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Guan B, Liu Q, Liu X, Gong X. Environment influences the genetic structure and genetic differentiation of Sassafras tzumu (Lauraceae). BMC Ecol Evol 2024; 24:80. [PMID: 38872114 PMCID: PMC11170782 DOI: 10.1186/s12862-024-02264-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 05/24/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Sassafras tzumu, an elegant deciduous arboreal species, belongs to the esteemed genus Sassafras within the distinguished family Lauraceae. With its immense commercial value, escalating market demands and unforeseen human activities within its natural habitat have emerged as new threats to S. tzumu in recent decades, so it is necessary to study its genetic diversity and influencing factors, to propose correlative conservation strategies. RESULTS By utilizing genotyping-by-sequence (GBS) technology, we acquired a comprehensive database of single nucleotide polymorphisms (SNPs) from a cohort of 106 individuals sourced from 13 diverse Sassafras tzumu natural populations, scattered across various Chinese mountainous regions. Through our meticulous analysis, we aimed to unravel the intricate genetic diversity and structure within these S. tzumu populations, while simultaneously investigating the various factors that potentially shape genetic distance. Our preliminary findings unveiled a moderate level of genetic differentiation (FST = 0.103, p < 0.01), accompanied by a reasonably high genetic diversity among the S. tzumu populations. Encouragingly, our principal component analysis painted a vivid picture of two distinct genetic and geographical regions across China, where gene flow appeared to be somewhat restricted. Furthermore, employing the sophisticated multiple matrix regression with randomization (MMRR) analysis method, we successfully ascertained that environmental distance exerted a more pronounced impact on genetic distance when compared to geographical distance (βE = 0.46, p < 0.01; βD = 0.16, p < 0.01). This intriguing discovery underscores the potential significance of environmental factors in shaping the genetic landscape of S. tzumu populations. CONCLUSIONS The genetic variance among populations of S. tzumu in our investigation exhibited a moderate degree of differentiation, alongside a heightened level of genetic diversity. The environmental distance of S. tzumu had a greater impact on its genetic diversity than geographical distance. It is of utmost significance to formulate and implement meticulous management and conservation strategies to safeguard the invaluable genetic resources of S. tzumu.
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Affiliation(s)
- Bicai Guan
- School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Qian Liu
- School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Xiang Liu
- School of Life Sciences, Nanchang University, Nanchang, 330031, China
| | - Xi Gong
- School of Life Sciences, Nanchang University, Nanchang, 330031, China.
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Baloch FS, Guizado SJV, Altaf MT, Yüce I, Çilesiz Y, Bedir M, Nadeem MA, Hatipoglu R, Gómez JCC. Applicability of inter-primer binding site iPBS- retrotransposon marker system for the assessment of genetic diversity and population structure of Peruvian rosewood (Aniba rosaeodora Ducke) germplasm. Mol Biol Rep 2022; 49:2553-2564. [PMID: 35023008 DOI: 10.1007/s11033-021-07056-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/02/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Rosewood (Aniba rosaeodora Ducke), which has a great demand due to its essential oil globally, is an evergreen tree of the Amazon forests. Rosewood natural stands have been depleted through deforestation and the destruction of habitat. Currently, rosewood is included in the ICUN red list of endangered species. METHODS AND RESULTS The 11 highly polymorphic primers amplified total 305 bands of which 301 (98.69%) were polymorphic. The number of effective alleles (Ne), Shannon's information index (I), overall gene diversity (Ht), gene diversity (h), and polymorphism information content (PIC) were (1.562), (0.505), (0.330), (0.337) and (0.343), respectively. These diversity indices explored high genetic diversity in rosewood germplasm. Among studied germplasm, the Santa Marta population was found most diverse by reflecting higher values of diversity indices while the Zungarococha population was found least diverse. The analysis of molecular variance (AMOVA) revealed that 79% of the genetic variation was within the populations. The STRUCTURE algorithm, unweighted pair group with arithmetic mean (UPGMA), and principal coordinate's analysis (PCoA) separated all germplasms into different population groups according to their geographic locations. Santa Marta population was found more diverse by reflecting higher values of diversity indices. The maximum genetic distance (0.868) was found between the Huajoya-10 and Nanay-3. In this investigation, iPBS- retrotransposon marker system was used to explore the genetic diversity of Peruvian rosewood germplasm. CONCLUSIONS The results in this study such as higher genetic diversity indices, AMOVA (79%) within population and PIC value (0.343) showed the utility and reproducibility of iPBS-retrotransposons in this species successfully. The STRUCTURE algorithm separated the germplasms into six population groups according to their geographic locations. These results have valuable information for the conservation, management strategies and future breeding activities of rosewood.
