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dc.contributor.author Caldu-Primo, Jose Luis
dc.contributor.author Mastretta-Yanes, Alicia
dc.contributor.author Wegier, Ana
dc.contributor.author Piñero, Daniel
dc.coverage.spatial Mexico
dc.date.accessioned 2017-04-18T18:19:38Z
dc.date.available 2017-04-18T18:19:38Z
dc.date.issued 2017-04-18
dc.identifier doi:10.5061/dryad.j2n8q
dc.identifier.citation Caldu-Primo JL, Mastretta-Yanes A, Wegier A, Piñero D (2017) Finding a needle in a haystack: distinguishing Mexican maize landraces using a small number of SNPs. Frontiers in Genetics 8: 45.
dc.identifier.issn 1664-8021
dc.identifier.uri http://hdl.handle.net/10255/dryad.141897
dc.description In Mexico's territory, the center of origin and domestication of maize (Zea mays), there is a large phenotypic diversity of this crop. This diversity has been classified into “landraces.” Previous studies have reported that genomic variation in Mexican maize is better explained by environmental factors, particularly those related with altitude, than by landrace. Still, landraces are extensively used by agronomists, who recognize them as stable and discriminatory categories for the classification of samples. In order to investigate the genomic foundation of maize landraces, we analyzed genomic data (35,909 SNPs from Illumina MaizeSNP50 BeadChip) obtained from 50 samples representing five maize landraces (Comiteco, Conejo, Tehua, Zapalote Grande, and Zapalote Chico), and searched for markers suitable for landrace assignment. Landrace clusters could not be identified taking all the genomic information, but they become manifest taking only a subset of SNPs with high FST among landraces. Discriminant analysis of principal components was conducted to classify samples using SNP data. Two classification analyses were done, first classifying samples by landrace and then by altitude category. Through this classification method, we identified 20 landrace-informative SNPs and 14 altitude-informative SNPs, with only 6 SNPs in common for both analyses. These results show that Mexican maize phenotypic diversity can be classified in landraces using a small number of genomic markers, given the fact that landrace genomic diversity is influenced by environmental factors as well as artificial selection due to bio-cultural practices.
dc.relation.haspart doi:10.5061/dryad.j2n8q/1
dc.relation.haspart doi:10.5061/dryad.j2n8q/2
dc.relation.isreferencedby doi:10.3389/fgene.2017.00045
dc.subject maize diversity
dc.subject artificial selection
dc.subject Maize SNP50K BeadChip
dc.subject maize genomics
dc.title Data from: Finding a needle in a haystack: distinguishing Mexican maize landraces using a small number of SNPs
dc.type Article
dwc.ScientificName Zea mays
dc.contributor.correspondingAuthor Caldu-Primo, Jose Luis
prism.publicationName Frontiers in Genetics
dryad.citationInProgress false

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