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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Veröffentlicht in:PloS one 2024-06, Vol.19 (6), p.e0302313-e0302313
Hauptverfasser: Ji, Qun, Li, Feng, Huang, Xinfang, Li, Shuangmei, Wang, Zhixin, Liu, Zhengwei, Huang, Laichun, Yang, Yingnan, Zhu, Honglian, Ke, Weidong
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container_issue 6
container_start_page e0302313
container_title PloS one
container_volume 19
creator Ji, Qun
Li, Feng
Huang, Xinfang
Li, Shuangmei
Wang, Zhixin
Liu, Zhengwei
Huang, Laichun
Yang, Yingnan
Zhu, Honglian
Ke, Weidong
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.
doi_str_mv 10.1371/journal.pone.0302313
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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. 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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.</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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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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