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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Autores principales:	Charlotte Jones, Jose De Vega, David Lloyd, Matthew Hegarty, Sarah Ayling, Wayne Powell, Leif Skøt
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4b903f6690654efb92621e3c75c5d021
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spelling	oai:doaj.org-article:4b903f6690654efb92621e3c75c5d0212021-12-02T14:59:12ZPopulation structure and genetic diversity in red clover (Trifolium pratense L.) germplasm10.1038/s41598-020-64989-z2045-2322https://doaj.org/article/4b903f6690654efb92621e3c75c5d0212020-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-64989-zhttps://doaj.org/toc/2045-2322Abstract 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.Charlotte JonesJose De VegaDavid LloydMatthew HegartySarah AylingWayne PowellLeif SkøtNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-12 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q 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
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.
format	article
author	Charlotte Jones Jose De Vega David Lloyd Matthew Hegarty Sarah Ayling Wayne Powell Leif Skøt
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 Portfolio
publishDate	2020
url	https://doaj.org/article/4b903f6690654efb92621e3c75c5d021
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Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm

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