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Article: Genome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber

TitleGenome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber
Authors
Issue Date2015
Citation
Plant Cell, 2015, v. 27, n. 6, p. 1595-1604 How to Cite?
Abstract© 2015 American Society of Plant Biologists. All rights reserved. Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated break-induced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber.
Persistent Identifierhttp://hdl.handle.net/10722/251112
ISSN
2023 Impact Factor: 10.0
2023 SCImago Journal Rankings: 3.616
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorZhang, Zhonghua-
dc.contributor.authorMao, Linyong-
dc.contributor.authorChen, Huiming-
dc.contributor.authorBu, Fengjiao-
dc.contributor.authorLi, Guangcun-
dc.contributor.authorSun, Jinjing-
dc.contributor.authorLi, Shuai-
dc.contributor.authorSun, Honghe-
dc.contributor.authorJiao, Chen-
dc.contributor.authorBlakely, Rachel-
dc.contributor.authorPan, Junsong-
dc.contributor.authorCai, Run-
dc.contributor.authorLuo, Ruibang-
dc.contributor.authorVan de Peer, Yves-
dc.contributor.authorJacobsen, Evert-
dc.contributor.authorFei, Zhangjun-
dc.contributor.authorHuang, Sanwen-
dc.date.accessioned2018-02-01T01:54:37Z-
dc.date.available2018-02-01T01:54:37Z-
dc.date.issued2015-
dc.identifier.citationPlant Cell, 2015, v. 27, n. 6, p. 1595-1604-
dc.identifier.issn1040-4651-
dc.identifier.urihttp://hdl.handle.net/10722/251112-
dc.description.abstract© 2015 American Society of Plant Biologists. All rights reserved. Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated break-induced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber.-
dc.languageeng-
dc.relation.ispartofPlant Cell-
dc.titleGenome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber-
dc.typeArticle-
dc.description.naturelink_to_OA_fulltext-
dc.identifier.doi10.1105/tpc.114.135848-
dc.identifier.pmid26002866-
dc.identifier.scopuseid_2-s2.0-84936931699-
dc.identifier.volume27-
dc.identifier.issue6-
dc.identifier.spage1595-
dc.identifier.epage1604-
dc.identifier.eissn1532-298X-
dc.identifier.isiWOS:000357718800005-
dc.identifier.issnl1040-4651-

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