Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm

Charlotte Jones, Jose de Vega, David Lloyd, Matthew Hegarty, Sarah Ayling, Wayne Powell, Leif Skot

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Red clover (Trifolium pratense L.) is a highly adaptable forage crop for temperate livestock agriculture. Genetic variation can be identified, via molecular techniques, and used to assess diversity among populations that may otherwise be indistinguishable. Here we have used genotyping by sequencing (GBS) to determine the genetic variation and population structure in red clover natural populations from Europe and Asia, and varieties or synthetic populations. Cluster analysis differentiated the collection into four large regional groups: Asia, Iberia, UK, and Central Europe. The five varieties clustered with the geographical area from which they were derived. Two methods (BayeScan and Samβada) were used to search for outlier loci indicating signatures of selection. A total of 60 loci were identified by both methods, but no specific genomic region was highlighted. The rate of decay in linkage disequilibrium was fast, and no significant evidence of any bottlenecks was found. Phenotypic analysis showed that a more prostrate and spreading growth habit was predominantly found among populations from Iberia and the UK. A genome wide association study identified a single nucleotide polymorphism (SNP) located in a homologue of the VEG2 gene from pea, associated with flowering time. The identification of genetic variation within the natural populations is likely to be useful for enhancing the breeding of red clover in the future.
Original languageEnglish
Article number8364
Number of pages12
JournalScientific Reports
Issue number1
Early online date20 May 2020
Publication statusPublished - 01 Dec 2020


  • Asia
  • Chromosome Mapping
  • Cluster Analysis
  • Crops, Agricultural/genetics
  • Genome, Plant/genetics
  • Genome-Wide Association Study
  • Linkage Disequilibrium
  • Phylogeography
  • Plant Breeding
  • Polymorphism, Single Nucleotide
  • Selection, Genetic
  • Spain
  • Trifolium/genetics
  • United Kingdom


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