Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement

Jose J De Vega, Sarah Ayling, Matthew Hegarty, Dave Kudrna, Jose L Goicoechea, Åshild Ergon, Odd A Rognli, Charlotte Jones, Martin Swain, Rene Geurts, Chunting Lang, Klaus F X Mayer, Stephan Rössner, Steven Yates, Kathleen J Webb, Iain S Donnison, Giles E D Oldroyd, Rod A Wing, Mario Caccamo, Wayne PowellMichael T Abberton, Leif Skøt

Research output: Contribution to journalArticle

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Abstract

Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems. It is an attractive component of grassland farming, because of its high yield and protein content, nutritional value and ability to fix atmospheric nitrogen. Enhancing its role further in sustainable agriculture requires genetic improvement of persistency, disease resistance, and tolerance to grazing. To help address these challenges, we have assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection.

Original languageEnglish
Article number17394
JournalScientific Reports
Volume5
DOIs
Publication statusPrint publication - 30 Nov 2015

Fingerprint

Trifolium
Agriculture
Genome
Livestock
Medicago truncatula
Synteny
Disease Resistance
Nutritive Value
Multigene Family
Genomics
Fabaceae
Breeding
Nitrogen
Chromosomes
Genotype
Population
Genes
Proteins

Keywords

  • Computational Biology/methods
  • Genes, Plant
  • Genome, Plant
  • Genomics/methods
  • Linkage Disequilibrium
  • Molecular Sequence Annotation
  • Multigene Family
  • Phenotype
  • Quantitative Trait, Heritable
  • Sequence Analysis, DNA
  • Trifolium/genetics

Cite this

De Vega, J. J., Ayling, S., Hegarty, M., Kudrna, D., Goicoechea, J. L., Ergon, Å., ... Skøt, L. (2015). Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. Scientific Reports, 5, [17394]. https://doi.org/10.1038/srep17394
De Vega, Jose J ; Ayling, Sarah ; Hegarty, Matthew ; Kudrna, Dave ; Goicoechea, Jose L ; Ergon, Åshild ; Rognli, Odd A ; Jones, Charlotte ; Swain, Martin ; Geurts, Rene ; Lang, Chunting ; Mayer, Klaus F X ; Rössner, Stephan ; Yates, Steven ; Webb, Kathleen J ; Donnison, Iain S ; Oldroyd, Giles E D ; Wing, Rod A ; Caccamo, Mario ; Powell, Wayne ; Abberton, Michael T ; Skøt, Leif. / Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. In: Scientific Reports. 2015 ; Vol. 5.
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abstract = "Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems. It is an attractive component of grassland farming, because of its high yield and protein content, nutritional value and ability to fix atmospheric nitrogen. Enhancing its role further in sustainable agriculture requires genetic improvement of persistency, disease resistance, and tolerance to grazing. To help address these challenges, we have assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection.",
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De Vega, JJ, Ayling, S, Hegarty, M, Kudrna, D, Goicoechea, JL, Ergon, Å, Rognli, OA, Jones, C, Swain, M, Geurts, R, Lang, C, Mayer, KFX, Rössner, S, Yates, S, Webb, KJ, Donnison, IS, Oldroyd, GED, Wing, RA, Caccamo, M, Powell, W, Abberton, MT & Skøt, L 2015, 'Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement', Scientific Reports, vol. 5, 17394. https://doi.org/10.1038/srep17394

Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. / De Vega, Jose J; Ayling, Sarah; Hegarty, Matthew; Kudrna, Dave; Goicoechea, Jose L; Ergon, Åshild; Rognli, Odd A; Jones, Charlotte; Swain, Martin; Geurts, Rene; Lang, Chunting; Mayer, Klaus F X; Rössner, Stephan; Yates, Steven; Webb, Kathleen J; Donnison, Iain S; Oldroyd, Giles E D; Wing, Rod A; Caccamo, Mario; Powell, Wayne; Abberton, Michael T; Skøt, Leif.

In: Scientific Reports, Vol. 5, 17394, 30.11.2015.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement

AU - De Vega, Jose J

AU - Ayling, Sarah

AU - Hegarty, Matthew

AU - Kudrna, Dave

AU - Goicoechea, Jose L

AU - Ergon, Åshild

AU - Rognli, Odd A

AU - Jones, Charlotte

AU - Swain, Martin

AU - Geurts, Rene

AU - Lang, Chunting

AU - Mayer, Klaus F X

AU - Rössner, Stephan

AU - Yates, Steven

AU - Webb, Kathleen J

AU - Donnison, Iain S

AU - Oldroyd, Giles E D

AU - Wing, Rod A

AU - Caccamo, Mario

AU - Powell, Wayne

AU - Abberton, Michael T

AU - Skøt, Leif

PY - 2015/11/30

Y1 - 2015/11/30

N2 - Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems. It is an attractive component of grassland farming, because of its high yield and protein content, nutritional value and ability to fix atmospheric nitrogen. Enhancing its role further in sustainable agriculture requires genetic improvement of persistency, disease resistance, and tolerance to grazing. To help address these challenges, we have assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection.

AB - Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems. It is an attractive component of grassland farming, because of its high yield and protein content, nutritional value and ability to fix atmospheric nitrogen. Enhancing its role further in sustainable agriculture requires genetic improvement of persistency, disease resistance, and tolerance to grazing. To help address these challenges, we have assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection.

KW - Computational Biology/methods

KW - Genes, Plant

KW - Genome, Plant

KW - Genomics/methods

KW - Linkage Disequilibrium

KW - Molecular Sequence Annotation

KW - Multigene Family

KW - Phenotype

KW - Quantitative Trait, Heritable

KW - Sequence Analysis, DNA

KW - Trifolium/genetics

U2 - 10.1038/srep17394

DO - 10.1038/srep17394

M3 - Article

C2 - 26617401

VL - 5

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

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ER -

De Vega JJ, Ayling S, Hegarty M, Kudrna D, Goicoechea JL, Ergon Å et al. Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. Scientific Reports. 2015 Nov 30;5. 17394. https://doi.org/10.1038/srep17394