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Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array.

Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, International Wheat Genome Sequencing ConsortiumLillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E - Plant Biotechnol. J. (2014)

Bottom Line: We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations.The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin.The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.

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Examples of  alleles in the wheat genome. (a) Assay IWB17050 detecting a  allele; (b) Assay IWB12859 detects a co-dominant single nucleotide polymorphism locus that also shows the evidence of a  allele; (c) Frequency of s in the populations of different geographical origin.
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fig04: Examples of alleles in the wheat genome. (a) Assay IWB17050 detecting a allele; (b) Assay IWB12859 detects a co-dominant single nucleotide polymorphism locus that also shows the evidence of a allele; (c) Frequency of s in the populations of different geographical origin.

Mentions: The ability of the clustering algorithms implemented in the polyploid version of GS to detect clusters of any shape allowed for the identification of alleles (clusters with low signal intensity) resulting from either the deletion of single-copy genes in the wheat genome or the divergence of genotyping probe annealing sites (Figure 4). A total of 1660 single-locus SNPs showed evidence for alleles. We investigated the molecular basis of allele origin by comparing the sequences of SNP probes detecting these alleles in wheat cultivar Chinese Spring with the genomic sequence of this cultivar. Based on the comparison of flanking sequences of 94 SNP assays detecting the alleles in cultivar Chinese Spring, 46 assays did not have annealing sites in the genome. This result suggests that about 50% of alleles result from gene deletions and remaining are the consequence of sequence divergence at the SNP probe annealing sites.


Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array.

Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, International Wheat Genome Sequencing ConsortiumLillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E - Plant Biotechnol. J. (2014)

Examples of  alleles in the wheat genome. (a) Assay IWB17050 detecting a  allele; (b) Assay IWB12859 detects a co-dominant single nucleotide polymorphism locus that also shows the evidence of a  allele; (c) Frequency of s in the populations of different geographical origin.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4265271&req=5

fig04: Examples of alleles in the wheat genome. (a) Assay IWB17050 detecting a allele; (b) Assay IWB12859 detects a co-dominant single nucleotide polymorphism locus that also shows the evidence of a allele; (c) Frequency of s in the populations of different geographical origin.
Mentions: The ability of the clustering algorithms implemented in the polyploid version of GS to detect clusters of any shape allowed for the identification of alleles (clusters with low signal intensity) resulting from either the deletion of single-copy genes in the wheat genome or the divergence of genotyping probe annealing sites (Figure 4). A total of 1660 single-locus SNPs showed evidence for alleles. We investigated the molecular basis of allele origin by comparing the sequences of SNP probes detecting these alleles in wheat cultivar Chinese Spring with the genomic sequence of this cultivar. Based on the comparison of flanking sequences of 94 SNP assays detecting the alleles in cultivar Chinese Spring, 46 assays did not have annealing sites in the genome. This result suggests that about 50% of alleles result from gene deletions and remaining are the consequence of sequence divergence at the SNP probe annealing sites.

Bottom Line: We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations.The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin.The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.

Show MeSH