A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

Ashley S. Chaffin; Yung-Fen Huang; Scott Smith; Wubishet A. Bekele; Ebrahiem Babiker; Belaghihalli N. Gnanesh; Bradley J. Foresman; Steven G. Blanchard; Jeremy J. Jay; Robert W. Reid; Charlene P. Wight; Shiaoman Chao; Rebekah E. Oliver; Emir Islamovic; Frederic L. Kolb; Curt Mccartney; Jennifer W. Mitchell Fetch; Aaron D. Beattie; Åsmund Bjørnstad; J. Michael Bonman; Timothy Langdon; Catherine Howarth; Cory R. Brouwer; Eric N. Jellen; Kathy Esvelt Klos; Jesse A. Poland; Tzung-fu Hsieh; Ryan Brown; Eric W. Jackson; Jessica A. Schlueter; Nicholas A. Tinker

doi:10.3835/plantgenome2015.10.0102

A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

Ashley S. Chaffin, Yung-Fen Huang, Scott Smith, Wubishet A. Bekele, Ebrahiem Babiker, Belaghihalli N. Gnanesh, Bradley J. Foresman, Steven G. Blanchard, Jeremy J. Jay, Robert W. Reid, Charlene P. Wight, Shiaoman Chao, Rebekah E. Oliver, Emir Islamovic, Frederic L. Kolb, Curt Mccartney, Jennifer W. Mitchell Fetch, Aaron D. Beattie, Åsmund Bjørnstad, J. Michael BonmanTimothy Langdon, Catherine Howarth, Cory R. Brouwer, Eric N. Jellen, Kathy Esvelt Klos, Jesse A. Poland, Tzung-fu Hsieh, Ryan Brown, Eric W. Jackson, Jessica A. Schlueter, Nicholas A. Tinker

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Abstract

Hexaploid oat (Avena sativa L., 2n = 6x = 42) is a member of the Poaceae family and has a large genome (∼12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice (Oryza sativa L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.

Original language	English
Article number	0102
Number of pages	21
Journal	The Plant Genome
Volume	9
Issue number	2
DOIs	https://doi.org/10.3835/plantgenome2015.10.0102
Publication status	Published - 01 Jul 2016

Keywords

Avena/genetics
Chromosome Mapping
Chromosomes, Plant/genetics
Genetic Linkage
Genome, Plant/genetics
Genotype
North America
Polymorphism, Single Nucleotide
Polyploidy
Synteny

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A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome RearrangementFinal published version, 3.14 MBLicence: CC BY-NC-ND
Supporting InformationData, 2.1 MBLicence: CC BY

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Chaffin, A. S., Huang, Y.-F., Smith, S., Bekele, W. A., Babiker, E., Gnanesh, B. N., Foresman, B. J., Blanchard, S. G., Jay, J. J., Reid, R. W., Wight, C. P., Chao, S., Oliver, R. E., Islamovic, E., Kolb, F. L., Mccartney, C., Mitchell Fetch, J. W., Beattie, A. D., Bjørnstad, Å., ... Tinker, N. A. (2016). A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement. The Plant Genome, 9(2), Article 0102. https://doi.org/10.3835/plantgenome2015.10.0102

@article{c7d7bf330df24b488d15570c82209bc7,

title = "A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement",

abstract = "Hexaploid oat (Avena sativa L., 2n = 6x = 42) is a member of the Poaceae family and has a large genome (∼12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice (Oryza sativa L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.",

keywords = "Avena/genetics, Chromosome Mapping, Chromosomes, Plant/genetics, Genetic Linkage, Genome, Plant/genetics, Genotype, North America, Polymorphism, Single Nucleotide, Polyploidy, Synteny",

author = "Chaffin, {Ashley S.} and Yung-Fen Huang and Scott Smith and Bekele, {Wubishet A.} and Ebrahiem Babiker and Gnanesh, {Belaghihalli N.} and Foresman, {Bradley J.} and Blanchard, {Steven G.} and Jay, {Jeremy J.} and Reid, {Robert W.} and Wight, {Charlene P.} and Shiaoman Chao and Oliver, {Rebekah E.} and Emir Islamovic and Kolb, {Frederic L.} and Curt Mccartney and {Mitchell Fetch}, {Jennifer W.} and Beattie, {Aaron D.} and {\AA}smund Bj{\o}rnstad and Bonman, {J. Michael} and Timothy Langdon and Catherine Howarth and Brouwer, {Cory R.} and Jellen, {Eric N.} and {Esvelt Klos}, Kathy and Poland, {Jesse A.} and Tzung-fu Hsieh and Ryan Brown and Jackson, {Eric W.} and Schlueter, {Jessica A.} and Tinker, {Nicholas A.}",

note = "Funding Information: ASC, Y-FH, and SS contributed equally as first authors; JAS and NAT contributed equally as senior corresponding authors. The authors acknowledge the generous support for this project provided to the Collaborative Oat Research Enterprise by General Mills, the North American Millers? Association, the Prairie Oat Growers? Association of Canada, USDANIFA, and Agriculture and Agri-food Canada. We are also grateful to the students and many sponsors of the Plant Pathways Elucidation Project (http://p2ep.org, accessed 9 Mar. 2016). We are indebted to many others, too numerous to mention, who provided excellent advice and technical support to the authors. Financial support to JAS was provided by National Science Foundation (NSF) Award #1444575. Publisher Copyright: {\textcopyright} Her Majesty the Queen in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada. This is an open access article distributed under the CC BY-NC-ND license.",

