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Spatial structure and climatic adaptation in African maize revealed by surveying SNP diversity in relation to global breeding and landrace panels.

Westengen OT, Berg PR, Kent MP, Brysting AK - PLoS ONE (2012)

Bottom Line: Environmental association analysis was used to detect SNPs associated with three climatic variables based on the full 43,963 SNP dataset.Controlling for population history in a linear model, we identify 79 SNPs associated with maximum temperature during the growing season.The associations located in genes of known importance for abiotic stress tolerance are interesting candidates for local adaptations.

View Article: PubMed Central - PubMed

Affiliation: Centre for Development and the Environment, SUM, University of Oslo, Oslo, Norway. ola.westengen@sum.uio.no

ABSTRACT

Background: Climate change threatens maize productivity in sub-Saharan Africa. To ensure food security, access to locally adapted genetic resources and varieties is an important adaptation measure. Most of the maize grown in Africa is a genetic mix of varieties introduced at different historic times following the birth of the trans-Atlantic economy, and knowledge about geographic structure and local adaptations is limited.

Methodology: A panel of 48 accessions of maize representing various introduction routes and sources of historic and recent germplasm introductions in Africa was genotyped with the MaizeSNP50 array. Spatial genetic structure and genetic relationships in the African panel were analysed separately and in the context of a panel of 265 inbred lines representing global breeding material (based on 26,900 SNPs) and a panel of 1127 landraces from the Americas (270 SNPs). Environmental association analysis was used to detect SNPs associated with three climatic variables based on the full 43,963 SNP dataset.

Conclusions: The genetic structure is consistent between subsets of the data and the markers are well suited for resolving relationships and admixture among the accessions. The African accessions are structured in three clusters reflecting historical and current patterns of gene flow from the New World and within Africa. The Sahelian cluster reflects original introductions of Meso-American landraces via Europe and a modern introduction of temperate breeding material. The Western cluster reflects introduction of Coastal Brazilian landraces, as well as a Northeast-West spread of maize through Arabic trade routes across the continent. The Eastern cluster most strongly reflects gene flow from modern introduced tropical varieties. Controlling for population history in a linear model, we identify 79 SNPs associated with maximum temperature during the growing season. The associations located in genes of known importance for abiotic stress tolerance are interesting candidates for local adaptations.

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SNP associations with maximum temperature during growing season.Manhattan plot of the log10P-values for 43,963 SNPs along the chromosomes (Y-axis) for association with maximum temperature during the growing season. Dotted line indicates significance at 1% false discovery rate (FDR) threshold. Highlighted SNPs are described specifically in the main text.
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pone-0047832-g005: SNP associations with maximum temperature during growing season.Manhattan plot of the log10P-values for 43,963 SNPs along the chromosomes (Y-axis) for association with maximum temperature during the growing season. Dotted line indicates significance at 1% false discovery rate (FDR) threshold. Highlighted SNPs are described specifically in the main text.

Mentions: The environmental association analysis with GLM resulted in identification of loci significantly correlated with climatic variables in the dataset with 22 accessions for which colour is used as a phenotypic marker for presence of early introduced material. None of the models applied reveal significant associations in the dataset with the 43 African accessions in which only accessions with known modern ancestry were excluded. The GLM for associations with maximum temperature during growing season identifies 79 significant SNPs after applying a 1% false discovery rate (FDR) control in the 22 accession dataset (Fig. 5). Likewise, the GLM for association with mean precipitation detects 22 significant SNPs. Analysis with the MLM model does not identify significant associations after FDR control for any of the two datasets analysed. The 79 significant associations from the GLM are listed in Table S6, which also indicates chromosome position and gene affiliation


Spatial structure and climatic adaptation in African maize revealed by surveying SNP diversity in relation to global breeding and landrace panels.

Westengen OT, Berg PR, Kent MP, Brysting AK - PLoS ONE (2012)

SNP associations with maximum temperature during growing season.Manhattan plot of the log10P-values for 43,963 SNPs along the chromosomes (Y-axis) for association with maximum temperature during the growing season. Dotted line indicates significance at 1% false discovery rate (FDR) threshold. Highlighted SNPs are described specifically in the main text.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3472975&req=5

pone-0047832-g005: SNP associations with maximum temperature during growing season.Manhattan plot of the log10P-values for 43,963 SNPs along the chromosomes (Y-axis) for association with maximum temperature during the growing season. Dotted line indicates significance at 1% false discovery rate (FDR) threshold. Highlighted SNPs are described specifically in the main text.
Mentions: The environmental association analysis with GLM resulted in identification of loci significantly correlated with climatic variables in the dataset with 22 accessions for which colour is used as a phenotypic marker for presence of early introduced material. None of the models applied reveal significant associations in the dataset with the 43 African accessions in which only accessions with known modern ancestry were excluded. The GLM for associations with maximum temperature during growing season identifies 79 significant SNPs after applying a 1% false discovery rate (FDR) control in the 22 accession dataset (Fig. 5). Likewise, the GLM for association with mean precipitation detects 22 significant SNPs. Analysis with the MLM model does not identify significant associations after FDR control for any of the two datasets analysed. The 79 significant associations from the GLM are listed in Table S6, which also indicates chromosome position and gene affiliation

Bottom Line: Environmental association analysis was used to detect SNPs associated with three climatic variables based on the full 43,963 SNP dataset.Controlling for population history in a linear model, we identify 79 SNPs associated with maximum temperature during the growing season.The associations located in genes of known importance for abiotic stress tolerance are interesting candidates for local adaptations.

View Article: PubMed Central - PubMed

Affiliation: Centre for Development and the Environment, SUM, University of Oslo, Oslo, Norway. ola.westengen@sum.uio.no

ABSTRACT

Background: Climate change threatens maize productivity in sub-Saharan Africa. To ensure food security, access to locally adapted genetic resources and varieties is an important adaptation measure. Most of the maize grown in Africa is a genetic mix of varieties introduced at different historic times following the birth of the trans-Atlantic economy, and knowledge about geographic structure and local adaptations is limited.

Methodology: A panel of 48 accessions of maize representing various introduction routes and sources of historic and recent germplasm introductions in Africa was genotyped with the MaizeSNP50 array. Spatial genetic structure and genetic relationships in the African panel were analysed separately and in the context of a panel of 265 inbred lines representing global breeding material (based on 26,900 SNPs) and a panel of 1127 landraces from the Americas (270 SNPs). Environmental association analysis was used to detect SNPs associated with three climatic variables based on the full 43,963 SNP dataset.

Conclusions: The genetic structure is consistent between subsets of the data and the markers are well suited for resolving relationships and admixture among the accessions. The African accessions are structured in three clusters reflecting historical and current patterns of gene flow from the New World and within Africa. The Sahelian cluster reflects original introductions of Meso-American landraces via Europe and a modern introduction of temperate breeding material. The Western cluster reflects introduction of Coastal Brazilian landraces, as well as a Northeast-West spread of maize through Arabic trade routes across the continent. The Eastern cluster most strongly reflects gene flow from modern introduced tropical varieties. Controlling for population history in a linear model, we identify 79 SNPs associated with maximum temperature during the growing season. The associations located in genes of known importance for abiotic stress tolerance are interesting candidates for local adaptations.

Show MeSH