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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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(a) Alignment of chromosome 2 consensus maps with genetic maps from individual bi-parental crosses. BTS/AUS = BT-Schomburgk × AUS33384, Cha/Glen = Chara × Glenlea, Op/Syn = W7984 × Opata M85, Sun/AUS = Sundor × AUS30604, Wes/Kauz = Westonia × Kauz, Yo/AUS = Young × AUS33414. Chromosome 2B from Yo/AUS was excluded from consensus map construction due to the presence of the alien Sr36 introgression in cultivar Young, whose presence restricts recombination and complicates map construction. (b) Comparative analysis of the order of single nucleotide polymorphism (SNP) loci in the wheat genome based on SNPs showing segregation at two (left) and three (right) duplicated loci.
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fig03: (a) Alignment of chromosome 2 consensus maps with genetic maps from individual bi-parental crosses. BTS/AUS = BT-Schomburgk × AUS33384, Cha/Glen = Chara × Glenlea, Op/Syn = W7984 × Opata M85, Sun/AUS = Sundor × AUS30604, Wes/Kauz = Westonia × Kauz, Yo/AUS = Young × AUS33414. Chromosome 2B from Yo/AUS was excluded from consensus map construction due to the presence of the alien Sr36 introgression in cultivar Young, whose presence restricts recombination and complicates map construction. (b) Comparative analysis of the order of single nucleotide polymorphism (SNP) loci in the wheat genome based on SNPs showing segregation at two (left) and three (right) duplicated loci.

Mentions: Six of the doubled-haploid mapping populations were used to construct a consensus SNP map containing 40 267 loci (Table S13). Comparison of the consensus map order with that obtained for individual populations showed high collinearity across chromosomes, confirming the high accuracy of genotype calling using the polyploid GS (Figure 3a). Comparative analysis of SNP order revealed by assays detecting segregation at nontarget SNPs (see below) showed the high level of gene order conservation between homoeologous chromosomes, as well as frequent gene duplications across chromosomes (Figure 3b). These assays provide insights into the structural organization of the wheat genome revealing new and previously characterized re-arrangements (Devos et al., 1995).


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)

(a) Alignment of chromosome 2 consensus maps with genetic maps from individual bi-parental crosses. BTS/AUS = BT-Schomburgk × AUS33384, Cha/Glen = Chara × Glenlea, Op/Syn = W7984 × Opata M85, Sun/AUS = Sundor × AUS30604, Wes/Kauz = Westonia × Kauz, Yo/AUS = Young × AUS33414. Chromosome 2B from Yo/AUS was excluded from consensus map construction due to the presence of the alien Sr36 introgression in cultivar Young, whose presence restricts recombination and complicates map construction. (b) Comparative analysis of the order of single nucleotide polymorphism (SNP) loci in the wheat genome based on SNPs showing segregation at two (left) and three (right) duplicated loci.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig03: (a) Alignment of chromosome 2 consensus maps with genetic maps from individual bi-parental crosses. BTS/AUS = BT-Schomburgk × AUS33384, Cha/Glen = Chara × Glenlea, Op/Syn = W7984 × Opata M85, Sun/AUS = Sundor × AUS30604, Wes/Kauz = Westonia × Kauz, Yo/AUS = Young × AUS33414. Chromosome 2B from Yo/AUS was excluded from consensus map construction due to the presence of the alien Sr36 introgression in cultivar Young, whose presence restricts recombination and complicates map construction. (b) Comparative analysis of the order of single nucleotide polymorphism (SNP) loci in the wheat genome based on SNPs showing segregation at two (left) and three (right) duplicated loci.
Mentions: Six of the doubled-haploid mapping populations were used to construct a consensus SNP map containing 40 267 loci (Table S13). Comparison of the consensus map order with that obtained for individual populations showed high collinearity across chromosomes, confirming the high accuracy of genotype calling using the polyploid GS (Figure 3a). Comparative analysis of SNP order revealed by assays detecting segregation at nontarget SNPs (see below) showed the high level of gene order conservation between homoeologous chromosomes, as well as frequent gene duplications across chromosomes (Figure 3b). These assays provide insights into the structural organization of the wheat genome revealing new and previously characterized re-arrangements (Devos et al., 1995).

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