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Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey.
| | - Stalin Juan Vasquez Guizado
- Specialized Unit of Biotechnology, Research Center of Natural Resources of the Amazon, National University of the Peruvian Amazon, Iquitos, 1600, Peru
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey
| | - Ilker Yüce
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey
| | - Yeter Çilesiz
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey
| | - Mehmet Bedir
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey
| | - Rustu Hatipoglu
- Department of Field Crops, Faculty of Agricultural, University of Cukurova, 01380, Adana, Turkey
| | - Juan Carlos Castro Gómez
- Specialized Unit of Biotechnology, Research Center of Natural Resources of the Amazon, National University of the Peruvian Amazon, Iquitos, 1600, Peru
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Determining the Optimal Density of Phoebe bournei Plantations Based on Dynamic Programming under Close-to-Nature Management Measures. SUSTAINABILITY 2022. [DOI: 10.3390/su14020847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Close-to-nature management (CTNM) is the most promising option for plantation silviculture and has received widespread attention in recent years. Stand density is a key variable in CTNM, as it directly influences growth and yield. Research for the optimal density that maximizes the total harvest has been ongoing. In this paper, a dynamic programming model was applied to the CTNM of Phoebe bournei plantations for the first time to solve the problem of stand density and target tree density control. This paper took Phoebe bournei plantations in Jindong Forest Farm of Hunan Province as the research object. Based on the data of seven consecutive years from 2015 to 2021, Richard’s growth equation was used to fit the height growth equation and basal area growth equation of Phoebe bournei. Stand growth was divided into five development stages according to the forest growth process and characteristics. Stand density and basal area were selected as two-dimensional state variables, and the maximum total harvest in the entire stand growth process was used as the objective function to establish a dynamic programming model. The optimal stand density and target tree density at each growth stage of the stand under three different site conditions were determined. According to the results obtained, the objective forest shape was designed for the stand under three types of site conditions, which can provide a theoretical basis for the CTNM of Phoebe bournei plantations to make the stand achieve the maximum harvest.
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Zhou Q, Zhou PY, Zou WT, Li YG. EST-SSR marker development based on transcriptome sequencing and genetic analyses of Phoebe bournei (Lauraceae). Mol Biol Rep 2021; 48:2201-2208. [PMID: 33629201 DOI: 10.1007/s11033-021-06228-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
High-throughput sequencing of the Phoebe bournei transcriptome was performed, and novel SSR markers were identified. A total of 73,518 nonredundant unigenes were assembled and annotated by sequence similarity searching in diverse public databases. A total of 40,853 SSRs were identified from 73,518 unigenes. Twenty-three pairs of polymorphic EST-SSR markers were selected from 98 markers and used for genetic analyses in 75 individuals from three P. bournei populations. The 23 pairs of markers could detect abundant genetic information from the samples (PIC = 0.769), and cross-species amplification was successfully performed in other related species. Three populations had high level of genetic diversity (He = 0.658 in average), of which the population YS from Jiangxi province had the most abundant genetic diversity (He = 0.722). The results of genetic structure analyses showed that the population YS from Jiangxi province had obvious genetic differences from the other two populations, and the genetic information of the population SX from Fujian province was related to that of the population LC from Guangdong province and the population YS. The transcriptomic resources and EST-SSR markers are valuable tools not only for the ecological conservation of P. bournei but also for phylogenetic studies.
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Affiliation(s)
- Qi Zhou
- Zhejiang Academy of Forestry, Hangzhou, 310023, China
| | | | - Wen-Tao Zou
- Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Yin-Gang Li
- Zhejiang Academy of Forestry, Hangzhou, 310023, China.
