Characterization of polyploid wheat genomic diversity using a high-density 90000 single nucleotide polymorphism array

S. Wang; D. Wong; K. Forrest; A. Allen; S. Chao; B.E. Huang; M. Maccaferri; S. Salvi; S.G. Milner; L. Cattivelli; A.M. Mastrangelo; A. Whan; S. Stephen; G. Barker; R. Wieseke; J. Plieske; M. Lillemo; D. Mather; R. Appels; R. Dolferus; G. Brown-Guedira; A. Korol; A.R. Akhunova; C. Feuillet; J. Salse; M. Morgante; C. Pozniak; M-C Luo; J. Dvorak; M. Morell; J. Dubcovsky; M. Ganal; R. Tuberosa; C. Lawley; I. Mikoulitch; C. Cavanagh; K.J. Edwards; M. Hayden; E. Akhunov

doi:10.1111/pbi.12183

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Characterization of polyploid wheat genomic diversity using a high-density 90000 single nucleotide polymorphism array

Journal article

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Characterization of polyploid wheat genomic diversity using a high-density 90000 single nucleotide polymorphism array

S. Wang, D. Wong, K. Forrest, A. Allen, S. Chao, B.E. Huang, M. Maccaferri, S. Salvi, S.G. Milner, L. Cattivelli, …

Plant Biotechnology Journal, Vol.12(6), pp.787-796

2014

DOI: https://doi.org/10.1111/pbi.12183

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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.

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Title: Characterization of polyploid wheat genomic diversity using a high-density 90000 single nucleotide polymorphism array
Authors/Creators: S. Wang (Author/Creator) - Kansas State University
D. Wong (Author/Creator) - Department of Environment, Land, Water and Planning
K. Forrest (Author/Creator) - Department of Environment, Land, Water and Planning
A. Allen (Author/Creator) - University of Bristol
S. Chao (Author/Creator) - US Department of Agriculture–Agricultural Research Service Biosciences Research Laboratory
B.E. Huang (Author/Creator) - Health Sciences and Nutrition
M. Maccaferri (Author/Creator) - University of Bologna
S. Salvi (Author/Creator) - University of Bologna
S.G. Milner (Author/Creator) - University of Bologna
L. Cattivelli (Author/Creator) - Consiglio per la ricerca e la sperimentazione in agricoltura
A.M. Mastrangelo (Author/Creator) - Consiglio per la ricerca e la sperimentazione in agricoltura
A. Whan (Author/Creator) - Health Sciences and Nutrition
S. Stephen (Author/Creator) - Health Sciences and Nutrition
G. Barker (Author/Creator)
R. Wieseke (Author/Creator) - TraitGenetics GmbH
J. Plieske (Author/Creator) - TraitGenetics GmbH
M. Lillemo (Author/Creator) - Norwegian University of Life Sciences
D. Mather (Author/Creator) - The University of Adelaide
R. Appels (Author/Creator) - Murdoch University
R. Dolferus (Author/Creator) - Health Sciences and Nutrition
G. Brown-Guedira (Author/Creator) - US Department of Agriculture, Agricultural Research Service Eastern Regional Small Grains Genotyping Laboratory
A. Korol (Author/Creator) - University of Haifa
A.R. Akhunova (Author/Creator) - Kansas State University
C. Feuillet (Author/Creator) - Institut Pascal
J. Salse (Author/Creator) - Institut Pascal
M. Morgante (Author/Creator) - University of Udine
C. Pozniak (Author/Creator) - University of Saskatchewan
M-C Luo (Author/Creator) - University of California, Berkeley
J. Dvorak (Author/Creator) - University of California, Berkeley
M. Morell (Author/Creator) - Health Sciences and Nutrition
J. Dubcovsky (Author/Creator) - University of California, Berkeley
M. Ganal (Author/Creator) - TraitGenetics GmbH
R. Tuberosa (Author/Creator) - University of Bologna
C. Lawley (Author/Creator) - Illumina (United States)
I. Mikoulitch (Author/Creator) - Illumina (United States)
C. Cavanagh (Author/Creator) - Health Sciences and Nutrition
K.J. Edwards (Author/Creator) - School of Biological Sciences
M. Hayden (Author/Creator) - Department of Environment, Land, Water and Planning
E. Akhunov (Author/Creator) - Kansas State University
Publication Details: Plant Biotechnology Journal, Vol.12(6), pp.787-796
Publisher: Blackwell Publishing Inc.
Identifiers: 991005540926007891
Copyright: © 2014 The Authors
Murdoch Affiliation: Centre for Comparative Genomics
Language: English
Resource Type: Journal article

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Collaboration types: Industry collaboration; Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Biotechnology & Applied Microbiology; Plant Sciences
ESI research areas: Plant & Animal Science