title: Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array.
abstract: High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. 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. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. 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.
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
authors.forename: Shichen
authors.initials: S
authors.lastname: Wang
authors.forename: Debbie
authors.initials: D
authors.lastname: Wong
authors.forename: Kerrie
authors.initials: K
authors.lastname: Forrest
authors.forename: Alexandra
authors.initials: A
authors.lastname: Allen
authors.forename: Shiaoman
authors.initials: S
authors.lastname: Chao
authors.forename: Bevan E
authors.initials: BE
authors.lastname: Huang
authors.forename: Marco
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authors.lastname: Maccaferri
authors.forename: Silvio
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authors.lastname: Salvi
authors.forename: Sara G
authors.initials: SG
authors.lastname: Milner
authors.forename: Luigi
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authors.lastname: Cattivelli
authors.forename: Anna M
authors.initials: AM
authors.lastname: Mastrangelo
authors.forename: Alex
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authors.lastname: Whan
authors.forename: Stuart
authors.initials: S
authors.lastname: Stephen
authors.forename: Gary
authors.initials: G
authors.lastname: Barker
authors.forename: Ralf
authors.initials: R
authors.lastname: Wieseke
authors.forename: Joerg
authors.initials: J
authors.lastname: Plieske
authors.forename: Morten
authors.initials: M
authors.lastname: Lillemo
authors.forename: Diane
authors.initials: D
authors.lastname: Mather
authors.forename: Rudi
authors.initials: R
authors.lastname: Appels
authors.forename: Rudy
authors.initials: R
authors.lastname: Dolferus
authors.forename: Gina
authors.initials: G
authors.lastname: Brown-Guedira
authors.forename: Abraham
authors.initials: A
authors.lastname: Korol
authors.forename: Alina R
authors.initials: AR
authors.lastname: Akhunova
authors.forename: Catherine
authors.initials: C
authors.lastname: Feuillet
authors.forename: Jerome
authors.initials: J
authors.lastname: Salse
authors.forename: Michele
authors.initials: M
authors.lastname: Morgante
authors.forename: Curtis
authors.initials: C
authors.lastname: Pozniak
authors.forename: Ming-Cheng
authors.initials: MC
authors.lastname: Luo
authors.forename: Jan
authors.initials: J
authors.lastname: Dvorak
authors.forename: Matthew
authors.initials: M
authors.lastname: Morell
authors.forename: Jorge
authors.initials: J
authors.lastname: Dubcovsky
authors.forename: Martin
authors.initials: M
authors.lastname: Ganal
authors.forename: Roberto
authors.initials: R
authors.lastname: Tuberosa
authors.forename: Cindy
authors.initials: C
authors.lastname: Lawley
authors.forename: Ivan
authors.initials: I
authors.lastname: Mikoulitch
authors.forename: Colin
authors.initials: C
authors.lastname: Cavanagh
authors.forename: Keith J
authors.initials: KJ
authors.lastname: Edwards
authors.forename: Matthew
authors.initials: M
authors.lastname: Hayden
authors.forename: Eduard
authors.initials: E
authors.lastname: Akhunov
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D016000:Cluster Analysis; D005787:Gene Frequency / Q000235:genetics; D056426:Genetic Loci; D005819:Genetic Markers; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011123:Polyploidy; D014908:Triticum / Q000235:genetics*
chemical_list: D005819:Genetic Markers
keywords: genetic diversity; genotyping; high-density map; polyploid wheat; single nucleotide polymorphism; wheat iSelect array