Dataset Information

Finding a Needle in a Haystack: Distinguishing Mexican Maize Landraces Using a Small Number of SNPs.

ABSTRACT: 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.

SUBMITTER: Caldu-Primo JL

PROVIDER: S-EPMC5394175 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Finding a Needle in a Haystack: Distinguishing Mexican Maize Landraces Using a Small Number of SNPs.

Caldu-Primo Jose L JL Mastretta-Yanes Alicia A Wegier Ana A Piñero Daniel D

Frontiers in genetics 20170418

In Mexico's territory, the center of origin and domestication of maize (<i>Zea mays</i>), 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 classif ...[more]

PMID: 28458682

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Project description:Local adaptation of populations results from an interplay between their environment and genetics. If functional trait variation influences plant performance, populations can adapt to their local environment. However, populations may also respond plastically to environmental challenges, altering phenotype without shifting allele frequencies. The level of local adaptation in crop landraces and their capacity for plasticity in response to environmental change may predict their continued utility to farmers facing climate change. Yet we understand little about how physiological traits potentially underlying local adaptation of cultivars influence fitness. Farmers in Mexico-the crop center of origin for maize-manage and rely upon a high diversity of landraces. We studied maize grown in Chiapas, Mexico, where strong elevational gradients cover a relatively small geographic area. We reciprocally transplanted 12 populations sourced from three elevational zones (600, 1550 and 2150 m) back into those elevations for two years using a modified split-split plot design to model effects of environment, genetics, and their interaction. We studied physiological and growth traits, including photosynthetic rate, stomatal conductance, stomatal density, relative growth rate (RGR), and seed production. Maize fitness showed indications of local adaptation with highland and midland types performing poorly at warmer lowland locations, though patterns depended on the year. Several physiological traits, including stomatal conductance, were affected by G x E interactions, some of which indicated non-adaptive plastic responses with potential fitness implications. We discerned a significant positive relationship between fitness and relative growth rate. Growth rates in highland landraces were outperformed by midland and lowland landraces grown in high temperature, lowland garden. Lowland landrace stomatal conductance was diminished compared to that of highland landraces in the cooler highland garden. Thus, both adaptive and non-adaptive physiological responses of maize landraces in southern Mexico may have implications for fitness, as well as responses to climate change.

Dataset Information

Finding a Needle in a Haystack: Distinguishing Mexican Maize Landraces Using a Small Number of SNPs.

Publications

Finding a Needle in a Haystack: Distinguishing Mexican Maize Landraces Using a Small Number of SNPs.

Similar Datasets

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