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Geographic population genetic structure and diversity of Sophora moorcroftiana based on genotyping-by-sequencing (GBS)

Sophora moorcroftiana is a perennial leguminous low shrub endemic to the Yarlung Zangbo River basin in Tibet with irreplaceable economic and ecological value. To determine the drivers of evolution in this species, 225 individuals belonging to 15 populations from different geographic locations were s...

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Autores principales: Liu, Ying, Yi, Fei, Yang, Guijuan, Wang, Yuting, Pubu, Ciren, He, Runhua, Xiao, Yao, Wang, Junchen, Lu, Nan, Wang, Junhui, Ma, Wenjun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7676378/
https://www.ncbi.nlm.nih.gov/pubmed/33240581
http://dx.doi.org/10.7717/peerj.9609
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author Liu, Ying
Yi, Fei
Yang, Guijuan
Wang, Yuting
Pubu, Ciren
He, Runhua
Xiao, Yao
Wang, Junchen
Lu, Nan
Wang, Junhui
Ma, Wenjun
author_facet Liu, Ying
Yi, Fei
Yang, Guijuan
Wang, Yuting
Pubu, Ciren
He, Runhua
Xiao, Yao
Wang, Junchen
Lu, Nan
Wang, Junhui
Ma, Wenjun
author_sort Liu, Ying
collection PubMed
description Sophora moorcroftiana is a perennial leguminous low shrub endemic to the Yarlung Zangbo River basin in Tibet with irreplaceable economic and ecological value. To determine the drivers of evolution in this species, 225 individuals belonging to 15 populations from different geographic locations were sampled, and population genetics was studied using high-throughput genotyping-by-sequencing (GBS). Based on genetic diversity analysis, phylogenetic analysis, principal component analysis, and structure analysis, 15 natural populations were clustered into the following five subgroups: subgroup I (Shigatse subgroup) was located in the upper reaches of the Yarlung Zangbo River with a relatively high level of population genetic variation (means for PIC, Shannon and PI were 0.173, 0.326 and 0.0000305, respectively), and gene flow within the subgroup was also high (mean value for Nm was 4.67). Subgroup II (including Pop 7 and Pop 8; means for PIC, Shannon and PI were 0.182, 0.345 and 0.0000321, respectively), located in the middle reaches of the Yarlung Zangbo River had relatively high levels of gene flow with the populations distributed in the upper and lower reaches. The Nm between subgroup II with subgroups I and III was 3.271 and 2.894, respectively. Considering all the genetic diversity indices Pop 8 had relatively high genetic diversity. Subgroup III (the remaining mixed subgroup of Lhasa and Shannan) was located in the middle reaches of the Yarlung Zangbo River and the means for PIC, Shannon and PI were 0.172, 0.324 and 0.0000303, respectively. Subgroup IV (Nyingchi subgroup), located in the lower reaches of the Yarlung Zangbo River basin, showed a further genetic distance from the other subgroups and the means for PIC, Shannon and PI were 0.147, 0.277 and 0.0000263, respectively. Subgroup V (Nyingchi Gongbu Jiangda subgroup), located in the upper reaches of the Niyang River, had the lowest level of genetic variation (means for PIC, Shannon and PI were 0.106, 0.198 and 0.0000187, respectively) and gene flow with other populations (mean value for Nm was 0.42). According to the comprehensive analysis, the S. moorcroftiana populations generally expanded from upstream to downstream and displayed a high level of genetic differentiation in the populations in the upper and lower reaches. There were high levels of gene exchange between the central populations with upstream and downstream populations, and wind-induced seed dispersal was an important factor in the formation of this gene exchange mode.
