Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm
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 se...
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doaj-4b903f6690654efb92621e3c75c5d0212021-05-23T11:38:44ZengNature Publishing GroupScientific Reports2045-23222020-05-0110111210.1038/s41598-020-64989-zPopulation structure and genetic diversity in red clover (Trifolium pratense L.) germplasmCharlotte Jones0Jose De Vega1David Lloyd2Matthew Hegarty3Sarah Ayling4Wayne Powell5Leif Skøt6Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityThe Earlham Institute, Norwich Research ParkInstitute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityInstitute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityThe Earlham Institute, Norwich Research ParkInstitute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityInstitute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAbstract 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.https://doi.org/10.1038/s41598-020-64989-z |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Charlotte Jones Jose De Vega David Lloyd Matthew Hegarty Sarah Ayling Wayne Powell Leif Skøt |
spellingShingle |
Charlotte Jones Jose De Vega David Lloyd Matthew Hegarty Sarah Ayling Wayne Powell Leif Skøt Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm Scientific Reports |
author_facet |
Charlotte Jones Jose De Vega David Lloyd Matthew Hegarty Sarah Ayling Wayne Powell Leif Skøt |
author_sort |
Charlotte Jones |
title |
Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm |
title_short |
Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm |
title_full |
Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm |
title_fullStr |
Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm |
title_full_unstemmed |
Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm |
title_sort |
population structure and genetic diversity in red clover (trifolium pratense l.) germplasm |
publisher |
Nature Publishing Group |
series |
Scientific Reports |
issn |
2045-2322 |
publishDate |
2020-05-01 |
description |
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. |
url |
https://doi.org/10.1038/s41598-020-64989-z |
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