Evaluation of genetic diversity and population structure of Annamocarya sinensis using SCoT markers
Annamocarya sinensis (Dode) Leroy, a relict plant from the Tertiary period, is a member of Annamocarya genus in the Juglandaceae family. Despite its wide distribution in Guangxi Province, the habitats of this species had become fragmented and isolated, causing it facing deterioration. For protecting...
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| description | Annamocarya sinensis (Dode) Leroy, a relict plant from the Tertiary period, is a member of Annamocarya genus in the Juglandaceae family. Despite its wide distribution in Guangxi Province, the habitats of this species had become fragmented and isolated, causing it facing deterioration. For protecting this endangered species, it is crucial to understand its status in the wild and genetic diversity. In this study, 216 A. sinensis accessions from 18 populations in Guangxi were examined using Start Codon Target Polymorphism (SCoT) markers for PCR amplification, genetic diversity, and population structure analysis. Out of the 20 SCoT primers used, 222 sites were amplified, with 185 being polymorphic (PPB of 83.33%). Polymorphic information content values ranged from 0.4380 to 0.4999, Nei's genetic diversity index ranging from 0.1573 to 0.2503, and Shannon diversity index ranged from 0.1583 to 0.3812. Through AMOVA analysis, the total genetic diversity and genetic diversity within populations was calculated out as 0.3271 and 0.1542 respectively, the genetic differentiation coefficient between populations was 0.5286, with a gene flow 0.4458. Cluster analysis categorized A. sinensis germplasm into three groups, while population structure analysis divided all accessions into three ancestral sources with 19.91% showing mixed ancestral origins. No significant correlation was observed between genetic and geographical distance on the Mentel test (r = 0.07348, p = 0.7468). Overall, A. sinensis displays a relatively rich genetic diversity at the species level, albeit with a fairly uniform genetic background and high genetic differentiation. This study provides a crucial basis for the conservation and innovative use of A. sinensis germplasm resources. |
| doi_str_mv | 10.1371/journal.pone.0309283 |
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Despite its wide distribution in Guangxi Province, the habitats of this species had become fragmented and isolated, causing it facing deterioration. For protecting this endangered species, it is crucial to understand its status in the wild and genetic diversity. In this study, 216 A. sinensis accessions from 18 populations in Guangxi were examined using Start Codon Target Polymorphism (SCoT) markers for PCR amplification, genetic diversity, and population structure analysis. Out of the 20 SCoT primers used, 222 sites were amplified, with 185 being polymorphic (PPB of 83.33%). Polymorphic information content values ranged from 0.4380 to 0.4999, Nei's genetic diversity index ranging from 0.1573 to 0.2503, and Shannon diversity index ranged from 0.1583 to 0.3812. Through AMOVA analysis, the total genetic diversity and genetic diversity within populations was calculated out as 0.3271 and 0.1542 respectively, the genetic differentiation coefficient between populations was 0.5286, with a gene flow 0.4458. Cluster analysis categorized A. sinensis germplasm into three groups, while population structure analysis divided all accessions into three ancestral sources with 19.91% showing mixed ancestral origins. No significant correlation was observed between genetic and geographical distance on the Mentel test (r = 0.07348, p = 0.7468). Overall, A. sinensis displays a relatively rich genetic diversity at the species level, albeit with a fairly uniform genetic background and high genetic differentiation. This study provides a crucial basis for the conservation and innovative use of A. sinensis germplasm resources.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0309283</identifier><identifier>PMID: 39231174</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Amplification ; Annamocarya sinensis ; Biological diversity ; Biology and Life Sciences ; Botanical research ; China ; Cluster analysis ; Codon, Initiator - genetics ; Differentiation ; Distribution ; Earth Sciences ; Ecology and Environmental Sciences ; Endangered & extinct species ; Endangered species ; Environmental aspects ; Gene Flow ; Genetic analysis ; Genetic diversity ; Genetic Markers ; Genetic testing ; Genetic Variation ; Genetics, Population ; Genomes ; Geographical distribution ; Germplasm ; Leaves ; Natural history ; People and Places ; Phylogeny ; Polymorphism ; Polymorphism, Genetic ; Population biology ; Population genetics ; Population