Utilizing SSR-based core collection development to improve conservation and utilization of Corylus L. genetic resources
Hazelnuts are traditional woody oilseed plants. Corylus L. resources are rich in variety and widely distributed in China. However, the identification of germplasm varieties and the selection of superior varieties remain quite limited. This study aimed to analyze the genetic diversity of 331 Corylus...
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| description | Hazelnuts are traditional woody oilseed plants. Corylus L. resources are rich in variety and widely distributed in China. However, the identification of germplasm varieties and the selection of superior varieties remain quite limited. This study aimed to analyze the genetic diversity of 331 Corylus L. germplasms using 16 simple sequence repeat (SSR) markers. Based on this, 11 pairs of core primers were selected, a fingerprint database of germplasm resources was constructed, and a primary core collection was screened. The results indicated that these tested Corylus L. germplasms exhibited a high level of genetic diversity, with an average number of alleles (Na) per locus of 14.5 and a polymorphic information content of 0.777. The phylogenetic relationships among various hazelnut cultivars were characterized by complexity, and they were delineated into four distinct groups facilitated by genetic distance analyses. An SSR fingerprint database for 331 Corylus L. germplasms was successfully constructed using the 11 obtained core SSR markers to increase the discrimination efficiency. Ultimately, 127 primary core accessions of Corylus L. were selected. The retention rate for the observed Na and MAF (the minor allele frequency) in the primary core germplasm constructed based on a sampling proportion of 38.36% was 100% and 94.7%, respectively. Shannon's information index (I) was highly consistent between the core and original germplasms, indicating that the core germplasm could fully represent the genetic diversity of the original germplasm. Additionally, the principal coordinate analysis of the selected primary core germplasm was essentially consistent with that of the entire original germplasm, further supporting the broad representativeness of the core germplasm. This study provided a basis for precisely identifying and efficiently utilizing Corylus L. accession. |
| doi_str_mv | 10.1371/journal.pone.0312116 |
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Corylus L. resources are rich in variety and widely distributed in China. However, the identification of germplasm varieties and the selection of superior varieties remain quite limited. This study aimed to analyze the genetic diversity of 331 Corylus L. germplasms using 16 simple sequence repeat (SSR) markers. Based on this, 11 pairs of core primers were selected, a fingerprint database of germplasm resources was constructed, and a primary core collection was screened. The results indicated that these tested Corylus L. germplasms exhibited a high level of genetic diversity, with an average number of alleles (Na) per locus of 14.5 and a polymorphic information content of 0.777. The phylogenetic relationships among various hazelnut cultivars were characterized by complexity, and they were delineated into four distinct groups facilitated by genetic distance analyses. An SSR fingerprint database for 331 Corylus L. germplasms was successfully constructed using the 11 obtained core SSR markers to increase the discrimination efficiency. Ultimately, 127 primary core accessions of Corylus L. were selected. The retention rate for the observed Na and MAF (the minor allele frequency) in the primary core germplasm constructed based on a sampling proportion of 38.36% was 100% and 94.7%, respectively. Shannon's information index (I) was highly consistent between the core and original germplasms, indicating that the core germplasm could fully represent the genetic diversity of the original germplasm. Additionally, the principal coordinate analysis of the selected primary core germplasm was essentially consistent with that of the entire original germplasm, further supporting the broad representativeness of the core germplasm. This study provided a basis for precisely identifying and efficiently utilizing Corylus L. accession.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0312116</identifier><identifier>PMID: 39471201</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adaptability ; Alleles ; Analysis ; Biological diversity ; Biology and Life Sciences ; China ; Cladistic analysis ; Collection development ; Conservation of Natural Resources - methods ; Conserved sequence ; Corylus ; Corylus - genetics ; Corylus - growth & development ; Cultivars ; DNA fingerprints ; Ecology and Environmental Sciences ; Efficiency ; Fingerprints ; Gene frequency ; Genetic analysis ; Genetic distance ; Genetic diversity ; Genetic Markers ; Genetic resources ; Genetic Variation ; Germplasm ; Germplasm resources ; Hazelnuts ; Methods ; Microsatellite Repeats - genetics ; Nucleotide sequence ; Phylogenetics ; Phylogeny ; Polymorphism, Genetic</subject><ispartof>PloS one, 2024-10, Vol.19 (10), p.e0312116</ispartof><rights>Copyright: © 2024 Yang 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 Yang 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 Yang et al 2024 Yang et al</rights><rights>2024 Yang 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-c506t-162f7db4a4cec3515c4ba4076fc91054ad7f7c003ca9341b146198ff338c5c493</cites><orcidid>0009-0004-1464-5341</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/PMC11521296/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11521296/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39471201$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yang, Weicong</creatorcontrib><creatorcontrib>Yang, Boning</creatorcontrib><creatorcontrib>Lu, Liyuan</creatorcontrib><creatorcontrib>Zhang, Xuemei</creatorcontrib><creatorcontrib>Sun, Jun</creatorcontrib><creatorcontrib>Wang, Liwei</creatorcontrib><creatorcontrib>Zheng, Zeyang</creatorcontrib><creatorcontrib>Liang, Dejun</creatorcontrib><creatorcontrib>Wang, Kehan</creatorcontrib><creatorcontrib>Yan, Xinyu</creatorcontrib><creatorcontrib>Yang, Chenchen</creatorcontrib><creatorcontrib>Liu, Zhenpan</creatorcontrib><title>Utilizing SSR-based core collection development to improve conservation and utilization of Corylus L. genetic resources</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Hazelnuts are traditional woody oilseed plants. Corylus L. resources are rich in variety and widely distributed in China. However, the identification of germplasm varieties and the selection of superior varieties remain quite limited. This study aimed to analyze the genetic diversity of 331 Corylus L. germplasms using 16 simple sequence repeat (SSR) markers. Based on this, 11 pairs of core primers were selected, a fingerprint database of germplasm resources was constructed, and a primary core collection was screened. The results indicated that these tested Corylus L. germplasms exhibited a high level of genetic diversity, with an average number of alleles (Na) per locus of 14.5 and a polymorphic information content of 0.777. The phylogenetic relationships among various hazelnut cultivars were characterized by complexity, and they were delineated into four distinct groups facilitated by genetic distance analyses. An SSR fingerprint database for 331 Corylus L. germplasms was successfully constructed using the 11 obtained core SSR markers to increase the discrimination efficiency. Ultimately, 127 primary core accessions of Corylus L. were selected. The retention rate for the observed Na and MAF (the minor allele frequency) in the primary core germplasm constructed based on a sampling proportion of 38.36% was 100% and 94.7%, respectively. Shannon's information index (I) was highly consistent between the core and original germplasms, indicating that the core germplasm could fully represent the genetic diversity of the original germplasm. Additionally, the principal coordinate analysis of the selected primary core germplasm was essentially consistent with that of the entire original germplasm, further supporting the broad representativeness of the core germplasm. This study provided a basis for precisely identifying and efficiently utilizing Corylus L. accession.</description><subject>Adaptability</subject><subject>Alleles</subject><subject>Analysis</subject><subject>Biological diversity</subject><subject>Biology and Life Sciences</subject><subject>China</subject><subject>Cladistic analysis</subject><subject>Collection development</subject><subject>Conservation of Natural Resources - methods</subject><subject>Conserved sequence</subject><subject>Corylus</subject><subject>Corylus - genetics</subject><subject>Corylus - growth & development</subject><subject>Cultivars</subject><subject>DNA fingerprints</subject><subject>Ecology and Environmental Sciences</subject><subject>Efficiency</subject><subject>Fingerprints</subject><subject>Gene frequency</subject><subject>Genetic analysis</subject><subject>Genetic distance</subject><subject>Genetic diversity</subject><subject>Genetic Markers</subject><subject>Genetic resources</subject><subject>Genetic Variation</subject><subject>Germplasm</subject><subject>Germplasm resources</subject><subject>Hazelnuts</subject><subject>Methods</subject><subject>Microsatellite Repeats - 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methods</topic><topic>Conserved sequence</topic><topic>Corylus</topic><topic>Corylus - genetics</topic><topic>Corylus - growth & development</topic><topic>Cultivars</topic><topic>DNA fingerprints</topic><topic>Ecology and Environmental Sciences</topic><topic>Efficiency</topic><topic>Fingerprints</topic><topic>Gene frequency</topic><topic>Genetic analysis</topic><topic>Genetic distance</topic><topic>Genetic diversity</topic><topic>Genetic Markers</topic><topic>Genetic resources</topic><topic>Genetic Variation</topic><topic>Germplasm</topic><topic>Germplasm resources</topic><topic>Hazelnuts</topic><topic>Methods</topic><topic>Microsatellite Repeats - genetics</topic><topic>Nucleotide