Geographical distribution of genetic diversity in Secale landrace and wild accessions
Abstract Background Rye, Secale cereale L. , has historically been a crop of major importance and is still a key cereal in many parts of Europe. Single populations of cultivated rye have been shown to capture a large proportion of the genetic diversity present in the species, but the distribution of...
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ftbiomed:oai:biomedcentral.com:s12870-016-0710-y 2023-05-15T16:13:47+02:00 Geographical distribution of genetic diversity in Secale landrace and wild accessions Hagenblad, Jenny Oliveira, Hugo Forsberg, Nils Leino, Matti 2016-01-19 http://www.biomedcentral.com/1471-2229/16/23 en eng BioMed Central Ltd. http://www.biomedcentral.com/1471-2229/16/23 Copyright 2016 Hagenblad et al. Rye Population structure SNP Ascertainment bias Genetic variation Phylogeography Research article 2016 ftbiomed 2016-01-24T01:08:33Z Abstract Background Rye, Secale cereale L. , has historically been a crop of major importance and is still a key cereal in many parts of Europe. Single populations of cultivated rye have been shown to capture a large proportion of the genetic diversity present in the species, but the distribution of genetic diversity in subspecies and across geographical areas is largely unknown. Here we explore the structure of genetic diversity in landrace rye and relate it to that of wild and feral relatives. Results A total of 567 SNPs were analysed in 434 individuals from 76 accessions of wild, feral and cultivated rye. Genetic diversity was highest in cultivated rye, slightly lower in feral rye taxa and significantly lower in the wild S. strictum Presl. and S. africanum Stapf. Evaluation of effects from ascertainment bias suggests underestimation of diversity primarily in S. strictum and S. africanum . Levels of ascertainment bias, STRUCTURE and principal component analyses all supported the proposed classification of S. africanum and S. strictum as a separate species from S. cereale. S. afghanicum (Vav.) Roshev , S. ancestrale Zhuk. , S. dighoricum (Vav.) Roshev , S. segetale (Zhuk.) Roshev and S. vavilovii Grossh. seemed, in contrast, to share the same gene pool as S. cereale and their genetic clustering was more dependent on geographical origin than taxonomic classification. S. vavilovii was found to be the most likely wild ancestor of cultivated rye. Among cultivated rye landraces from Europe, Asia and North Africa five geographically discrete genetic clusters were identified. These had only limited overlap with major agro-climatic zones. Slash-and-burn rye from the Finnmark area in Scandinavia formed a distinct cluster with little similarity to other landrace ryes. Regional studies of Northern and South-West Europe demonstrate different genetic distribution patterns as a result of varying cultivation intensity. Conclusions With the exception of S. strictum and S. africanum different rye taxa share the majority of the genetic variation. Due to the vast sharing of genetic diversity within the S. cereale clade, ascertainment bias seems to be a lesser problem in rye than in predominantly selfing species. By exploiting within accession diversity geographic structure can be shown on a much finer scale than previously reported. Article in Journal/Newspaper Finnmark Finnmark BioMed Central |
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BioMed Central |
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English |
topic |
Rye Population structure SNP Ascertainment bias Genetic variation Phylogeography |
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Rye Population structure SNP Ascertainment bias Genetic variation Phylogeography Hagenblad, Jenny Oliveira, Hugo Forsberg, Nils Leino, Matti Geographical distribution of genetic diversity in Secale landrace and wild accessions |
topic_facet |
Rye Population structure SNP Ascertainment bias Genetic variation Phylogeography |
description |
Abstract Background Rye, Secale cereale L. , has historically been a crop of major importance and is still a key cereal in many parts of Europe. Single populations of cultivated rye have been shown to capture a large proportion of the genetic diversity present in the species, but the distribution of genetic diversity in subspecies and across geographical areas is largely unknown. Here we explore the structure of genetic diversity in landrace rye and relate it to that of wild and feral relatives. Results A total of 567 SNPs were analysed in 434 individuals from 76 accessions of wild, feral and cultivated rye. Genetic diversity was highest in cultivated rye, slightly lower in feral rye taxa and significantly lower in the wild S. strictum Presl. and S. africanum Stapf. Evaluation of effects from ascertainment bias suggests underestimation of diversity primarily in S. strictum and S. africanum . Levels of ascertainment bias, STRUCTURE and principal component analyses all supported the proposed classification of S. africanum and S. strictum as a separate species from S. cereale. S. afghanicum (Vav.) Roshev , S. ancestrale Zhuk. , S. dighoricum (Vav.) Roshev , S. segetale (Zhuk.) Roshev and S. vavilovii Grossh. seemed, in contrast, to share the same gene pool as S. cereale and their genetic clustering was more dependent on geographical origin than taxonomic classification. S. vavilovii was found to be the most likely wild ancestor of cultivated rye. Among cultivated rye landraces from Europe, Asia and North Africa five geographically discrete genetic clusters were identified. These had only limited overlap with major agro-climatic zones. Slash-and-burn rye from the Finnmark area in Scandinavia formed a distinct cluster with little similarity to other landrace ryes. Regional studies of Northern and South-West Europe demonstrate different genetic distribution patterns as a result of varying cultivation intensity. Conclusions With the exception of S. strictum and S. africanum different rye taxa share the majority of the genetic variation. Due to the vast sharing of genetic diversity within the S. cereale clade, ascertainment bias seems to be a lesser problem in rye than in predominantly selfing species. By exploiting within accession diversity geographic structure can be shown on a much finer scale than previously reported. |
format |
Article in Journal/Newspaper |
author |
Hagenblad, Jenny Oliveira, Hugo Forsberg, Nils Leino, Matti |
author_facet |
Hagenblad, Jenny Oliveira, Hugo Forsberg, Nils Leino, Matti |
author_sort |
Hagenblad, Jenny |
title |
Geographical distribution of genetic diversity in Secale landrace and wild accessions |
title_short |
Geographical distribution of genetic diversity in Secale landrace and wild accessions |
title_full |
Geographical distribution of genetic diversity in Secale landrace and wild accessions |
title_fullStr |
Geographical distribution of genetic diversity in Secale landrace and wild accessions |
title_full_unstemmed |
Geographical distribution of genetic diversity in Secale landrace and wild accessions |
title_sort |
geographical distribution of genetic diversity in secale landrace and wild accessions |
publisher |
BioMed Central Ltd. |
publishDate |
2016 |
url |
http://www.biomedcentral.com/1471-2229/16/23 |
genre |
Finnmark Finnmark |
genre_facet |
Finnmark Finnmark |
op_relation |
http://www.biomedcentral.com/1471-2229/16/23 |
op_rights |
Copyright 2016 Hagenblad et al. |
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1765999625455534080 |