structure ; Populations ; Protected species ; Relict species ; Seeds ; Software ; Species diversity ; Structural analysis ; Tertiary ; Wildlife conservation</subject><ispartof>PloS one, 2024-09, Vol.19 (9), p.e0309283</ispartof><rights>Copyright: © 2024 Pan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</rights><rights>COPYRIGHT 2024 Public Library of Science</rights><rights>2024 Pan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2024 Pan et al 2024 Pan et al</rights><rights>2024 Pan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c526t-ec617a1cda899b985c05f7a59389de9456472724c2b8a7a9efeb2d62845e58733</cites><orcidid>0009-0004-5928-6565</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373820/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11373820/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39231174$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Kordrostami, Mojtaba</contributor><creatorcontrib>Pan, Hong</creatorcontrib><creatorcontrib>Deng, Libao</creatorcontrib><creatorcontrib>Zhu, Kaixian</creatorcontrib><creatorcontrib>Shi, Deju</creatorcontrib><creatorcontrib>Wang, Feiyong</creatorcontrib><creatorcontrib>Cui, Guofa</creatorcontrib><title>Evaluation of genetic diversity and population structure of Annamocarya sinensis using SCoT markers</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Annamocarya sinensis (Dode) Leroy, a relict plant from the Tertiary period, is a member of Annamocarya genus in the Juglandaceae family. Despite its wide distribution in Guangxi Province, the habitats of this species had become fragmented and isolated, causing it facing deterioration. For protecting this endangered species, it is crucial to understand its status in the wild and genetic diversity. In this study, 216 A. sinensis accessions from 18 populations in Guangxi were examined using Start Codon Target Polymorphism (SCoT) markers for PCR amplification, genetic diversity, and population structure analysis. Out of the 20 SCoT primers used, 222 sites were amplified, with 185 being polymorphic (PPB of 83.33%). Polymorphic information content values ranged from 0.4380 to 0.4999, Nei's genetic diversity index ranging from 0.1573 to 0.2503, and Shannon diversity index ranged from 0.1583 to 0.3812. Through AMOVA analysis, the total genetic diversity and genetic diversity within populations was calculated out as 0.3271 and 0.1542 respectively, the genetic differentiation coefficient between populations was 0.5286, with a gene flow 0.4458. Cluster analysis categorized A. sinensis germplasm into three groups, while population structure analysis divided all accessions into three ancestral sources with 19.91% showing mixed ancestral origins. No significant correlation was observed between genetic and geographical distance on the Mentel test (r = 0.07348, p = 0.7468). Overall, A. sinensis displays a relatively rich genetic diversity at the species level, albeit with a fairly uniform genetic background and high genetic differentiation. This study provides a crucial basis for the conservation and innovative use of A. sinensis germplasm resources.</description><subject>Amplification</subject><subject>Annamocarya sinensis</subject><subject>Biological diversity</subject><subject>Biology and Life Sciences</subject><subject>Botanical research</subject><subject>China</subject><subject>Cluster analysis</subject><subject>Codon, Initiator - genetics</subject><subject>Differentiation</subject><subject>Distribution</subject><subject>Earth Sciences</subject><subject>Ecology and Environmental Sciences</subject><subject>Endangered & extinct species</subject><subject>Endangered species</subject><subject>Environmental aspects</subject><subject>Gene Flow</subject><subject>Genetic analysis</subject><subject>Genetic diversity</subject><subject>Genetic Markers</subject><subject>Genetic testing</subject><subject>Genetic Variation</subject><subject>Genetics, Population</subject><subject>Genomes</subject><subject>Geographical distribution</subject><subject>Germplasm</subject><subject>Leaves</subject><subject>Natural history</subject><subject>People and Places</subject><subject>Phylogeny</subject><subject>Polymorphism</subject><subject>Polymorphism, Genetic</subject><subject>Population biology</subject><subject>Population genetics</subject><subject>Population structure</subject><subject>Populations</subject><subject>Protected species</subject><subject>Relict species</subject><subject>Seeds</subject><subject>Software</subject><subject>Species diversity</subject><subject>Structural analysis</subject><subject>Tertiary</subject><subject>Wildlife 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of genetic diversity and population structure of Annamocarya sinensis using SCoT markers</title><author>Pan, Hong ; Deng, Libao ; Zhu, Kaixian ; Shi, Deju ; Wang, Feiyong ; Cui, Guofa</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c526t-ec617a1cda899b985c05f7a59389de9456472724c2b8a7a9efeb2d62845e58733</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Amplification</topic><topic>Annamocarya sinensis</topic><topic>Biological diversity</topic><topic>Biology and Life Sciences</topic><topic>Botanical research</topic><topic>China</topic><topic>Cluster analysis</topic><topic>Codon, Initiator - genetics</topic><topic>Differentiation</topic><topic>Distribution</topic><topic>Earth Sciences</topic><topic>Ecology and Environmental Sciences</topic><topic>Endangered & extinct species</topic><topic>Endangered species</topic><topic>Environmental aspects</topic><topic>Gene 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Feiyong</au><au>Cui, Guofa</au><au>Kordrostami, Mojtaba</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Evaluation of genetic diversity and population structure of Annamocarya sinensis using SCoT markers</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2024-09-04</date><risdate>2024</risdate><volume>19</volume><issue>9</issue><spage>e0309283</spage><pages>e0309283-</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Annamocarya sinensis (Dode) Leroy, a relict plant from the Tertiary period, is a member of Annamocarya genus in the Juglandaceae family. Despite its wide distribution in Guangxi Province, the habitats of this species had become fragmented and isolated, causing it facing deterioration. For protecting this endangered species, it is crucial to understand its status in the wild and genetic diversity. In this study, 216 A. sinensis accessions from 18 populations in Guangxi were examined using Start Codon Target Polymorphism (SCoT) markers for PCR amplification, genetic diversity, and population structure analysis. Out of the 20 SCoT primers used, 222 sites were amplified, with 185 being polymorphic (PPB of 83.33%). Polymorphic information content values ranged from 0.4380 to 0.4999, Nei's genetic diversity index ranging from 0.1573 to 0.2503, and Shannon diversity index ranged from 0.1583 to 0.3812. Through AMOVA analysis, the total genetic diversity and genetic diversity within populations was calculated out as 0.3271 and 0.1542 respectively, the genetic differentiation coefficient between populations was 0.5286, with a gene flow 0.4458. Cluster analysis categorized A. sinensis germplasm into three groups, while population structure analysis divided all accessions into three ancestral sources with 19.91% showing mixed ancestral origins. No significant correlation was observed between genetic and geographical distance on the Mentel test (r = 0.07348, p = 0.7468). Overall, A. sinensis displays a relatively rich genetic diversity at the species level, albeit with a fairly uniform genetic background and high genetic differentiation. This study provides a crucial basis for the conservation and innovative use of A. sinensis germplasm resources.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>39231174</pmid><doi>10.1371/journal.pone.0309283</doi><tpages>e0309283</tpages><orcidid>https://orcid.org/0009-0004-5928-6565</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Amplification Annamocarya sinensis Biological diversity Biology and Life Sciences Botanical research China Cluster analysis Codon, Initiator - genetics Differentiation Distribution Earth Sciences Ecology and Environmental Sciences Endangered & extinct species Endangered species Environmental aspects Gene Flow Genetic analysis Genetic diversity Genetic Markers Genetic testing Genetic Variation Genetics, Population Genomes Geographical distribution Germplasm Leaves Natural history People and Places Phylogeny Polymorphism Polymorphism, Genetic Population biology Population genetics Population structure Populations Protected species Relict species Seeds Software Species diversity Structural analysis Tertiary Wildlife conservation |
| title | Evaluation of genetic diversity and population structure of Annamocarya sinensis using SCoT markers |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-06T12%3A38%3A25IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Evaluation%20of%20genetic%20diversity%20and%20population%20structure%20of%20Annamocarya%20sinensis%20using%20SCoT%20markers&rft.jtitle=PloS%20one&rft.au=Pan,%20Hong&rft.date=2024-09-04&rft.volume=19&rft.issue=9&rft.spage=e0309283&rft.pages=e0309283-&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0309283&rft_dat=%3Cgale_plos_%3EA807251501%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=3100825613&rft_id=info:pmid/39231174&rft_galeid=A807251501&rft_doaj_id=oai_doaj_org_article_5de39d3a8f2b4ae6aa2254bc0f9601fa&rfr_iscdi=true |