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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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Relationship between African maize and global reference panels.Rooted Neighbor-joining tree of the combined African panel (Eastern, Sahelian, and Western Africa), Association Panel (NSS, SS and TS) and Landrace Panel (branches are named and coloured according to the clusters identified with K = 5 in the STRUCTURE analysis) based on 259 SNPs with bootstrap values in % from 1000 replications.
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pone-0047832-g004: Relationship between African maize and global reference panels.Rooted Neighbor-joining tree of the combined African panel (Eastern, Sahelian, and Western Africa), Association Panel (NSS, SS and TS) and Landrace Panel (branches are named and coloured according to the clusters identified with K = 5 in the STRUCTURE analysis) based on 259 SNPs with bootstrap values in % from 1000 replications.

Mentions: NJ analysis of the merged dataset (259 SNPs), including the African panel, AP, LP and teosinte as an outgroup, allows further investigation of the relationship between the clusters. The rooted NJ tree in Fig. 4 are based on the clusters defined by STRUCTURE for K = 5 for the LP and K = 3 for the AP and the African panel. The West and Highland Mexico group is sister to the remaining ingroup in 95% of the trees from the bootstrap replicates, reflecting the origin of domesticated maize in this region. The Eastern African samples cluster with the TS cluster from the AP and the Meso-American Lowland and Coastal Brazil cluster from the LP with 100% bootstrap support. The differentiation of the temperate and tropical landraces from the breeding material is less well supported by bootstrap values, but the overall pattern is geographically meaningful and regionally close ecogeographic groups, such as the Lowland South American group and the Andean group, cluster with high bootstrap support. Basic diversity statistics for the panels and clusters are presented in Table 2. At the panel level the African panel and the LP do not display significantly (P< 0.05) different heterozygosity. Heterozygosity is significantly (P<0.05) different between clusters within Africa and between all clusters within the LP, except between the two clusters Lowland South America and Northern America. West and Highland Mexico has significantly (P<0.05) higher heterozygosity than all other LP clusters and only the Eastern African cluster within the African panel has not significantly lower heterozygosity.


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)

Relationship between African maize and global reference panels.Rooted Neighbor-joining tree of the combined African panel (Eastern, Sahelian, and Western Africa), Association Panel (NSS, SS and TS) and Landrace Panel (branches are named and coloured according to the clusters identified with K = 5 in the STRUCTURE analysis) based on 259 SNPs with bootstrap values in % from 1000 replications.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0047832-g004: Relationship between African maize and global reference panels.Rooted Neighbor-joining tree of the combined African panel (Eastern, Sahelian, and Western Africa), Association Panel (NSS, SS and TS) and Landrace Panel (branches are named and coloured according to the clusters identified with K = 5 in the STRUCTURE analysis) based on 259 SNPs with bootstrap values in % from 1000 replications.
Mentions: NJ analysis of the merged dataset (259 SNPs), including the African panel, AP, LP and teosinte as an outgroup, allows further investigation of the relationship between the clusters. The rooted NJ tree in Fig. 4 are based on the clusters defined by STRUCTURE for K = 5 for the LP and K = 3 for the AP and the African panel. The West and Highland Mexico group is sister to the remaining ingroup in 95% of the trees from the bootstrap replicates, reflecting the origin of domesticated maize in this region. The Eastern African samples cluster with the TS cluster from the AP and the Meso-American Lowland and Coastal Brazil cluster from the LP with 100% bootstrap support. The differentiation of the temperate and tropical landraces from the breeding material is less well supported by bootstrap values, but the overall pattern is geographically meaningful and regionally close ecogeographic groups, such as the Lowland South American group and the Andean group, cluster with high bootstrap support. Basic diversity statistics for the panels and clusters are presented in Table 2. At the panel level the African panel and the LP do not display significantly (P< 0.05) different heterozygosity. Heterozygosity is significantly (P<0.05) different between clusters within Africa and between all clusters within the LP, except between the two clusters Lowland South America and Northern America. West and Highland Mexico has significantly (P<0.05) higher heterozygosity than all other LP clusters and only the Eastern African cluster within the African panel has not significantly lower heterozygosity.

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