New DArT markers for oat provide enhanced map coverage and global germplasm characterization

Nicholas A. Tinker; Andrzej Kilian; Charlene P. Wight; Katarzyna Heller-Uszynska; Peter Wenzl; Howard W. Rines; Åsmund Bjørnstad; Catherine J. Howarth; Jean Luc Jannink; Joseph M. Anderson; Brian G. Rossnagel; Deon D. Stuthman; Mark E. Sorrells; Eric W. Jackson; Stine Tuvesson; Frederic L. Kolb; Olof Olsson; Luiz Federizzi; Marty L. Carson; Herbert W. Ohm; Stephen J. Molnar; Graham J. Scoles; Peter E. Eckstein; J. Michael Bonman; Alf Ceplitis; Tim Langdon

doi:10.1186/1471-2164-10-39

New DArT markers for oat provide enhanced map coverage and global germplasm characterization

Nicholas A. Tinker^*
, Andrzej Kilian
, Charlene P. Wight
, Katarzyna Heller-Uszynska
, Peter Wenzl
, Howard W. Rines
, Åsmund Bjørnstad
, Catherine J. Howarth
, Jean Luc Jannink
, Joseph M. Anderson
, Brian G. Rossnagel
, Deon D. Stuthman
, Mark E. Sorrells
, Eric W. Jackson
, Stine Tuvesson
, Frederic L. Kolb
, Olof Olsson
, Luiz Federizzi
, Marty L. Carson
, Herbert W. Ohm

Stephen J. Molnar, Graham J. Scoles, Peter E. Eckstein, J. Michael Bonman, Alf Ceplitis, Tim Langdon

^*Corresponding author for this work

Institute of Biological, Environmental, and Rural Sciences

Guelph Research and Development Centre
Diversity Arrays Technology P/L
University of Minnesota
Norwegian University of Life Sciences
Cornell University
Purdue University West Lafayette
University of Saskatchewan
National Animal Disease Center
Cereal Breeding Department
University of Illinois Urbana-Champaign
University of Gothenburg
Universidade Federal do Rio Grande do Sul

Research output: Contribution to journal › Article › peer-review

138 Citations (Scopus)

230 Downloads (Pure)

Abstract

Background
Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT).

Results
Approximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' × 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure.

Conclusion
These markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity.

Original language	English
Article number	39
Number of pages	22
Journal	BMC Genomics
Volume	10
Issue number	1
DOIs	https://doi.org/10.1186/1471-2164-10-39
Publication status	Published - 21 Jan 2009

Keywords

Avena/genetics
Chromosome Mapping/methods
Cluster Analysis
DNA, Plant/genetics
Genetic Markers
Genome, Plant
Genomic Library
Genotype
Oligonucleotide Array Sequence Analysis
Polymorphism, Genetic
Sequence Analysis, DNA

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10.1186/1471-2164-10-39Licence: CC BY

ArticleFinal published version, 1.01 MBLicence: CC BY
Supplementary MaterialData, 4.34 MBLicence: CC BY

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Tinker, N. A., Kilian, A., Wight, C. P., Heller-Uszynska, K., Wenzl, P., Rines, H. W., Bjørnstad, Å., Howarth, C. J., Jannink, J. L., Anderson, J. M., Rossnagel, B. G., Stuthman, D. D., Sorrells, M. E., Jackson, E. W., Tuvesson, S., Kolb, F. L., Olsson, O., Federizzi, L., Carson, M. L., ... Langdon, T. (2009). New DArT markers for oat provide enhanced map coverage and global germplasm characterization. BMC Genomics, 10(1), Article 39. https://doi.org/10.1186/1471-2164-10-39

@article{659c850a2ef74dafb913db71522829ad,

title = "New DArT markers for oat provide enhanced map coverage and global germplasm characterization",

abstract = "Background Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT). Results Approximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' {\texttimes} 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99\% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure. Conclusion These markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity.",

keywords = "Avena/genetics, Chromosome Mapping/methods, Cluster Analysis, DNA, Plant/genetics, Genetic Markers, Genome, Plant, Genomic Library, Genotype, Oligonucleotide Array Sequence Analysis, Polymorphism, Genetic, Sequence Analysis, DNA",

author = "Tinker, \{Nicholas A.\} and Andrzej Kilian and Wight, \{Charlene P.\} and Katarzyna Heller-Uszynska and Peter Wenzl and Rines, \{Howard W.\} and {\AA}smund Bj{\o}rnstad and Howarth, \{Catherine J.\} and Jannink, \{Jean Luc\} and Anderson, \{Joseph M.\} and Rossnagel, \{Brian G.\} and Stuthman, \{Deon D.\} and Sorrells, \{Mark E.\} and Jackson, \{Eric W.\} and Stine Tuvesson and Kolb, \{Frederic L.\} and Olof Olsson and Luiz Federizzi and Carson, \{Marty L.\} and Ohm, \{Herbert W.\} and Molnar, \{Stephen J.\} and Scoles, \{Graham J.\} and Eckstein, \{Peter E.\} and Bonman, \{J. Michael\} and Alf Ceplitis and Tim Langdon",

