Intraspecific diversification of the crop wild relative Brassica cretica Lam. using demographic model selection
dc.contributor.author | Kioukis, A | |
dc.contributor.author | Michalopoulou, VA | |
dc.contributor.author | Briers, L | |
dc.contributor.author | Pirintsos, S | |
dc.contributor.author | Studholme, DJ | |
dc.contributor.author | Pavlidis, P | |
dc.contributor.author | Sarris, PF | |
dc.date.accessioned | 2020-01-24T09:06:19Z | |
dc.date.issued | 2020-01-14 | |
dc.description.abstract | BACKGROUND: Crop wild relatives (CWRs) contain genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops to adapt to changing conditions that they experience due to climate change. An impressive global effort for the conservation of various CWR will facilitate their use in crop breeding for food security. The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage), a species native to southern and western Europe, has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves. Brassica cretica Lam. (Bc) is a CWR in the brassica group and B. cretica subsp. nivea (Bcn) has been suggested as a separate subspecies. The species Bc has been proposed as a potential gene donor to brassica crops, including broccoli, cabbage, cauliflower, oilseed rape, etc. RESULTS: We sequenced genomes of four Bc individuals, including two Bcn and two Bc. Demographic analysis based on our whole-genome sequence data suggests that populations of Bc are not isolated. Classification of the Bc into distinct subspecies is not supported by the data. Using only the non-coding part of the data (thus, the parts of the genome that has evolved nearly neutrally), we find the gene flow between different Bc population is recent and its genomic diversity is high. CONCLUSIONS: Despite predictions on the disruptive effect of gene flow in adaptation, when selection is not strong enough to prevent the loss of locally adapted alleles, studies show that gene flow can promote adaptation, that local adaptations can be maintained despite high gene flow, and that genetic architecture plays a fundamental role in the origin and maintenance of local adaptation with gene flow. Thus, in the genomic era it is important to link the selected demographic models with the underlying processes of genomic variation because, if this variation is largely selectively neutral, we cannot assume that a diverse population of crop wild relatives will necessarily exhibit the wide-ranging adaptive diversity required for further crop improvement. | en_GB |
dc.description.sponsorship | Gatsby Foundation | en_GB |
dc.identifier.citation | Vol. 21, article 48 | en_GB |
dc.identifier.doi | 10.1186/s12864-019-6439-x | |
dc.identifier.uri | http://hdl.handle.net/10871/40552 | |
dc.language.iso | en | en_GB |
dc.publisher | BMC (part of Springer Nature) | en_GB |
dc.relation.url | https://www.ncbi.nlm.nih.gov/pubmed/31937246 | en_GB |
dc.rights | © The Author(s). 2020. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. | en_GB |
dc.subject | Brassica cretica Lam. | en_GB |
dc.subject | Brassica oleracea | en_GB |
dc.subject | Crop wild relatives | en_GB |
dc.subject | Draft genome | en_GB |
dc.subject | de novo sequencing | en_GB |
dc.title | Intraspecific diversification of the crop wild relative Brassica cretica Lam. using demographic model selection | en_GB |
dc.type | Article | en_GB |
dc.date.available | 2020-01-24T09:06:19Z | |
exeter.place-of-publication | England | en_GB |
dc.description | This is the final version. Available from BMC via the DOI in this record. | en_GB |
dc.description | All genome sequence assemblies and genomic sequence reads are freely available from GenBank and the Sequence Read Archive respectively under BioProject accession PRJNA470925. The GenBank accession numbers for the assemblies are: Brassica cretica PFS-1207/04: GCA_003260655.1 & GCA_003260655.2; Brassica cretica PFS-001/15: GCA_003260635.1 & GCA_003260635.2; Brassica cretica PFS-109/04: GCA_003260675.1 & GCA_003260675.2; and Brassica cretica PFS-102/07: GCA_003260695.1 & GCA_003260695.2. | en_GB |
dc.identifier.journal | BMC Genomics | en_GB |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | en_GB |
dcterms.dateAccepted | 2019-12-29 | |
exeter.funder | ::Gatsby Foundation | en_GB |
rioxxterms.version | VoR | en_GB |
rioxxterms.licenseref.startdate | 2019-12-29 | |
rioxxterms.type | Journal Article/Review | en_GB |
refterms.dateFCD | 2020-01-24T08:58:43Z | |
refterms.versionFCD | VoR | |
refterms.dateFOA | 2020-01-24T09:06:33Z | |
refterms.panel | A | en_GB |
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Except where otherwise noted, this item's licence is described as © The Author(s). 2020. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.