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

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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., 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, [17394]. https://doi.org/10.1038/srep17394