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 Oliver, Emir Islamovic, Frederic L. Kolb, Curt McCartney, Jennifer W. Mitchell Fetch, Aaron D. Beattie, Åsmund Bjørnstad, J. Michael BonmanTim Langdon, Catherine J. Howarth, Cory R. Brouwer, Eric N. Jellen, Kathy Esvelt Klos, Jesse A. Poland, Tzung Fu Hsieh, Ryan Brown, Eric Jackson, Jessica A. Schlueter, Nicholas A. Tinker

Research output: Contribution to journalArticle

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 languageEnglish (US)
JournalPlant Genome
Volume9
Issue number2
DOIs
StatePublished - Jul 2016

Fingerprint

Synteny
hexaploidy
Poaceae
oats
Consensus
Genome
grasses
chromosomes
Chromosomes
genome
linkage groups
Chromosomes, Human, Pair 21
chromosome mapping
Population
chromosome translocation
Avena sativa
North America
Diploidy
inbred lines
genotyping

ASJC Scopus subject areas

  • Genetics
  • Agronomy and Crop Science
  • Plant Science

Cite this

Chaffin, A. S., Huang, Y. F., Smith, S., Bekele, W. A., Babiker, E., Gnanesh, B. N., ... Tinker, N. A. (2016). A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial subgenome rearrangement. Plant Genome, 9(2). https://doi.org/10.3835/plantgenome2015.10.0102

A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial subgenome rearrangement. / Chaffin, Ashley S.; Huang, Yung Fen; Smith, Scott; Bekele, Wubishet A.; Babiker, Ebrahiem; Gnanesh, Belaghihalli N.; Foresman, Bradley J.; Blanchard, Steven G.; Jay, Jeremy J.; Reid, Robert W.; Wight, Charlene P.; Chao, Shiaoman; Oliver, Rebekah; Islamovic, Emir; Kolb, Frederic L.; McCartney, Curt; Mitchell Fetch, Jennifer W.; Beattie, Aaron D.; Bjørnstad, Åsmund; Michael Bonman, J.; Langdon, Tim; Howarth, Catherine J.; Brouwer, Cory R.; Jellen, Eric N.; Klos, Kathy Esvelt; Poland, Jesse A.; Hsieh, Tzung Fu; Brown, Ryan; Jackson, Eric; Schlueter, Jessica A.; Tinker, Nicholas A.

In: Plant Genome, Vol. 9, No. 2, 07.2016.

Research output: Contribution to journalArticle

Chaffin, AS, Huang, YF, Smith, S, Bekele, WA, Babiker, E, Gnanesh, BN, Foresman, BJ, Blanchard, SG, Jay, JJ, Reid, RW, Wight, CP, Chao, S, Oliver, R, Islamovic, E, Kolb, FL, McCartney, C, Mitchell Fetch, JW, Beattie, AD, Bjørnstad, Å, Michael Bonman, J, Langdon, T, Howarth, CJ, Brouwer, CR, Jellen, EN, Klos, KE, Poland, JA, Hsieh, TF, Brown, R, Jackson, E, Schlueter, JA & Tinker, NA 2016, 'A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial subgenome rearrangement', Plant Genome, vol. 9, no. 2. https://doi.org/10.3835/plantgenome2015.10.0102
Chaffin, Ashley S. ; Huang, Yung Fen ; Smith, Scott ; Bekele, Wubishet A. ; Babiker, Ebrahiem ; Gnanesh, Belaghihalli N. ; Foresman, Bradley J. ; Blanchard, Steven G. ; Jay, Jeremy J. ; Reid, Robert W. ; Wight, Charlene P. ; Chao, Shiaoman ; Oliver, Rebekah ; Islamovic, Emir ; Kolb, Frederic L. ; McCartney, Curt ; Mitchell Fetch, Jennifer W. ; Beattie, Aaron D. ; Bjørnstad, Åsmund ; Michael Bonman, J. ; Langdon, Tim ; Howarth, Catherine J. ; Brouwer, Cory R. ; Jellen, Eric N. ; Klos, Kathy Esvelt ; Poland, Jesse A. ; Hsieh, Tzung Fu ; Brown, Ryan ; Jackson, Eric ; Schlueter, Jessica A. ; Tinker, Nicholas A. / A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial subgenome rearrangement. In: Plant Genome. 2016 ; Vol. 9, No. 2.
@article{808b08d8a741415a994b076d58f7835f,
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.",
author = "Chaffin, {Ashley S.} and Huang, {Yung Fen} 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 Rebekah Oliver 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 {Michael Bonman}, J. and Tim Langdon and Howarth, {Catherine J.} and Brouwer, {Cory R.} and Jellen, {Eric N.} and Klos, {Kathy Esvelt} and Poland, {Jesse A.} and Hsieh, {Tzung Fu} and Ryan Brown and Eric Jackson and Schlueter, {Jessica A.} and Tinker, {Nicholas A.}",
year = "2016",
month = "7",
doi = "10.3835/plantgenome2015.10.0102",
language = "English (US)",
volume = "9",
journal = "Plant Genome",
issn = "1940-3372",
publisher = "Crop Science Society of America",
number = "2",

}

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

AU - Islamovic, Emir

AU - Kolb, Frederic L.

AU - McCartney, Curt

AU - Mitchell Fetch, Jennifer W.

AU - Beattie, Aaron D.

AU - Bjørnstad, Åsmund

AU - Michael Bonman, J.

AU - Langdon, Tim

AU - Howarth, Catherine J.

AU - Brouwer, Cory R.

AU - Jellen, Eric N.

AU - Klos, Kathy Esvelt

AU - Poland, Jesse A.

AU - Hsieh, Tzung Fu

AU - Brown, Ryan

AU - Jackson, Eric

AU - Schlueter, Jessica A.

AU - Tinker, Nicholas A.

PY - 2016/7

Y1 - 2016/7

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.

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

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

U2 - 10.3835/plantgenome2015.10.0102

DO - 10.3835/plantgenome2015.10.0102

M3 - Article

C2 - 27898818

AN - SCOPUS:84969885731

VL - 9

JO - Plant Genome

JF - Plant Genome

SN - 1940-3372

IS - 2

ER -