Assessment of phylogenetic relationships and genetic diversity of Sagittaria trifolia using phenotypic traits and SNP markers
The aquatic perennial herb Sagittaria trifolia L. commonly known as arrowhead, has been utilized in China both as a culinary vegetable and in traditional medicines. Characterizing the phylogenetic relationships and genetic diversity of arrowheads is crucial for improved management, conservation, and...
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description | The aquatic perennial herb Sagittaria trifolia L. commonly known as arrowhead, has been utilized in China both as a culinary vegetable and in traditional medicines. Characterizing the phylogenetic relationships and genetic diversity of arrowheads is crucial for improved management, conservation, and efficient utilization of the germplasm resources associated with this species. Herein, we presented the phenotypic traits and genome-wide DNA marker-based analyses of 111 arrowhead accessions, most of which were from China. Cluster analysis revealed that arrowhead could be categorized into two clusters based on 11 phenotypic traits, with Cluster 1 comprising two subclusters. All accessions were clustered into three sub-clusters based primarily on leaf shape and tuber weight. A set of 759,237 high-quality single-nucleotide polymorphisms was identified and used to assess the phylogenetic relationships. Population structure and phylogenetic tree analyses suggested that the accessions could be classified into two major groups, Group I was further subdivided into two subgroups, aligning with the clusters identified through morphological classification. By employing Sagittaria lichuanensis as an outgroup, the rooted tree revealed that the evolutionary relationships within the three groups followed a progression from Group I-1 to Group I-2 and finally to Group II. The landraces were clustered into one group along with the remaining wild accessions. The level of genetic diversity for Group I (π = 0.26) was slightly lower than that which was estimated for Group II (π = 0.29). The lowest pairwise differentiation levels (Fst, 0.008) were obtained from the comparison between groups I-2 and II, indicating that the two groups were the most closely related. This study provides novel insights into germplasm classification, evolutionary relationships, genomics and arrowhead breeding. |
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Characterizing the phylogenetic relationships and genetic diversity of arrowheads is crucial for improved management, conservation, and efficient utilization of the germplasm resources associated with this species. Herein, we presented the phenotypic traits and genome-wide DNA marker-based analyses of 111 arrowhead accessions, most of which were from China. Cluster analysis revealed that arrowhead could be categorized into two clusters based on 11 phenotypic traits, with Cluster 1 comprising two subclusters. All accessions were clustered into three sub-clusters based primarily on leaf shape and tuber weight. A set of 759,237 high-quality single-nucleotide polymorphisms was identified and used to assess the phylogenetic relationships. Population structure and phylogenetic tree analyses suggested that the accessions could be classified into two major groups, Group I was further subdivided into two subgroups, aligning with the clusters identified through morphological classification. By employing Sagittaria lichuanensis as an outgroup, the rooted tree revealed that the evolutionary relationships within the three groups followed a progression from Group I-1 to Group I-2 and finally to Group II. The landraces were clustered into one group along with the remaining wild accessions. The level of genetic diversity for Group I (π = 0.26) was slightly lower than that which was estimated for Group II (π = 0.29). The lowest pairwise differentiation levels (Fst, 0.008) were obtained from the comparison between groups I-2 and II, indicating that the two groups were the most closely related. This study provides novel insights into germplasm classification, evolutionary relationships, genomics and arrowhead breeding.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0302313</identifier><identifier>PMID: 38829862</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Asexual reproduction ; Biogeography ; Biological diversity ; Biological evolution ; Biology and Life Sciences ; Biomarkers ; Ceramics ; China ; Chloroplasts ; Classification ; Cluster analysis ; Clusters ; Computer and Information Sciences ; Earth Sciences ; Ecology and Environmental Sciences ; Evolution ; Flowers & plants ; Genetic diversity ; Genetic Markers ; Genetic Variation ; Genomes ; Genomics ; Germplasm ; Morphology ; Nucleotides ; Phenotype ; Phylogenetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Population structure ; Sagittaria - anatomy & histology ; Sagittaria - classification ; Sagittaria - genetics ; Sagittaria trifolia ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Subgroups ; Vegetables</subject><ispartof>PloS one, 2024-06, Vol.19 (6), p.e0302313-e0302313</ispartof><rights>Copyright: © 2024 Ji 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 Ji 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 Ji et al 2024 Ji et al</rights><rights>2024 Ji 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-c572t-9afd8004eb32cabe251e2c6d027460d76baa68c403f575d947372cff05990ca63</cites><orcidid>0000-0001-7018-3875 ; 0000-0003-2350-735X ; 0009-0007-6727-4793</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/PMC11146740/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11146740/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38829862$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ji, Qun</creatorcontrib><creatorcontrib>Li, Feng</creatorcontrib><creatorcontrib>Huang, Xinfang</creatorcontrib><creatorcontrib>Li, Shuangmei</creatorcontrib><creatorcontrib>Wang, Zhixin</creatorcontrib><creatorcontrib>Liu, Zhengwei</creatorcontrib><creatorcontrib>Huang, Laichun</creatorcontrib><creatorcontrib>Yang, Yingnan</creatorcontrib><creatorcontrib>Zhu, Honglian</creatorcontrib><creatorcontrib>Ke, Weidong</creatorcontrib><title>Assessment of phylogenetic relationships and genetic diversity of Sagittaria trifolia using phenotypic traits and SNP markers</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The aquatic perennial herb Sagittaria trifolia L. commonly known as arrowhead, has been utilized in China both as a culinary vegetable and in traditional