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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Publications at this Location » Publication #300111
Title: Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array

Author
item WANG, SHICHEN - Kansas State University
item WONG, DEBBIE - Department Of Environment And Primary Industries
item FORREST, KERRIE - Department Of Environment And Primary Industries
item ALLEN, ALEXANDRA - University Of Bristol
item Chao, Shiaoman
item HUANG, EMMA - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item MACCAFERRI, MARCO - University Of Bologna, Italy
item SALVI, SILVIO - University Of Bologna, Italy
item MILNER, SARA - University Of Bologna, Italy
item CATTIVELLI, LUIGI - Agricultural Research Council (CRA)
item MASTRANGELO, ANNA - Agricultural Research Council (CRA)
item STEPHEN, STUART - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item LUO, MING-CHENG - Traitgenetics
item DVORAK, JAN - Traitgenetics
item MATHER, DIANE - Eversole Associates
item APPELS, RUDI - Eversole Associates
item DULFEROS, RUDI - Eversole Associates
item Brown-Guedira, Gina
item AKHUNOVA, ALINA - Murdoch University
item FEUILLET, CATHERINE - University Of Haifa
item SALSE, JEROME - Institut National De La Recherche Agronomique (INRA)
item MORGANTE, MICHELE - Kansas State University
item POZNIAK, CURTIS - Institut National De La Recherche Agronomique (INRA)
item WIESEKE, RALF - Bayer Corporation
item PLIESKE, JOERG - Bayer Corporation
item MORELL, MATTHEW - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item DUBCOVSKY, JORGE - Traitgenetics
item GANAL, MARTIN - Bayer Corporation
item TUBEROSA, ROBERTO - University Of Bologna, Italy
item LAWLEY, CINDY - University Of Saskatchewan
item MIKOULITCH, IVAN - University Of Saskatchewan
item CAVANAGH, COLIN - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item EDWARDS, KEITH - University Of Bristol
item HAYDEN, MATTHEW - Department Of Environment And Primary Industries
item AKHUNOV, EDUARD - Kansas State University
item WHAN, A - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item BARKER, G - University Of Bristol
item LILLEMO, M - Norwegian University Of Life Sciences
item KOROL, A - University Of Haifa

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/6/2014
Publication Date: 3/1/2014
Citation: Wang, S., Wong, D., Forrest, K., Allen, A., Chao, S., Huang, B.E., Maccaferri, M., Salvi, S., Milner, S.G., Cattivelli, L., Mastrangelo, A.M., Whan, A., Stephen, S., Barker, G., Wieseke, R., Plieske, J., International Wheat Genome Sequencing Consortium, Lillemo, M., Mather, D., Appels, R., Dulferos, R., Brown-Guedira, G., Korol, A., Akhunova, A.R., Feuillet, C., Salse, J., Morgante, M., Pozniak, C., Luo, M.-C., Dvorak, J., Morell, M., Dubcovsky, J., Ganal, M., Tuberosa, R., Lawley, C., Mikoulitch, I., Cavanagh, C., Edwards, K.J., Hayden, M., Akhunov, E. 2014. Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnology Journal. 12:787-796.

Interpretive Summary: A resource of 90,000 DNA markers detecting genetic variations at a single nucleotide base level in the wheat genomes was developed that served as a powerful tool for various genetic and breeding applications in polyploid wheat. The objective was to evaluate the utility of this high-density DNA marker tool using the improved software algorithms to facilitate the analysis of complex datasets obtained due to polyploidy nature of the wheat genomes. Wheat samples from diverse geographic areas in the US and elsewhere in the world were surveyed. Similar levels of genetic diversity were detected in samples among different areas, demonstrating the general marker utility applied to the wheat community at large. A total of 46,362 markers were located and placed on each of the 21 wheat chromosomes, that provides road maps for studying genetic architecture underlying important agronomic traits. A protocol on the use of the improved algorithms was prepared and can guide users to correctly obtain high quality marker data for their own studies.

Technical Abstract: High-density single nucleotide polymorphism (SNP) genotyping chips are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships among 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 geographic origin. We utilized new density-based spatial clustering algorithms to enable high-throughput genotype calling in complex datasets obtained for polyploid wheat. We show that these model-free clustering algorithms can be successfully used for 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. The SNP assays detecting low intensity clusters provided insight into the distribution of presence-absence variation (PAV) in wheat populations and across the polyploid genome. A total of 46,362 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.