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Chen B, Zeng Y, Li C, Xu B, Zhang C, Chen W, Li S, Liu W. Characterization of the complete chloroplast genome of the Phoebe bournei. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1810153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Beibei Chen
- Enshi Tujia and Miao Autonomous Prefecture Academy of Forestry, Enshi, People’s Republic of China
| | - Yong Zeng
- Enshi Tujia and Miao Autonomous Prefecture Academy of Forestry, Enshi, People’s Republic of China
| | - Chunlin Li
- Enshi Tujia and Miao Autonomous Prefecture Academy of Forestry, Enshi, People’s Republic of China
| | - Bing Xu
- Fujian Academy of Forestry Sciences, Fuzhou, People’s Republic of China
| | - Chuan Zhang
- Enshi Tujia and Miao Autonomous Prefecture Academy of Forestry, Enshi, People’s Republic of China
| | - Wei Chen
- Enshi Tujia and Miao Autonomous Prefecture Academy of Forestry, Enshi, People’s Republic of China
| | - Shuanglong Li
- Enshi Tujia and Miao Autonomous Prefecture Academy of Forestry, Enshi, People’s Republic of China
| | - Weiyi Liu
- Enshi Tujia and Miao Autonomous Prefecture Academy of Forestry, Enshi, People’s Republic of China
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Li Y, Xu W, Zou W, Jiang D, Liu X. Complete chloroplast genome sequences of two endangered Phoebe (Lauraceae) species. BOTANICAL STUDIES 2017; 58:37. [PMID: 28905330 PMCID: PMC5597560 DOI: 10.1186/s40529-017-0192-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/20/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND Phoebe (Lauraceae) comprises of evergreen trees or shrubs with approximately 100 species, distributed in tropical and subtropical Asia and Neotropical America. A total of 34 species and three varieties occur in China. Despite of economic and ecological value, only limited genomic resources are available for this genus. RESULTS We sequenced the two complete chloroplast (cp) genomes of Phoebe chekiangensis and P. bournei using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. We also performed comparative analyses with the cp genomes of P. sheareri and P. sheareri var. oineiensis previously reported. The chloroplast genomes of P. chekiangensis and P. bournei identically contain 112 genes consisting of 78 protein coding genes, 30 tRNA genes, and 4 rRNA genes, with the size of 152,849 and 152,853 bp, respectively. From the two chloroplast genomes, 131 SSRs were identified and 12 different SSRs located in five protein coding genes. The analysis showed the extremely conserved structure of chloroplast genomes with surprisingly little variations at the LSC/IR and SSC/IR boundaries. Moreover, the mean nucleotide diversity was found to be 0.162% for 77 regions, suggesting an extraordinarily low level of sequence divergence. Four highest divergent regions (trnH-psbA, rps14-trnT, petA-psbJ, ccsA-ndhD) with the percentage of nucleotide diversity higher than 0.50% were identified, which had potential use for species identification and phylogenetic studies. CONCLUSION This study will facilitate our understanding of population genetics, phylogenetic relationship and plant evolution of Phoebe species.
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Affiliation(s)
- Yingang Li
- Zhejiang Academy of Forestry, Hangzhou, 310023 China
| | - Wuqin Xu
- Key Laboratory of Conservation Biology for Endangered Wildlife of Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Wentao Zou
- Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520 China
| | - Dongyue Jiang
- Zhejiang Academy of Forestry, Hangzhou, 310023 China
| | - Xinhong Liu
- Zhejiang Academy of Forestry, Hangzhou, 310023 China
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Phylogeographic pattern suggests a general northeastward dispersal in the distribution of Machilus pauhoi in South China. PLoS One 2017; 12:e0184456. [PMID: 28886133 PMCID: PMC5590941 DOI: 10.1371/journal.pone.0184456] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/24/2017] [Indexed: 11/19/2022] Open
Abstract
Machilus pauhoi Kanehira is an important timber species in China. A provenance trial was recently set up to evaluate the growth performance of trees from different localities, with the aim of designing seed transfer guidelines. Here, we tested twelve nuclear microsatellite markers derived from other species of the Lauraceae family and investigated population genetic structure in M. pauhoi. Both the number of observed alleles per locus (Na) and the polymorphic information content (PIC) significantly decreased against the latitude, but showed an insignificant decrease against the longitude. Heterozygosity (Ho) and gene diversity (h) exhibited a weak correlation with geographic location. Private alleles were present in multiple populations, and a moderate level of population genetic differentiation was detected (Gst = 0.1691). The joint pattern of genetic diversity (Na, PIC, Ho, and h) suggests that general northeastward dispersal led to the current distribution of M. pauhoi. Significant but weak effects of isolation-by-distance (IBD) occurred, implicating the mountain ranges as the major barrier to gene flow. Both STRUCTURE and hierarchical clustering analyses showed three distinct groups of populations related to the physical connectivity among mountain ranges. A priority in designing genetic conservation should be given to the populations at the southwest side of the species’ distribution. This conservation strategy can also be combined with the pattern of adaptive genetic variation from the provenance trial for comprehensive genetic resource management of native M. pauhoi.
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Ding Y, Zhang J, Lu Y, Lin E, Lou L, Tong Z. Development of EST-SSR markers and analysis of genetic diversity in natural populations of endemic and endangered plant Phoebe chekiangensis. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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