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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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Distribution of pairwise (a) Roger’s genetic distance among the landraces; (b) Roger’s genetic distance between landraces and controls; (c) relative kinship among landraces, and (d) relative kinship calculated between landraces and controls.
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Fig4: Distribution of pairwise (a) Roger’s genetic distance among the landraces; (b) Roger’s genetic distance between landraces and controls; (c) relative kinship among landraces, and (d) relative kinship calculated between landraces and controls.

Mentions: The pairwise Roger genetic distance between each of the 446 landraces ranged from 0.002 to 0.47 with an overall mean distance of 0.33. While such a high degree of divergence is uncommon for a national collection of self-pollinated landraces, this result is not without precedent; Semagn et al. [22] reported a similar mean distance of ~0.35 for a diverse set of CIMMYT maize inbred lines. Of the 99,235 pairwise distances, 75,015 (75.6%) fell between 0.3 and 0.4 (Figure 4a), with only 400 (0.4%) exhibiting values <0.1. Comparisons between selected controls resulted in a total of 19,624 pairwise distances, of which 16,833 (85.8%) fell between 0.3 and 0.4, and only 22 (0.11%) exhibited distances <0.2 (Figure 4b). Taken together, these results are indicative of a very low degree of genetic redundancy within this collection.Figure 4


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)

Distribution of pairwise (a) Roger’s genetic distance among the landraces; (b) Roger’s genetic distance between landraces and controls; (c) relative kinship among landraces, and (d) relative kinship calculated between landraces and controls.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Distribution of pairwise (a) Roger’s genetic distance among the landraces; (b) Roger’s genetic distance between landraces and controls; (c) relative kinship among landraces, and (d) relative kinship calculated between landraces and controls.
Mentions: The pairwise Roger genetic distance between each of the 446 landraces ranged from 0.002 to 0.47 with an overall mean distance of 0.33. While such a high degree of divergence is uncommon for a national collection of self-pollinated landraces, this result is not without precedent; Semagn et al. [22] reported a similar mean distance of ~0.35 for a diverse set of CIMMYT maize inbred lines. Of the 99,235 pairwise distances, 75,015 (75.6%) fell between 0.3 and 0.4 (Figure 4a), with only 400 (0.4%) exhibiting values <0.1. Comparisons between selected controls resulted in a total of 19,624 pairwise distances, of which 16,833 (85.8%) fell between 0.3 and 0.4, and only 22 (0.11%) exhibited distances <0.2 (Figure 4b). Taken together, these results are indicative of a very low degree of genetic redundancy within this collection.Figure 4

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