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 (US)
Article number	17394
Journal	Scientific reports
Volume	5
DOIs	https://doi.org/10.1038/srep17394
State	Published - Nov 30 2015

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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. https://doi.org/10.1038/srep17394

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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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.",

author = "{De Vega}, {Jose J.} and Sarah Ayling and Matthew Hegarty and Dave Kudrna and Goicoechea, {Jose L.} and {\AA}shild Ergon and Rognli, {Odd A.} and Charlotte Jones and Martin Swain and Rene Geurts and Chunting Lang and Mayer, {Klaus F.X.} and Stephan R{\"o}ssner and Steven Yates and Webb, {Kathleen J.} and Donnison, {Iain S.} and Oldroyd, {Giles E.D.} and Wing, {Rod A.} and Mario Caccamo and Wayne Powell and Abberton, {Michael T.} and Leif Sk{\o}t",

note = "Funding Information: This work was funded by an Institute Programme Grant to IBERS (BB/J004405/1) from the Biotechnology and Biological Sciences Research Council (BBSRC), by the ERANET Plant Genomics programme (ERAPG038A-TRANSLEG) and by a Capacity, Capability Challenge Programme from TGAC. The R-script for the landscape plots of LD, the predicted r2 and the average LD was kindly provided by Lei Wang, Department of Molecular Biology and Genetics, Aarhus University, Denmark, and modifications of the R-scripts for red clover were provided by Dr Nastasiya F. Grinberg, Manchester Institute of Biotechnology, Manchester University, UK.",

year = "2015",

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day = "30",

doi = "10.1038/srep17394",

language = "English (US)",

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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

N1 - Funding Information: This work was funded by an Institute Programme Grant to IBERS (BB/J004405/1) from the Biotechnology and Biological Sciences Research Council (BBSRC), by the ERANET Plant Genomics programme (ERAPG038A-TRANSLEG) and by a Capacity, Capability Challenge Programme from TGAC. The R-script for the landscape plots of LD, the predicted r2 and the average LD was kindly provided by Lei Wang, Department of Molecular Biology and Genetics, Aarhus University, Denmark, and modifications of the R-scripts for red clover were provided by Dr Nastasiya F. Grinberg, Manchester Institute of Biotechnology, Manchester University, UK.

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.

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

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