note = "Funding Information: We are grateful to the following institutions for generous funding that contributed to this work: The Quaker Oats Company [55], Quaker Tropicana Gatorade Canada [56], North American Millers Association [57], CropTai-lor [58], Biotechnology and Biological Sciences Research Council [59], and Anderson -USDA-ARS project 3602-21220-010-00D. At DArT Pty Ltd, a number of people contributed to technology development and data production, especially Eric Huttner, Jason Carling, Vanessa Caig, and Ling Xia. We recognize the excellent technical and professional assistance of many staff and collaborators including Dr. Phillip San Miguel, Allison Witt, and Viktoria Krasnyanskaya. Finally, we thank the following for providing additional germplasm and related information that contributed to this study: Carla Adtorre, Ron Barnett, Aaron Beattie, Howard Bockelman, Vern Burrows, Hermann B{\"u}rstmayr, Gongshe Hu, Axel Diederichsen, Stephen Harrison, David Hoffman (deceased), Heidi Kaeppler, Art McElroy, Michael McMullen, Jennifer Mitchell Fetch, Rickard Johnsson, Don Obert, Marcelo Pacheco, John Valentine, Weikai Yan, and Ju-Kyung Yu. We also recognize that there are many others who have contributed indirectly but generously to this work.",

year = "2009",

month = jan,

day = "21",

doi = "10.1186/1471-2164-10-39",

language = "English",

volume = "10",

journal = "BMC Genomics",

issn = "1471-2164",

publisher = "Springer Nature",

number = "1",

}

Tinker, NA, Kilian, A, Wight, CP, Heller-Uszynska, K, Wenzl, P, Rines, HW, Bjørnstad, Å, Howarth, CJ, Jannink, JL, Anderson, JM, Rossnagel, BG, Stuthman, DD, Sorrells, ME, Jackson, EW, Tuvesson, S, Kolb, FL, Olsson, O, Federizzi, L, Carson, ML, Ohm, HW, Molnar, SJ, Scoles, GJ, Eckstein, PE, Bonman, JM, Ceplitis, A & Langdon, T 2009, 'New DArT markers for oat provide enhanced map coverage and global germplasm characterization', BMC Genomics, vol. 10, no. 1, 39. https://doi.org/10.1186/1471-2164-10-39

TY - JOUR

T1 - New DArT markers for oat provide enhanced map coverage and global germplasm characterization

AU - Tinker, Nicholas A.

AU - Kilian, Andrzej

AU - Wight, Charlene P.

AU - Heller-Uszynska, Katarzyna

AU - Wenzl, Peter

AU - Rines, Howard W.

AU - Bjørnstad, Åsmund

AU - Howarth, Catherine J.

AU - Jannink, Jean Luc

AU - Anderson, Joseph M.

AU - Rossnagel, Brian G.

AU - Stuthman, Deon D.

AU - Sorrells, Mark E.

AU - Jackson, Eric W.

AU - Tuvesson, Stine

AU - Kolb, Frederic L.

AU - Olsson, Olof

AU - Federizzi, Luiz

AU - Carson, Marty L.

AU - Ohm, Herbert W.

AU - Molnar, Stephen J.

AU - Scoles, Graham J.

AU - Eckstein, Peter E.

AU - Bonman, J. Michael

AU - Ceplitis, Alf

AU - Langdon, Tim

N1 - Funding Information: We are grateful to the following institutions for generous funding that contributed to this work: The Quaker Oats Company [55], Quaker Tropicana Gatorade Canada [56], North American Millers Association [57], CropTai-lor [58], Biotechnology and Biological Sciences Research Council [59], and Anderson -USDA-ARS project 3602-21220-010-00D. At DArT Pty Ltd, a number of people contributed to technology development and data production, especially Eric Huttner, Jason Carling, Vanessa Caig, and Ling Xia. We recognize the excellent technical and professional assistance of many staff and collaborators including Dr. Phillip San Miguel, Allison Witt, and Viktoria Krasnyanskaya. Finally, we thank the following for providing additional germplasm and related information that contributed to this study: Carla Adtorre, Ron Barnett, Aaron Beattie, Howard Bockelman, Vern Burrows, Hermann Bürstmayr, Gongshe Hu, Axel Diederichsen, Stephen Harrison, David Hoffman (deceased), Heidi Kaeppler, Art McElroy, Michael McMullen, Jennifer Mitchell Fetch, Rickard Johnsson, Don Obert, Marcelo Pacheco, John Valentine, Weikai Yan, and Ju-Kyung Yu. We also recognize that there are many others who have contributed indirectly but generously to this work.

PY - 2009/1/21

Y1 - 2009/1/21

N2 - Background Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT). Results Approximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' × 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure. Conclusion These markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity.

AB - Background Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT). Results Approximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' × 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure. Conclusion These markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity.

KW - Avena/genetics

KW - Chromosome Mapping/methods

KW - Cluster Analysis

KW - DNA, Plant/genetics

KW - Genetic Markers

KW - Genome, Plant

KW - Genomic Library

KW - Genotype

KW - Oligonucleotide Array Sequence Analysis

KW - Polymorphism, Genetic

KW - Sequence Analysis, DNA

UR - https://www.scopus.com/pages/publications/63349085766

U2 - 10.1186/1471-2164-10-39

DO - 10.1186/1471-2164-10-39

M3 - Article

C2 - 19159465

SN - 1471-2164

VL - 10

JO - BMC Genomics

JF - BMC Genomics

IS - 1

M1 - 39

ER -

New DArT markers for oat provide enhanced map coverage and global germplasm characterization

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Harnessing new technologies for sustainable oat production and utilisation (QUOATS)

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New DArT markers for oat provide enhanced map coverage and global germplasm characterization

Abstract

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Harnessing new technologies for sustainable oat production and utilisation (QUOATS)

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