sequence</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Polymorphism, Genetic</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yang, Weicong</creatorcontrib><creatorcontrib>Yang, Boning</creatorcontrib><creatorcontrib>Lu, Liyuan</creatorcontrib><creatorcontrib>Zhang, Xuemei</creatorcontrib><creatorcontrib>Sun, Jun</creatorcontrib><creatorcontrib>Wang, Liwei</creatorcontrib><creatorcontrib>Zheng, Zeyang</creatorcontrib><creatorcontrib>Liang, Dejun</creatorcontrib><creatorcontrib>Wang, Kehan</creatorcontrib><creatorcontrib>Yan, Xinyu</creatorcontrib><creatorcontrib>Yang, Chenchen</creatorcontrib><creatorcontrib>Liu, Zhenpan</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database (ProQuest)</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Complete (ProQuest Database)</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>ProQuest Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yang, Weicong</au><au>Yang, Boning</au><au>Lu, Liyuan</au><au>Zhang, Xuemei</au><au>Sun, Jun</au><au>Wang, Liwei</au><au>Zheng, Zeyang</au><au>Liang, Dejun</au><au>Wang, Kehan</au><au>Yan, Xinyu</au><au>Yang, Chenchen</au><au>Liu, Zhenpan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Utilizing SSR-based core collection development to improve conservation and utilization of Corylus L. genetic resources</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2024-10-29</date><risdate>2024</risdate><volume>19</volume><issue>10</issue><spage>e0312116</spage><pages>e0312116-</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Hazelnuts are traditional woody oilseed plants. Corylus L. resources are rich in variety and widely distributed in China. However, the identification of germplasm varieties and the selection of superior varieties remain quite limited. This study aimed to analyze the genetic diversity of 331 Corylus L. germplasms using 16 simple sequence repeat (SSR) markers. Based on this, 11 pairs of core primers were selected, a fingerprint database of germplasm resources was constructed, and a primary core collection was screened. The results indicated that these tested Corylus L. germplasms exhibited a high level of genetic diversity, with an average number of alleles (Na) per locus of 14.5 and a polymorphic information content of 0.777. The phylogenetic relationships among various hazelnut cultivars were characterized by complexity, and they were delineated into four distinct groups facilitated by genetic distance analyses. An SSR fingerprint database for 331 Corylus L. germplasms was successfully constructed using the 11 obtained core SSR markers to increase the discrimination efficiency. Ultimately, 127 primary core accessions of Corylus L. were selected. The retention rate for the observed Na and MAF (the minor allele frequency) in the primary core germplasm constructed based on a sampling proportion of 38.36% was 100% and 94.7%, respectively. Shannon's information index (I) was highly consistent between the core and original germplasms, indicating that the core germplasm could fully represent the genetic diversity of the original germplasm. Additionally, the principal coordinate analysis of the selected primary core germplasm was essentially consistent with that of the entire original germplasm, further supporting the broad representativeness of the core germplasm. This study provided a basis for precisely identifying and efficiently utilizing Corylus L. accession.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>39471201</pmid><doi>10.1371/journal.pone.0312116</doi><tpages>e0312116</tpages><orcidid>https://orcid.org/0009-0004-1464-5341</orcidid><oa>free_for_read</oa></addata></record> |
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| source | PLoS; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Adaptability Alleles Analysis Biological diversity Biology and Life Sciences China Cladistic analysis Collection development Conservation of Natural Resources - methods Conserved sequence Corylus Corylus - genetics Corylus - growth & development Cultivars DNA fingerprints Ecology and Environmental Sciences Efficiency Fingerprints Gene frequency Genetic analysis Genetic distance Genetic diversity Genetic Markers Genetic resources Genetic Variation Germplasm Germplasm resources Hazelnuts Methods Microsatellite Repeats - genetics Nucleotide sequence Phylogenetics Phylogeny Polymorphism, Genetic |
| title | Utilizing SSR-based core collection development to improve conservation and utilization of Corylus L. genetic resources |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-01T10%3A01%3A35IST&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=Utilizing%20SSR-based%20core%20collection%20development%20to%20improve%20conservation%20and%20utilization%20of%20Corylus%20L.%20genetic%20resources&rft.jtitle=PloS%20one&rft.au=Yang,%20Weicong&rft.date=2024-10-29&rft.volume=19&rft.issue=10&rft.spage=e0312116&rft.pages=e0312116-&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0312116&rft_dat=%3Cgale_plos_%3EA814099798%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=3122113804&rft_id=info:pmid/39471201&rft_galeid=A814099798&rfr_iscdi=true |