medicines. Characterizing the phylogenetic relationships and genetic diversity of arrowheads is crucial for improved management, conservation, and efficient utilization of the germplasm resources associated with this species. Herein, we presented the phenotypic traits and genome-wide DNA marker-based analyses of 111 arrowhead accessions, most of which were from China. Cluster analysis revealed that arrowhead could be categorized into two clusters based on 11 phenotypic traits, with Cluster 1 comprising two subclusters. All accessions were clustered into three sub-clusters based primarily on leaf shape and tuber weight. A set of 759,237 high-quality single-nucleotide polymorphisms was identified and used to assess the phylogenetic relationships. Population structure and phylogenetic tree analyses suggested that the accessions could be classified into two major groups, Group I was further subdivided into two subgroups, aligning with the clusters identified through morphological classification. By employing Sagittaria lichuanensis as an outgroup, the rooted tree revealed that the evolutionary relationships within the three groups followed a progression from Group I-1 to Group I-2 and finally to Group II. The landraces were clustered into one group along with the remaining wild accessions. The level of genetic diversity for Group I (π = 0.26) was slightly lower than that which was estimated for Group II (π = 0.29). The lowest pairwise differentiation levels (Fst, 0.008) were obtained from the comparison between groups I-2 and II, indicating that the two groups were the most closely related. This study provides novel insights into germplasm classification, evolutionary relationships, genomics and arrowhead breeding.</description><subject>Analysis</subject><subject>Asexual reproduction</subject><subject>Biogeography</subject><subject>Biological diversity</subject><subject>Biological evolution</subject><subject>Biology and Life Sciences</subject><subject>Biomarkers</subject><subject>Ceramics</subject><subject>China</subject><subject>Chloroplasts</subject><subject>Classification</subject><subject>Cluster analysis</subject><subject>Clusters</subject><subject>Computer and Information Sciences</subject><subject>Earth Sciences</subject><subject>Ecology and Environmental Sciences</subject><subject>Evolution</subject><subject>Flowers & plants</subject><subject>Genetic diversity</subject><subject>Genetic Markers</subject><subject>Genetic 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of phylogenetic relationships and genetic diversity of Sagittaria trifolia using phenotypic traits and SNP markers</title><author>Ji, Qun ; Li, Feng ; Huang, Xinfang ; Li, Shuangmei ; Wang, Zhixin ; Liu, Zhengwei ; Huang, Laichun ; Yang, Yingnan ; Zhu, Honglian ; Ke, Weidong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c572t-9afd8004eb32cabe251e2c6d027460d76baa68c403f575d947372cff05990ca63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Analysis</topic><topic>Asexual reproduction</topic><topic>Biogeography</topic><topic>Biological diversity</topic><topic>Biological evolution</topic><topic>Biology and Life Sciences</topic><topic>Biomarkers</topic><topic>Ceramics</topic><topic>China</topic><topic>Chloroplasts</topic><topic>Classification</topic><topic>Cluster analysis</topic><topic>Clusters</topic><topic>Computer and Information Sciences</topic><topic>Earth 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traditional medicines. Characterizing the phylogenetic relationships and genetic diversity of arrowheads is crucial for improved management, conservation, and efficient utilization of the germplasm resources associated with this species. Herein, we presented the phenotypic traits and genome-wide DNA marker-based analyses of 111 arrowhead accessions, most of which were from China. Cluster analysis revealed that arrowhead could be categorized into two clusters based on 11 phenotypic traits, with Cluster 1 comprising two subclusters. All accessions were clustered into three sub-clusters based primarily on leaf shape and tuber weight. A set of 759,237 high-quality single-nucleotide polymorphisms was identified and used to assess the phylogenetic relationships. Population structure and phylogenetic tree analyses suggested that the accessions could be classified into two major groups, Group I was further subdivided into two subgroups, aligning with the clusters identified through morphological classification. By employing Sagittaria lichuanensis as an outgroup, the rooted tree revealed that the evolutionary relationships within the three groups followed a progression from Group I-1 to Group I-2 and finally to Group II. The landraces were clustered into one group along with the remaining wild accessions. The level of genetic diversity for Group I (π = 0.26) was slightly lower than that which was estimated for Group II (π = 0.29). The lowest pairwise differentiation levels (Fst, 0.008) were obtained from the comparison between groups I-2 and II, indicating that the two groups were the most closely related. This study provides novel insights into germplasm classification, evolutionary relationships, genomics and arrowhead breeding.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>38829862</pmid><doi>10.1371/journal.pone.0302313</doi><tpages>e0302313</tpages><orcidid>https://orcid.org/0000-0001-7018-3875</orcidid><orcidid>https://orcid.org/0000-0003-2350-735X</orcidid><orcidid>https://orcid.org/0009-0007-6727-4793</orcidid><oa>free_for_read</oa></addata></record> |
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source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
subjects | Analysis Asexual reproduction Biogeography Biological diversity Biological evolution Biology and Life Sciences Biomarkers Ceramics China Chloroplasts Classification Cluster analysis Clusters Computer and Information Sciences Earth Sciences Ecology and Environmental Sciences Evolution Flowers & plants Genetic diversity Genetic Markers Genetic Variation Genomes Genomics Germplasm Morphology Nucleotides Phenotype Phylogenetics Phylogeny Polymorphism, Single Nucleotide Population structure Sagittaria - anatomy & histology Sagittaria - classification Sagittaria - genetics Sagittaria trifolia Single nucleotide polymorphisms Single-nucleotide polymorphism Subgroups Vegetables |
title | Assessment of phylogenetic relationships and genetic diversity of Sagittaria trifolia using phenotypic traits and SNP markers |
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