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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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Diversity of Afghan wheat landraces. Each province is identified using a different colour. Landraces with unknown origins and those collected from Ghazni, Kunduz, Parwan, and Wardak provinces were left unshaded. Individual clade dendrograms are shown in Additional file 2: Figure S2.
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Fig5: Diversity of Afghan wheat landraces. Each province is identified using a different colour. Landraces with unknown origins and those collected from Ghazni, Kunduz, Parwan, and Wardak provinces were left unshaded. Individual clade dendrograms are shown in Additional file 2: Figure S2.

Mentions: High-throughput SNP arrays were used to evaluate 446 KAWLR samples and 45 controls originating from landraces of neighbouring countries, along with improved Afghan varieties, and one durum wheat genotype. Phylogenetic analysis revealed the complex nature of the diversity present in these landraces, which could be divided into 14 major clades (FigureĀ 5, Additional file 2). Among these 14 clades, clade I accounted for ~30% of all landraces. This clade consisted of landraces collected from Badakhshan, Baghlan, Bamyan, and Takhar provinces, along with six landraces from Ghor, four from Kabul, two from Samangan, and one from Faryab. The provinces of Badakhshan, Baghlan, Bamyan, and Takhar are all located in the northeast region of Afghanistan, where their wheat landraces are expected to cluster together. More surprising was the inclusion of an Ishkashim landrace in this clade, considering its predecessor originated in Tajikistan. On the other hand, clade II was limited to landraces collected from Badakhshan province, with the exception of one landrace from Parwan. Landraces from the north central provinces of Balkh, Samangan, and Faryab clustered primarily within clade VIII. Clades VI and IX were comprised of landraces from Ghor, Herat, Wardak, Badghis, and Bamyan provinces, while clade X contained landraces collected from Ghor, Herat, and Wardak.Figure 5


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)

Diversity of Afghan wheat landraces. Each province is identified using a different colour. Landraces with unknown origins and those collected from Ghazni, Kunduz, Parwan, and Wardak provinces were left unshaded. Individual clade dendrograms are shown in Additional file 2: Figure S2.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig5: Diversity of Afghan wheat landraces. Each province is identified using a different colour. Landraces with unknown origins and those collected from Ghazni, Kunduz, Parwan, and Wardak provinces were left unshaded. Individual clade dendrograms are shown in Additional file 2: Figure S2.
Mentions: High-throughput SNP arrays were used to evaluate 446 KAWLR samples and 45 controls originating from landraces of neighbouring countries, along with improved Afghan varieties, and one durum wheat genotype. Phylogenetic analysis revealed the complex nature of the diversity present in these landraces, which could be divided into 14 major clades (FigureĀ 5, Additional file 2). Among these 14 clades, clade I accounted for ~30% of all landraces. This clade consisted of landraces collected from Badakhshan, Baghlan, Bamyan, and Takhar provinces, along with six landraces from Ghor, four from Kabul, two from Samangan, and one from Faryab. The provinces of Badakhshan, Baghlan, Bamyan, and Takhar are all located in the northeast region of Afghanistan, where their wheat landraces are expected to cluster together. More surprising was the inclusion of an Ishkashim landrace in this clade, considering its predecessor originated in Tajikistan. On the other hand, clade II was limited to landraces collected from Badakhshan province, with the exception of one landrace from Parwan. Landraces from the north central provinces of Balkh, Samangan, and Faryab clustered primarily within clade VIII. Clades VI and IX were comprised of landraces from Ghor, Herat, Wardak, Badghis, and Bamyan provinces, while clade X contained landraces collected from Ghor, Herat, and Wardak.Figure 5

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