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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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Population structures of Afghan wheat landraces according to collection site and botanical variety. Population structure analysis resulted in 15 sub-populations (K = 15). Details of the botanical variety composition are indicated for each group. Mixed type structure is defined as landraces lacking a specific botanical variety and those in which the province of origin is not known.
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Fig6: Population structures of Afghan wheat landraces according to collection site and botanical variety. Population structure analysis resulted in 15 sub-populations (K = 15). Details of the botanical variety composition are indicated for each group. Mixed type structure is defined as landraces lacking a specific botanical variety and those in which the province of origin is not known.

Mentions: To further clarify our diversity analysis and to better estimate population subdivisions, a population structure analysis was performed using only KAWLR samples. Samples were analysed using STRUCTURE software [23], revealing 15 distinct sub-populations (K = 15) within our germplasm. In order to differentiate these sub-populations, samples were further categorised based on collection site, taxonomy, and morphology (FigureĀ 6). The landraces of Badakhshan province alone were grouped into five different sub-populations, while the sub-population with the highest number of accessions (104 acc.) combined landraces collected from neighbouring Herat and Ghor provinces. When comparing sub-populations based upon botanical varieties, nine sub-populations could be identified as having unique botanical varieties. For instance, the var. milturum (Alef.) Velican from Badakhshan province was grouped exclusively with landraces collected from high elevations. Other examples include var. ferrugineum (Alef.) Velican and var. erythrospermum (Alef.) Velican, the major varieties found in our collection, which were often grouped together. Overall these results highlight the considerable diversity present in our germplasm, along with the ability of STRUCTURE analysis to better connect genomic diversity with its corresponding phenotypic outcomes, such as geographic distribution and botanical varieties.Figure 6


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)

Population structures of Afghan wheat landraces according to collection site and botanical variety. Population structure analysis resulted in 15 sub-populations (K = 15). Details of the botanical variety composition are indicated for each group. Mixed type structure is defined as landraces lacking a specific botanical variety and those in which the province of origin is not known.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig6: Population structures of Afghan wheat landraces according to collection site and botanical variety. Population structure analysis resulted in 15 sub-populations (K = 15). Details of the botanical variety composition are indicated for each group. Mixed type structure is defined as landraces lacking a specific botanical variety and those in which the province of origin is not known.
Mentions: To further clarify our diversity analysis and to better estimate population subdivisions, a population structure analysis was performed using only KAWLR samples. Samples were analysed using STRUCTURE software [23], revealing 15 distinct sub-populations (K = 15) within our germplasm. In order to differentiate these sub-populations, samples were further categorised based on collection site, taxonomy, and morphology (FigureĀ 6). The landraces of Badakhshan province alone were grouped into five different sub-populations, while the sub-population with the highest number of accessions (104 acc.) combined landraces collected from neighbouring Herat and Ghor provinces. When comparing sub-populations based upon botanical varieties, nine sub-populations could be identified as having unique botanical varieties. For instance, the var. milturum (Alef.) Velican from Badakhshan province was grouped exclusively with landraces collected from high elevations. Other examples include var. ferrugineum (Alef.) Velican and var. erythrospermum (Alef.) Velican, the major varieties found in our collection, which were often grouped together. Overall these results highlight the considerable diversity present in our germplasm, along with the ability of STRUCTURE analysis to better connect genomic diversity with its corresponding phenotypic outcomes, such as geographic distribution and botanical varieties.Figure 6

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