus mapping in an F 2  population derived from a cross between lowland and highland maize individuals.    Results  Introgression regions ranged in size from several hundred base pairs to Megabase-scale events. Gene density within introgression regions was comparable to the genome as a whole, and over 1,000 annotated genes were located within introgression events. Quantitative Trait Locus mapping identified a small number of loci linked to traits characteristic of Mexican highland maize.    Discussion  Although there was no strong evidence to associate quantitative trait loci with regions of introgression, we nonetheless identified many Mexican highland alleles of introgressed origin that carry potentially functional sequence variants. The impact of introgression on stress tolerance and yield in the highland environment remains to be fully characterized.

Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize