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Molecular evaluation of orphan Afghan common wheat (Triticum aestivum L.) landraces collected by Dr. Kihara using single nucleotide polymorphic markers.

Manickavelu A, Jighly A, Ban T - BMC Plant Biol. (2014)

Bottom Line: Here we used SNP analysis to demonstrate the importance of Afghan wheat landraces and found tremendous genetic diversity and province-specific characteristics unique to this geographic region.This result closely resembles existing agro-climatic zones within Afghanistan, as well as the wheat varieties commonly cultivated within these regions.Molecular variance analysis showed a higher proportion of intra-province variation among landraces compared with variation among all landraces as a whole.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Landraces are an important source of genetic diversity in common wheat, but archival collections of Afghan wheat landraces remain poorly characterised. The recent development of array based marker systems, particularly single nucleotide polymorphism (SNP) markers, provide an excellent tool for examining the genetic diversity of local populations. Here we used SNP analysis to demonstrate the importance of Afghan wheat landraces and found tremendous genetic diversity and province-specific characteristics unique to this geographic region.

Results: A total of 446 Afghan wheat landraces were analysed using genotype by sequencing (GBS) arrays containing ~10 K unique markers. Pair-wise genetic distance analyses revealed significant genetic distances between landraces, particularly among those collected from distanced provinces. From these analyses, we were able to divide the landraces into 14 major classes, with the greatest degree of diversity evident among landraces isolated from Badakhshan province. Population-based analyses revealed an additional 15 sub-populations within our germplasm, and significant correlations were evident in both the provincial and botanical varieties. Genetic distance analysis was used to identify differences among provinces, with the strongest correlations seen between landraces from Herat and Ghor province, followed closely by those between Badakhshan and Takhar provinces. This result closely resembles existing agro-climatic zones within Afghanistan, as well as the wheat varieties commonly cultivated within these regions. Molecular variance analysis showed a higher proportion of intra-province variation among landraces compared with variation among all landraces as a whole.

Conclusion: The SNP analyses presented here highlight the importance and genetic diversity of Afghan wheat landraces. Furthermore, these data strongly refute a previous analysis that suggested low genetic diverse within this germplasm. Ongoing analyses include phenotypic characterisation of these landraces to identify functional traits associated with individual genotypes. Taken together, these analyses can be used to help improve wheat cultivation in Afghanistan, while providing insights into the evolution and selective pressures underlying these distinct landraces.

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Principal component analysis of Afghan wheat landraces. The first coordinate explained 52.7% of the variability, while the second one accounted for an additional 17.6%.
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Fig8: Principal component analysis of Afghan wheat landraces. The first coordinate explained 52.7% of the variability, while the second one accounted for an additional 17.6%.

Mentions: The Nei genetic distance analyses were consistent with those of our PCA analysis, indicating a strong reproducibility across analytical methods (Table 2 and Figure 8). The first and the second principle coordinates account for over two-thirds of the total genetic variation among the nine sub-populations; the first coordinate accounted for 52.7% of the variability and the second for an additional 17.6%. Interestingly, the provinces of Badghis, Herat, and Ghor were clustered in both coordinates, while the provinces of Kabul, Samangan, and Bamyan were clustered close together on one coordinate but far apart on the second. Of the remaining provinces, Badakhshan and Takhar provinces clustered together tightly, while Kandahar failed to cluster with any of the other groups. These results are consistent with a previous study that examined the phylogeny and population structure of these regions.Figure 8


Molecular evaluation of orphan Afghan common wheat (Triticum aestivum L.) landraces collected by Dr. Kihara using single nucleotide polymorphic markers.

Manickavelu A, Jighly A, Ban T - BMC Plant Biol. (2014)

Principal component analysis of Afghan wheat landraces. The first coordinate explained 52.7% of the variability, while the second one accounted for an additional 17.6%.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4255927&req=5

Fig8: Principal component analysis of Afghan wheat landraces. The first coordinate explained 52.7% of the variability, while the second one accounted for an additional 17.6%.
Mentions: The Nei genetic distance analyses were consistent with those of our PCA analysis, indicating a strong reproducibility across analytical methods (Table 2 and Figure 8). The first and the second principle coordinates account for over two-thirds of the total genetic variation among the nine sub-populations; the first coordinate accounted for 52.7% of the variability and the second for an additional 17.6%. Interestingly, the provinces of Badghis, Herat, and Ghor were clustered in both coordinates, while the provinces of Kabul, Samangan, and Bamyan were clustered close together on one coordinate but far apart on the second. Of the remaining provinces, Badakhshan and Takhar provinces clustered together tightly, while Kandahar failed to cluster with any of the other groups. These results are consistent with a previous study that examined the phylogeny and population structure of these regions.Figure 8

Bottom Line: Here we used SNP analysis to demonstrate the importance of Afghan wheat landraces and found tremendous genetic diversity and province-specific characteristics unique to this geographic region.This result closely resembles existing agro-climatic zones within Afghanistan, as well as the wheat varieties commonly cultivated within these regions.Molecular variance analysis showed a higher proportion of intra-province variation among landraces compared with variation among all landraces as a whole.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Landraces are an important source of genetic diversity in common wheat, but archival collections of Afghan wheat landraces remain poorly characterised. The recent development of array based marker systems, particularly single nucleotide polymorphism (SNP) markers, provide an excellent tool for examining the genetic diversity of local populations. Here we used SNP analysis to demonstrate the importance of Afghan wheat landraces and found tremendous genetic diversity and province-specific characteristics unique to this geographic region.

Results: A total of 446 Afghan wheat landraces were analysed using genotype by sequencing (GBS) arrays containing ~10 K unique markers. Pair-wise genetic distance analyses revealed significant genetic distances between landraces, particularly among those collected from distanced provinces. From these analyses, we were able to divide the landraces into 14 major classes, with the greatest degree of diversity evident among landraces isolated from Badakhshan province. Population-based analyses revealed an additional 15 sub-populations within our germplasm, and significant correlations were evident in both the provincial and botanical varieties. Genetic distance analysis was used to identify differences among provinces, with the strongest correlations seen between landraces from Herat and Ghor province, followed closely by those between Badakhshan and Takhar provinces. This result closely resembles existing agro-climatic zones within Afghanistan, as well as the wheat varieties commonly cultivated within these regions. Molecular variance analysis showed a higher proportion of intra-province variation among landraces compared with variation among all landraces as a whole.

Conclusion: The SNP analyses presented here highlight the importance and genetic diversity of Afghan wheat landraces. Furthermore, these data strongly refute a previous analysis that suggested low genetic diverse within this germplasm. Ongoing analyses include phenotypic characterisation of these landraces to identify functional traits associated with individual genotypes. Taken together, these analyses can be used to help improve wheat cultivation in Afghanistan, while providing insights into the evolution and selective pressures underlying these distinct landraces.

Show MeSH