year = "2016",

month = jul,

day = "1",

doi = "10.3835/plantgenome2015.10.0102",

language = "English",

volume = "9",

journal = "The Plant Genome",

publisher = "Crop Science Society of America",

number = "2",

}

Chaffin, AS, Huang, Y-F, Smith, S, Bekele, WA, Babiker, E, Gnanesh, BN, Foresman, BJ, Blanchard, SG, Jay, JJ, Reid, RW, Wight, CP, Chao, S, Oliver, RE, Islamovic, E, Kolb, FL, Mccartney, C, Mitchell Fetch, JW, Beattie, AD, Bjørnstad, Å, Bonman, JM, Langdon, T , Howarth, C, Brouwer, CR, Jellen, EN, Esvelt Klos, K, Poland, JA, Hsieh, T, Brown, R, Jackson, EW, Schlueter, JA & Tinker, NA 2016, 'A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement', The Plant Genome, vol. 9, no. 2, 0102. https://doi.org/10.3835/plantgenome2015.10.0102

TY - JOUR

T1 - A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

AU - Chaffin, Ashley S.

AU - Huang, Yung-Fen

AU - Smith, Scott

AU - Bekele, Wubishet A.

AU - Babiker, Ebrahiem

AU - Gnanesh, Belaghihalli N.

AU - Foresman, Bradley J.

AU - Blanchard, Steven G.

AU - Jay, Jeremy J.

AU - Reid, Robert W.

AU - Wight, Charlene P.

AU - Chao, Shiaoman

AU - Oliver, Rebekah E.

AU - Islamovic, Emir

AU - Kolb, Frederic L.

AU - Mccartney, Curt

AU - Mitchell Fetch, Jennifer W.

AU - Beattie, Aaron D.

AU - Bjørnstad, Åsmund

AU - Bonman, J. Michael

AU - Langdon, Timothy

AU - Howarth, Catherine

AU - Brouwer, Cory R.

AU - Jellen, Eric N.

AU - Esvelt Klos, Kathy

AU - Poland, Jesse A.

AU - Hsieh, Tzung-fu

AU - Brown, Ryan

AU - Jackson, Eric W.

AU - Schlueter, Jessica A.

AU - Tinker, Nicholas A.

N1 - Funding Information: ASC, Y-FH, and SS contributed equally as first authors; JAS and NAT contributed equally as senior corresponding authors. The authors acknowledge the generous support for this project provided to the Collaborative Oat Research Enterprise by General Mills, the North American Millers? Association, the Prairie Oat Growers? Association of Canada, USDANIFA, and Agriculture and Agri-food Canada. We are also grateful to the students and many sponsors of the Plant Pathways Elucidation Project (http://p2ep.org, accessed 9 Mar. 2016). We are indebted to many others, too numerous to mention, who provided excellent advice and technical support to the authors. Financial support to JAS was provided by National Science Foundation (NSF) Award #1444575. Publisher Copyright: © Her Majesty the Queen in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada. This is an open access article distributed under the CC BY-NC-ND license.

PY - 2016/7/1

Y1 - 2016/7/1

N2 - Hexaploid oat (Avena sativa L., 2n = 6x = 42) is a member of the Poaceae family and has a large genome (∼12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice (Oryza sativa L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.

AB - Hexaploid oat (Avena sativa L., 2n = 6x = 42) is a member of the Poaceae family and has a large genome (∼12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice (Oryza sativa L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.

KW - Avena/genetics

KW - Chromosome Mapping

KW - Chromosomes, Plant/genetics

KW - Genetic Linkage

KW - Genome, Plant/genetics

KW - Genotype

KW - North America

KW - Polymorphism, Single Nucleotide

KW - Polyploidy

KW - Synteny

UR - http://hdl.handle.net/2160/43236

UR - http://www.scopus.com/inward/record.url?scp=84969885731&partnerID=8YFLogxK

U2 - 10.3835/plantgenome2015.10.0102

DO - 10.3835/plantgenome2015.10.0102

M3 - Article

C2 - 27898818

VL - 9

JO - The Plant Genome

JF - The Plant Genome

IS - 2

M1 - 0102

ER -

A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

Abstract

Keywords

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Catherine Howarth

Tim Langdon

Other countries partnering award, Canada; Common Genomics Platfomrs for Oat Breeding

Developing enhanced breeding methodologies for oats for human health and nutrition SEE 11855

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

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

Cite this

A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

Abstract

Keywords

Access to Document

Permanent link

Other files and links

Fingerprint

Profiles

Catherine Howarth

Tim Langdon

Projects

Other countries partnering award, Canada; Common Genomics Platfomrs for Oat Breeding

Developing enhanced breeding methodologies for oats for human health and nutrition SEE 11855

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

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

Cite this