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ToolsJones, Charlotte, De Vega, Jose, Lloyd, David, Hegarty, Matthew, Ayling, Sarah, Powell, Wayne and Skøt, Leif (2020) Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm. Scientific Reports, 10. ISSN 2045-2322
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Abstract
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.
| Item Type: | Article |
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| Additional Information: | Data availability: The genotypic data have been deposited as raw sequence reads in the NCBI database under BioProject PRJEB30826 and phenotypic data are available upon request from the corresponding author. Acknowledgements: This work was supported by an Industrial Partnership Award from the Biotechnology and Biological Sciences Research Council (BBSRC) to IBERS (BB/L023563/1) and the Earlham Institute (BB/L022257/1). We are grateful for the support from our industrial partner Germinal Holdings Ltd. We wish to thank Jim Vale and his team for assistance with the field trial. |
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| Depositing User: | LivePure Connector |
| Date Deposited: | 02 Sep 2025 14:30 |
| Last Modified: | 07 Sep 2025 06:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/100270 |
| DOI: | 10.1038/s41598-020-64989-z |
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