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Population structure of wild soybean (Glycine soja) based on SLAF-seq have implications for its conservation

BACKGROUND: Glycine soja Sieb. & Zucc. is the wild ancestor from which the important crop plant soybean was bred. G. soja provides important germplasm resources for the breeding and improvement of cultivated soybean crops, however the species is threatened by habitat loss and fragmentation, and...

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Autores principales: Meng, Jing, Yang, Guoqian, Li, Xuejiao, Zhao, Yan, He, Shuilian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10638924/
https://www.ncbi.nlm.nih.gov/pubmed/37953790
http://dx.doi.org/10.7717/peerj.16415
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author Meng, Jing
Yang, Guoqian
Li, Xuejiao
Zhao, Yan
He, Shuilian
author_facet Meng, Jing
Yang, Guoqian
Li, Xuejiao
Zhao, Yan
He, Shuilian
author_sort Meng, Jing
collection PubMed
description BACKGROUND: Glycine soja Sieb. & Zucc. is the wild ancestor from which the important crop plant soybean was bred. G. soja provides important germplasm resources for the breeding and improvement of cultivated soybean crops, however the species is threatened by habitat loss and fragmentation, and is experiencing population declines across its natural range. Understanding the patterns of genetic diversity in G. soja populations can help to inform conservation practices. METHODS: In this study, we analyzed the genetic diversity and differentiation of G. soja at different sites and investigated the gene flow within the species. We obtained 147 G. soja accessions collected from 16 locations across the natural range of the species from China, Korea and Japan. Samples were analyzed using SLAF-seq (Specific-Locus Amplified Fragment Sequencing). RESULTS: We obtained a total of 56,489 highly consistent SNPs. Our results suggested that G. soja harbors relatively high diversity and that populations of this species are highly differentiated. The populations harboring high genetic diversity, especially KR, should be considered first when devising conservation plans for the protection of G. soja, and in situ protection should be adopted in KR. G. soja populations from the Yangtze River, the Korean peninsula and northeastern China have a close relationship, although these areas are geographically disconnected. Other populations from north China clustered together. Analysis of gene flow suggested that historical migrations of G. soja may have occurred from the south northwards across the East-Asia land-bridge, but not across north China. All G. soja populations could be divided into one of two lineages, and these two lineages should be treated separately when formulating protection policies.
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spelling pubmed-106389242023-11-11 Population structure of wild soybean (Glycine soja) based on SLAF-seq have implications for its conservation Meng, Jing Yang, Guoqian Li, Xuejiao Zhao, Yan He, Shuilian PeerJ Bioinformatics BACKGROUND: Glycine soja Sieb. & Zucc. is the wild ancestor from which the important crop plant soybean was bred. G. soja provides important germplasm resources for the breeding and improvement of cultivated soybean crops, however the species is threatened by habitat loss and fragmentation, and is experiencing population declines across its natural range. Understanding the patterns of genetic diversity in G. soja populations can help to inform conservation practices. METHODS: In this study, we analyzed the genetic diversity and differentiation of G. soja at different sites and investigated the gene flow within the species. We obtained 147 G. soja accessions collected from 16 locations across the natural range of the species from China, Korea and Japan. Samples were analyzed using SLAF-seq (Specific-Locus Amplified Fragment Sequencing). RESULTS: We obtained a total of 56,489 highly consistent SNPs. Our results suggested that G. soja harbors relatively high diversity and that populations of this species are highly differentiated. The populations harboring high genetic diversity, especially KR, should be considered first when devising conservation plans for the protection of G. soja, and in situ protection should be adopted in KR. G. soja populations from the Yangtze River, the Korean peninsula and northeastern China have a close relationship, although these areas are geographically disconnected. Other populations from north China clustered together. Analysis of gene flow suggested that historical migrations of G. soja may have occurred from the south northwards across the East-Asia land-bridge, but not across north China. All G. soja populations could be divided into one of two lineages, and these two lineages should be treated separately when formulating protection policies. PeerJ Inc. 2023-11-08 /pmc/articles/PMC10638924/ /pubmed/37953790 http://dx.doi.org/10.7717/peerj.16415 Text en © 2023 Meng et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Meng, Jing
Yang, Guoqian
Li, Xuejiao
Zhao, Yan
He, Shuilian
Population structure of wild soybean (Glycine soja) based on SLAF-seq have implications for its conservation
title Population structure of wild soybean (Glycine soja) based on SLAF-seq have implications for its conservation
title_full Population structure of wild soybean (Glycine soja) based on SLAF-seq have implications for its conservation
title_fullStr Population structure of wild soybean (Glycine soja) based on SLAF-seq have implications for its conservation
title_full_unstemmed Population structure of wild soybean (Glycine soja) based on SLAF-seq have implications for its conservation
title_short Population structure of wild soybean (Glycine soja) based on SLAF-seq have implications for its conservation
title_sort population structure of wild soybean (glycine soja) based on slaf-seq have implications for its conservation
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10638924/
https://www.ncbi.nlm.nih.gov/pubmed/37953790
http://dx.doi.org/10.7717/peerj.16415
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