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

Autor: Debbie Wong, Abraham B. Korol, Eduard Akhunov, Catherine Feuillet, Gina Brown-Guedira, Ivan Mikoulitch, Jan Dvorak, Martin W. Ganal, Marco Maccaferri, Curtis J. Pozniak, Luigi Cattivelli, Joerg Plieske, Rudi Appels, Rudy Dolferus, Anna M. Mastrangelo, Ming-Cheng Luo, Bevan Emma Huang, Alexandra M. Allen, Jorge Dubcovsky, Matthew K. Morell, Michele Morgante, Cindy Lawley, Shichen Wang, Morten Lillemo, Sara Giulia Milner, Shiaoman Chao, Alex Whan, Alina Akhunova, Kerrie Forrest, Matthew J. Hayden, Gary L A Barker, Keith J. Edwards, Jérôme Salse, Stuart Stephen, Roberto Tuberosa, Colin Cavanagh, Silvio Salvi, Ralf Wieseke, Diane E. Mather
Přispěvatelé: Department of Plant Pathology, Shizuoka University, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, USDA-ARS : Agricultural Research Service, Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Department of Agricultural Sciences, Genomics Research Centre, Consiglio per la Ricerca e Sperimentazione in Agricoltura, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Waite Res Inst, Australian Ctr Plant Funct Genom, University of Adelaide, Institute of Evolution and Department of Evolutionary and Environmental Biology, University of Haifa [Haifa], Integrated Genomics Facility, Kansas State University, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Dipartimento di Produzione Vegetale e Tecnologie Agrarie, Università degli Studi di Udine - University of Udine [Italie], Plant Genetics and Bioinformatics, UC Davis Plant Sciences, University of Hradec Kralove, CSIRO Plant Industry, Department of Plant Sciences (DPS), University of Cambridge [UK] (CAM), Illumina, Inc., CSIRO Plant Industrie, Dept Plant Pathol, Department of Plant Sciences [Univ California Davis] (Plant - UC Davis), University of California [Davis] (UC Davis), University of California (UC)-University of California (UC)-University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), Università di Bologna [Bologna] (UNIBO), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), S. Wang, D. Wong, K. Forrest, A. Allen, S. Chao, B. Huang, M. Maccaferri, S. Salvi, S. Milner, L. Cattivelli, A. Mastrangelo, A. Whan, S. Stephen, G. Barker, R. Wieseke, J. Plieske, M. Lillemo, D. Mather, R. Appel, R. Dolferu, G. Brown-Guedira, A. Korol, A. Akhunova, C. w. Feuillet, J. Salse, M. Morgante, C. Pozniak, M. Luo, J. Dvorak, M. Morell, J. u. Dubcovsky, M. Ganal, R. Tuberosa, C. Lawley, I. Mikoulitch, C. Cavanagh, K. Edward, M. Hayden, E. Akhunov
Rok vydání: 2014
Předmět:
0106 biological sciences
Technology
SNP ARRAY
LINKAGE DISEQUILIBRIUM
Polyploid wheat
[SDV]Life Sciences [q-bio]
Plant Science
Medical and Health Sciences
01 natural sciences
Genetic diversity
Gene Frequency
single nucleotide polymorphism
Genotype
WIDE ASSOCIATION
Cluster Analysis
ComputingMilieux_MISCELLANEOUS
AEGILOPS-TAUSCHII
POPULATION
Triticum
Research Articles
Oligonucleotide Array Sequence Analysis
2. Zero hunger
Genetics
0303 health sciences
education.field_of_study
Genome
biology
Chromosome Mapping
food and beverages
Wheat iSelect array
Single Nucleotide
genetic diversity
Biological Sciences
SNP genotyping
DURUM-WHEAT
wheat iSelect array
Genome
Plant
Biotechnology
Genetic Markers
Genotyping
SNP DISCOVERY
Population
Single-nucleotide polymorphism
SEQUENCE
Polymorphism
Single Nucleotide
GENETIC ARCHITECTURE
Polyploidy
polyploid wheat
03 medical and health sciences
Genetic variation
Aegilops tauschii
Polymorphism
TRITICUM-AESTIVUM L
education
Alleles
030304 developmental biology
genotyping
high-density map
Genetic Loci
Genetic Variation
High-density map
Plant
biology.organism_classification
Single nucleotide polymorphism
High density map
Evolutionary biology
HEXAPLOWHEAT
Agronomy and Crop Science
010606 plant biology & botany
Zdroj: Plant Biotechnology Journal, vol 12, iss 6
Wang, S; Wong, D; Forrest, K; Allen, A; Chao, S; Huang, BE; et al.(2014). Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnology Journal. doi: 10.1111/pbi.12183. UC Davis: Retrieved from: http://www.escholarship.org/uc/item/3rv2p5j3
Plant Biotechnology Journal
Plant Biotechnology Journal, Wiley, 2014, 12 (6), pp.787-796. ⟨10.1111/pbi.12183⟩
Wang, S; Wong, D; Forrest, K; Allen, A; Chao, S; Huang, BE; et al.(2014). Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnology Journal, 12(6), 787-796. doi: 10.1111/pbi.12183. UC Davis: Retrieved from: http://www.escholarship.org/uc/item/23b137fg
Plant Biotechnology Journal, 2014, 12 (6), pp.787-796. ⟨10.1111/pbi.12183⟩
ISSN: 1467-7652
1467-7644
DOI: 10.1111/pbi.12183
Popis: 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. © 2014 The Authors Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
Databáze: OpenAIRE
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