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

被引:12
|
作者
Liu, Ying [1 ,2 ]
Yi, Fei [1 ]
Yang, Guijuan [1 ]
Wang, Yuting [3 ]
Pubu, Ciren [3 ]
He, Runhua [4 ]
Xiao, Yao [1 ]
Wang, Junchen [1 ,2 ]
Lu, Nan [1 ]
Wang, Junhui [1 ]
Ma, Wenjun [1 ]
机构
[1] Chinese Acad Forestry, State Key Lab Tree Genet & Breeding, State Forestry Adm, Key Lab Tree Breeding & Cultivat,Res Inst Forestr, Beijing, Peoples R China
[2] Northwest A&F Univ, Coll Forestry, Yangling, Shaanxi, Peoples R China
[3] Forest Sci Res Inst Tibet Municipal, Lhasa, Tibet, Peoples R China
[4] Cent South Univ Forestry & Technol, Coll Forestry, Changsha, Hunan, Peoples R China
来源
PEERJ | 2020年 / 8卷
关键词
Sophora moorcroftiana; Gene flow; GBS; SNP; Population genetics; Phylogeography; F-STATISTICS; AEOLIAN SAND; TIBET; IDENTIFICATION; HYPOTHESIS; CHINA; FLOW; TOOL;
D O I
10.7717/peerj.9609
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
引用
收藏
页数:25
相关论文
共 50 条
  • [1] Genetic Diversity and Population Structure of a Longan Germplasm in Thailand Revealed by Genotyping-By-Sequencing (GBS)
    Riangwong, Kanamon
    Saensuk, Chatree
    Pitaloka, Mutiara K.
    Dumhai, Reajina
    Ruanjaichon, Vinitchan
    Toojinda, Theerayut
    Wanchana, Samart
    Arikit, Siwaret
    [J]. HORTICULTURAE, 2023, 9 (06)
  • [2] Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS)
    Islam, A. S. M. Faridul
    Sanders, Dean
    Mishra, Amit Kumar
    Joshi, Vijay
    [J]. GENES, 2021, 12 (12)
  • [3] Genetic diversity and population structure of trifoliate yam (Dioscorea dumetorum Kunth) in Cameroon revealed by genotyping-by-sequencing (GBS)
    Christian Siadjeu
    Eike Mayland-Quellhorst
    Dirk C. Albach
    [J]. BMC Plant Biology, 18
  • [4] Genetic diversity and population structure of trifoliate yam (Dioscorea dumetorum Kunth) in Cameroon revealed by genotyping-by-sequencing (GBS)
    Siadjeu, Christian
    Mayland-Quellhorst, Eike
    Albach, Dirk C.
    [J]. BMC PLANT BIOLOGY, 2018, 18
  • [5] Genetic diversity and population structure of wild and cultivated Crotalaria species based on genotyping-by-sequencing
    Muli, Joshua Kiilu
    Neondo, Johnstone O.
    Kamau, Peter K.
    Michuki, George N.
    Odari, Eddy
    Budambula, Nancy L. M.
    [J]. PLOS ONE, 2022, 17 (09):
  • [6] Phylogeography and genetic structure of Papaver bracteatum populations in Iran based on genotyping-by-sequencing (GBS)
    Rahmati, Razieh
    Nemati, Zahra
    Naghavi, Mohammad Reza
    Pfanzelt, Simon
    Rahimi, Amir
    Kanzagh, Ali Ghaderi
    Blattner, Frank R.
    [J]. SCIENTIFIC REPORTS, 2024, 14 (01):
  • [7] Genetic Diversity and Population Structure Analysis of Bigleaf Hydrangea Using Genotyping-by-sequencing
    Wu, Xingbo
    Alexander, Lisa W.
    [J]. JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE, 2019, 144 (04) : 257 - 263
  • [8] Genetic Diversity and Structure of a Diverse Population of Picea sitchensis Using Genotyping-by-Sequencing
    Byrne, Tomas
    Farrelly, Niall
    Kelleher, Colin
    Hodkinson, Trevor R.
    Byrne, Stephen L.
    Barth, Susanne
    [J]. FORESTS, 2022, 13 (09):
  • [9] Genetic diversity and population structure ofQuercus fabriHance in China revealed by genotyping-by-sequencing
    Xiong, Shifa
    Zhao, Yunxiao
    Chen, Yicun
    Gao, Ming
    Wu, Liwen
    Wang, Yangdong
    [J]. ECOLOGY AND EVOLUTION, 2020, 10 (16): : 8949 - 8958
  • [10] Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing
    Yang, Xiu
    Tan, Binwen
    Liu, Haijiao
    Zhu, Wei
    Xu, Lili
    Wang, Yi
    Fan, Xing
    Sha, Lina
    Zhang, Haiqin
    Zeng, Jian
    Wu, Dandan
    Jiang, Yunfeng
    Hu, Xigui
    Chen, Guoyue
    Zhou, Yonghong
    Kang, Houyang
    [J]. FRONTIERS IN GENETICS, 2020, 11