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 Powell & 2 others Michael T Abberton, Leif Skøt

    Research output: Contribution to journalArticleResearchpeer-review

    33 Citations (Scopus)

    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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    month = "11",
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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 journalArticleResearchpeer-review

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    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

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    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

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    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