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.
authors.affiliation: The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK.|Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion SY23 3EB, UK.
authors.forename: Jose J
authors.initials: JJ
authors.lastname: De Vega
authors.affiliation: The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
authors.forename: Sarah
authors.initials: S
authors.lastname: Ayling
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion SY23 3EB, UK.
authors.forename: Matthew
authors.initials: M
authors.lastname: Hegarty
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson AZ 85721, USA.
authors.forename: Dave
authors.initials: D
authors.lastname: Kudrna
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson AZ 85721, USA.
authors.forename: Jose L
authors.initials: JL
authors.lastname: Goicoechea
authors.affiliation: Norwegian University of Life Sciences, Department of Plant Sciences, N-1432, Ås, Norway.
authors.forename: Åshild
authors.initials: Å
authors.lastname: Ergon
authors.affiliation: Norwegian University of Life Sciences, Department of Plant Sciences, N-1432, Ås, Norway.
authors.forename: Odd A
authors.initials: OA
authors.lastname: Rognli
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion SY23 3EB, UK.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Jones
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion SY23 3EB, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Swain
authors.affiliation: Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands.
authors.forename: Rene
authors.initials: R
authors.lastname: Geurts
authors.affiliation: Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands.
authors.forename: Chunting
authors.initials: C
authors.lastname: Lang
authors.affiliation: MIPS/Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, Ingolstädter Landstrasse 1, Neuherberg, Germany.
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.affiliation: MIPS/Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, Ingolstädter Landstrasse 1, Neuherberg, Germany.
authors.forename: Stephan
authors.initials: S
authors.lastname: Rössner
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion SY23 3EB, UK.|Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, CH-8092, Zurich, Switzerland.
authors.forename: Steven
authors.initials: S
authors.lastname: Yates
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion SY23 3EB, UK.
authors.forename: Kathleen J
authors.initials: KJ
authors.lastname: Webb
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion SY23 3EB, UK.
authors.forename: Iain S
authors.initials: IS
authors.lastname: Donnison
authors.affiliation: Department of Disease and Stress Biology, John Innes Centre, Norwich NR4 7UH, UK.
authors.forename: Giles E D
authors.initials: GE
authors.lastname: Oldroyd
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson AZ 85721, USA.
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
authors.affiliation: The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
authors.forename: Mario
authors.initials: M
authors.lastname: Caccamo
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion SY23 3EB, UK.|CGIAR Consortium Office 1000, Avenue Agropolis, F-34394, Montpellier, Cedex 5, France.
authors.forename: Wayne
authors.initials: W
authors.lastname: Powell
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion SY23 3EB, UK.|International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan, Nigeria.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Abberton
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion SY23 3EB, UK.
authors.forename: Leif
authors.initials: L
authors.lastname: Skøt
mesh_terms: D019295:Computational Biology / Q000379:methods; D017343:Genes, Plant; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D015810:Linkage Disequilibrium; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D010641:Phenotype; D019655:Quantitative Trait, Heritable; D017422:Sequence Analysis, DNA; D029921:Trifolium / Q000235:genetics*