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spelling pubmed-76763782020-11-24 Geographic population genetic structure and diversity of Sophora moorcroftiana based on genotyping-by-sequencing (GBS) Liu, Ying Yi, Fei Yang, Guijuan Wang, Yuting Pubu, Ciren He, Runhua Xiao, Yao Wang, Junchen Lu, Nan Wang, Junhui Ma, Wenjun PeerJ Biogeography Sophora moorcroftiana is a perennial leguminous low shrub endemic to the Yarlung Zangbo River basin in Tibet with irreplaceable economic and ecological value. To determine the drivers of evolution in this species, 225 individuals belonging to 15 populations from different geographic locations were sampled, and population genetics was studied using high-throughput genotyping-by-sequencing (GBS). Based on genetic diversity analysis, phylogenetic analysis, principal component analysis, and structure analysis, 15 natural populations were clustered into the following five subgroups: subgroup I (Shigatse subgroup) was located in the upper reaches of the Yarlung Zangbo River with a relatively high level of population genetic variation (means for PIC, Shannon and PI were 0.173, 0.326 and 0.0000305, respectively), and gene flow within the subgroup was also high (mean value for Nm was 4.67). Subgroup II (including Pop 7 and Pop 8; means for PIC, Shannon and PI were 0.182, 0.345 and 0.0000321, respectively), located in the middle reaches of the Yarlung Zangbo River had relatively high levels of gene flow with the populations distributed in the upper and lower reaches. The Nm between subgroup II with subgroups I and III was 3.271 and 2.894, respectively. Considering all the genetic diversity indices Pop 8 had relatively high genetic diversity. Subgroup III (the remaining mixed subgroup of Lhasa and Shannan) was located in the middle reaches of the Yarlung Zangbo River and the means for PIC, Shannon and PI were 0.172, 0.324 and 0.0000303, respectively. Subgroup IV (Nyingchi subgroup), located in the lower reaches of the Yarlung Zangbo River basin, showed a further genetic distance from the other subgroups and the means for PIC, Shannon and PI were 0.147, 0.277 and 0.0000263, respectively. Subgroup V (Nyingchi Gongbu Jiangda subgroup), located in the upper reaches of the Niyang River, had the lowest level of genetic variation (means for PIC, Shannon and PI were 0.106, 0.198 and 0.0000187, respectively) and gene flow with other populations (mean value for Nm was 0.42). According to the comprehensive analysis, the S. moorcroftiana populations generally expanded from upstream to downstream and displayed a high level of genetic differentiation in the populations in the upper and lower reaches. There were high levels of gene exchange between the central populations with upstream and downstream populations, and wind-induced seed dispersal was an important factor in the formation of this gene exchange mode. PeerJ Inc. 2020-08-06 /pmc/articles/PMC7676378/ /pubmed/33240581 http://dx.doi.org/10.7717/peerj.9609 Text en ©2020 Liu 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 Biogeography
Liu, Ying
Yi, Fei
Yang, Guijuan
Wang, Yuting
Pubu, Ciren
He, Runhua
Xiao, Yao
Wang, Junchen
Lu, Nan
Wang, Junhui
Ma, Wenjun
Geographic population genetic structure and diversity of Sophora moorcroftiana based on genotyping-by-sequencing (GBS)
title Geographic population genetic structure and diversity of Sophora moorcroftiana based on genotyping-by-sequencing (GBS)
title_full Geographic population genetic structure and diversity of Sophora moorcroftiana based on genotyping-by-sequencing (GBS)
title_fullStr Geographic population genetic structure and diversity of Sophora moorcroftiana based on genotyping-by-sequencing (GBS)
title_full_unstemmed Geographic population genetic structure and diversity of Sophora moorcroftiana based on genotyping-by-sequencing (GBS)
title_short Geographic population genetic structure and diversity of Sophora moorcroftiana based on genotyping-by-sequencing (GBS)
title_sort geographic population genetic structure and diversity of sophora moorcroftiana based on genotyping-by-sequencing (gbs)
topic Biogeography
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7676378/
https://www.ncbi.nlm.nih.gov/pubmed/33240581
http://dx.doi.org/10.7717/peerj.9609
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