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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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Wang S, Wang Y, Zhou J, Li P, Lin H, Peng Y, Yu L, Zhang Y, Wang Z. Genetic Diversity and Population Structure of an Arctic Tertiary Relict Tree Endemic to China ( Sassafras tzumu) Revealed by Novel Nuclear Microsatellite (nSSR) Markers. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11202706. [PMID: 36297730 PMCID: PMC9610890 DOI: 10.3390/plants11202706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/09/2022] [Accepted: 10/10/2022] [Indexed: 05/11/2023]
Abstract
Sassafras tzumu (Hemsl.) Hemsl., as an Arctic Tertiary relict woody species, is an ecologically and economically important deciduous tree endemic to southern China. Nonetheless, the genetic resources and backgrounds of S. tzumu are still lacking and remain largely unclear. Here, we predicted 16,215 candidate polymorphic nuclear microsatellite (nSSR) loci from the assembled nucleus databases of six geographic-distant individuals of S. tzumu via CandiSSR. Among these nSSRs, the di- (75.53%) and tri-nucleotide (19.75%) repeats were the most abundant, and 27 new polymorphic SSRs were developed and characterized in 136 individuals from six natural populations of S. tzumu. The majority of the above 27 SSRs (24 loci, 88.89%) presented moderate polymorphism (mean PIC = 0.356), and the transferability of these markers in other Sassafras species was high (85.19%). A moderately low level of genetic diversity and a high variation (FST = 0.286) of six wild populations of S. tzumu were illuminated by 16 selected polymorphic nSSRs, with the average expected heterozygosity (HE) of 0.430 at the species level and HE ranging from 0.195 to 0.387 at the population level. Meanwhile, a bottleneck effect was shown in two populations. Consistent with the results of the principal coordinate analysis (PCoA) and phylogenetic trees, structure analysis optimally divided these six S. tzumu populations into two clusters, and the further strong population subdivision appeared from K = 2 to K = 5, which corresponded to two evolutionarily significant units (ESUs). Moreover, the significant correlation between genetic and geographic distance was tested by the Mantel test (r = 0.742, p = 0.006), clarifying the effect about isolation by distance (IBD), which could be possibly explained by the low gene flow (Nm = 0.625), a relatively high degree of inbreeding (FIS = 0.166), a relatively large distribution, and mountainous barriers. Above all, our research not only enlarged the useful genetic resources for future studies of population genetics, molecular breeding, and germplasm management of S. tzumu and its siblings but also contributed to proposing scientific conservation strategies and schemes for the better preservation of S. tzumu and other Sassafras (Lauraceae) species.
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Affiliation(s)
- Shuang Wang
- College of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ying Wang
- College of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jingbo Zhou
- College of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hungwei Lin
- College of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ye Peng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Lipeng Yu
- Mount Longwang Nature Reserve, Huzhou 313300, China
| | - Yunyan Zhang
- College of Life Sciences, Nanjing University, Nanjing 210023, China
- Correspondence: (Y.Z.); (Z.W.); Tel.: +86-15261868978 (Y.Z.); +86-13770650868 (Z.W.)
| | - Zhongsheng Wang
- College of Life Sciences, Nanjing University, Nanjing 210023, China
- Correspondence: (Y.Z.); (Z.W.); Tel.: +86-15261868978 (Y.Z.); +86-13770650868 (Z.W.)
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Zhang C, Jia C, Liu X, Zhao H, Hou L, Li M, Cui B, Li Y. Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers. FRONTIERS IN PLANT SCIENCE 2022; 13:903674. [PMID: 35646027 PMCID: PMC9134938 DOI: 10.3389/fpls.2022.903674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
Elsholtzia stauntonii Benth. (Lamiaceae) is an economically important ornamental, medicinal and aromatic plant species. To meet the increasing market demand for E. stauntonii, it is necessary to assess genetic diversity within the species to accelerate the process of genetic improvement. Analysis of the transferability of simple sequence repeat (SSR) markers from related species or genera is a fast and economical method to evaluate diversity, and can ensure the availability of molecular markers in crops with limited genomic resources. In this study, the cross-genera transferability of 497 SSR markers selected from other members of the Lamiaceae (Salvia L., Perilla L., Mentha L., Hyptis Jacq., Leonurus L., Pogostemon Desf., Rosmarinus L., and Scutella L.) to E. stauntonii was 9.05% (45 primers). Among the 45 transferable markers, 10 markers revealed relatively high polymorphism in E. stauntonii. The genetic variation among 825 individuals from 18 natural populations of E. stauntonii in Hebei Province of China was analyzed using the 10 polymorphic SSR markers. On the basis of the SSR data, the average number of alleles (N A), expected heterozygosity (H E), and Shannon's information index (I) of the 10 primers pairs were 7.000, 0.478, and 0.688, respectively. Lower gene flow (N m = 1.252) and high genetic differentiation (F st = 0.181) were detected in the populations. Analysis of molecular variance (AMOVA) revealed that most of the variation (81.47%) was within the populations. Integrating the results of STRUCTURE, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and principal coordinate analysis, the 825 samples were grouped into two clusters associated with geographical provenance (southwestern and northeastern regions), which was consistent with the results of a Mantel test (r = 0.56, p < 0.001). Overall, SSR markers developed in related genera were effective to study the genetic structure and genetic diversity in geographical populations of E. stauntonii. The results provide a theoretical basis for conservation of genetic resources, genetic improvement, and construction of a core collection for E. stauntonii.
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Affiliation(s)
- Chenxing Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Chunfeng Jia
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, China
| | - Xinru Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Hanqing Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Lu Hou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Meng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Binbin Cui
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, China
| | - Yingyue Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
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