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; Michael T Abberton; Leif Skøt

doi:10.1038/srep17394

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

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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 language	English
Article number	17394
Journal	Scientific Reports
Volume	5
Early online date	30 Nov 2015
DOIs	https://doi.org/10.1038/srep17394
Publication status	First published - 30 Nov 2015

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

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De Vega, J. J., Ayling, S., Hegarty, M., Kudrna, D., Goicoechea, J. L., Ergon, Å., Rognli, O. A., Jones, C., Swain, M., Geurts, R., Lang, C., Mayer, K. F. X., Rössner, S., Yates, S., Webb, K. J., Donnison, I. S., Oldroyd, G. E. D., Wing, R. A., Caccamo, M., ... Skøt, L. (2015). Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. Scientific Reports, 5, Article 17394. Advance online publication. https://doi.org/10.1038/srep17394

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

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. ",

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",

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doi = "10.1038/srep17394",

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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

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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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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

SN - 2045-2322

VL - 5

JO - Scientific Reports

JF - Scientific Reports

M1 - 17394

ER -

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

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Keywords

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