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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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Chromosomal locations of SNP markers. Markers were arranged along the long arm (green), centromere (dark red), and short arm (blue), respectively. For the markers on chromosome 3B, there are no details regarding chromosome arm.
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Fig3: Chromosomal locations of SNP markers. Markers were arranged along the long arm (green), centromere (dark red), and short arm (blue), respectively. For the markers on chromosome 3B, there are no details regarding chromosome arm.

Mentions: Following GBS analysis, data were filtered to remove SNPs exhibiting a minor allele frequency ≤10%, resulting in a total of 8969 SNP markers. Of these markers, 2770 were identified as transition markers, while 1738 represented transversion SNPs. Chromosomal alignments were successful for 1264 markers, with SNPs distributed across all 21 chromosomes (Figure 3). The highest number of markers was found on chromosome 2A and the lowest in chromosome 4D; a majority of markers were located in close proximity to the centromeres. As expected, more markers were identified in the A and B genomes than in the D genome, consistent with a previous study [20], indicating a need for targeted marker development for the D genome. Preliminary efforts to address this deficiency include the development of a DArT marker array based on 81 Aegilops tauschii Coss accessions [21], although the resulting marker coverage remains lower than desired.Figure 3


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)

Chromosomal locations of SNP markers. Markers were arranged along the long arm (green), centromere (dark red), and short arm (blue), respectively. For the markers on chromosome 3B, there are no details regarding chromosome arm.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Chromosomal locations of SNP markers. Markers were arranged along the long arm (green), centromere (dark red), and short arm (blue), respectively. For the markers on chromosome 3B, there are no details regarding chromosome arm.
Mentions: Following GBS analysis, data were filtered to remove SNPs exhibiting a minor allele frequency ≤10%, resulting in a total of 8969 SNP markers. Of these markers, 2770 were identified as transition markers, while 1738 represented transversion SNPs. Chromosomal alignments were successful for 1264 markers, with SNPs distributed across all 21 chromosomes (Figure 3). The highest number of markers was found on chromosome 2A and the lowest in chromosome 4D; a majority of markers were located in close proximity to the centromeres. As expected, more markers were identified in the A and B genomes than in the D genome, consistent with a previous study [20], indicating a need for targeted marker development for the D genome. Preliminary efforts to address this deficiency include the development of a DArT marker array based on 81 Aegilops tauschii Coss accessions [21], although the resulting marker coverage remains lower than desired.Figure 3

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