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Pham MP, Vu DD, Bei C, Bui TTX, Vu DG, Shah SNM. Characterisation of the Cinnamomumparthenoxylon (Jack) Meisn (Lauraceae) transcriptome using Illumina paired-end sequencing and EST-SSR markers development for population genetics. Biodivers Data J 2024; 12:e123405. [PMID: 38919771 PMCID: PMC11196892 DOI: 10.3897/bdj.12.e123405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024] Open
Abstract
Cinnamomumparthenoxylon is an endemic and endangered species with significant economic and ecological value in Vietnam. A better understanding of the genetic architecture of the species will be useful when planning management and conservation. We aimed to characterize the transcriptome of C.parthenoxylon, develop novel molecular markers, and assess the genetic variability of the species. First, transcriptome sequencing of five trees (C.parthenoxylon) based on root, leaf, and stem tissues was performed for functional annotation analysis and development of novel molecular markers. The transcriptomes of C.parthenoxylon were analyzed via an Illumina HiSeqTM 4000 sequencing system. A total of 27,363,199 bases were generated for C.parthenoxylon. De novo assembly indicated that a total of 160,435 unigenes were generated (average length = 548.954 bp). The 51,691 unigenes were compared against different databases, i.e. COG, GO, KEGG, KOG, Pfam, Swiss-Prot, and NR for functional annotation. Furthermore, a total of 12,849 EST-SSRs were identified. Of the 134 primer pairs, 54 were randomly selected for testing, with 15 successfully amplified across nine populations of C.parthenoxylon. We uncovered medium levels of genetic diversity (PIC = 0.52, Na = 3.29, Ne = 2.18, P = 94.07%, Ho = 0.56 and He = 0.47) within the studied populations. The molecular variance was 10% among populations and low genetic differentiation (Fst = 0.06) indicated low gene flow (Nm = 2.16). A reduction in the population size of C.parthenoxylon was detected using BOTTLENECK (VP population). The structure analysis suggested two optimal genetic clusters related to gene flow among the populations. Analysis of molecular variance (AMOVA) revealed higher genetic variation within populations (90%) than among populations (10%). The UPGMA approach and DAPC divided the nine populations into three main clusters. Our findings revealed a significant fraction of the transcriptome sequences and these newlydeveloped novel EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity and molecular marker-assisted selection in C.parthenoxylon. This study provides comprehensive genetic resources for the breeding and conservation of different varieties of C.parthenoxylon.
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Affiliation(s)
- Mai-Phuong Pham
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology, Hanoi, VietnamGraduate University of Science and Technology (GUST), Vietnam Academy of Science and TechnologyHanoiVietnam
- Join Vietnam–Russia Tropical Science and Technology Research Center, Hanoi, VietnamJoin Vietnam–Russia Tropical Science and Technology Research CenterHanoiVietnam
| | - Dinh Duy Vu
- Join Vietnam–Russia Tropical Science and Technology Research Center, Hanoi, VietnamJoin Vietnam–Russia Tropical Science and Technology Research CenterHanoiVietnam
| | - Cui Bei
- Jiangsu Vocational Institute of Architectural Technology, School of Architectural Decoration, Xuzhou 221100, Jiangsu, ChinaJiangsu Vocational Institute of Architectural Technology, School of Architectural Decoration, Xuzhou 221100JiangsuChina
| | - Thi Tuyet Xuan Bui
- Institute of Ecology and Biological Resource, Vietnam Academy of Science and Technology, Hanoi, VietnamInstitute of Ecology and Biological Resource, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Dinh Giap Vu
- Institute of Technology, Hanoi University of Industry (HaUI), Hanoi, VietnamInstitute of Technology, Hanoi University of Industry (HaUI)HanoiVietnam
| | - Syed Noor Muhammad Shah
- Department of Horticulture, Faculty of Agriculture, Gomal University, Dera Ismail Khan, PakistanDepartment of Horticulture, Faculty of Agriculture, Gomal UniversityDera Ismail KhanPakistan
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Lu Z, Ma Z, Fu M, Su J. Clustering Analysis of Natural D-borneol Resource Plants Based on Simple Sequence Repeat (SSR) Markers, Leaf Morphology, and Chemical Composition. Biochem Genet 2024:10.1007/s10528-024-10755-z. [PMID: 38554199 DOI: 10.1007/s10528-024-10755-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/21/2024] [Indexed: 04/01/2024]
Abstract
D-borneol is a double-loop monoterpene with a wide use in the pharmaceutical, food, and cosmetics industries. Natural D-borneol can be extracted from branches and leaves of D-borneol resource plants. With the widespread use of natural D-borneol, the identification of D-borneol resource plants and the protection of germplasm resources have become the focus of research. In this study, plant leaf morphology, chemical composition, and simple sequence repeat (SSR) molecular marker analysis were used to analyze and cluster 5 species of D-borneol resource plants and their closely related species. It was found that all three analysis methods could distinguish and cluster these D-borneol resource plants to some degree. The result of SSR analysis using capillary electrophoresis was the best, and it could distinguish Mei Pian tree from Yin Xiang as well as Longnao Zhang from An Zhang. The correlation analysis between SSR similarity matrix and leaf morphology analysis and between SSR similarity matrix and chemical composition similarity matrix revealed that they both had significant correlations (P < 0.0001) and the correlation (r = 0.588) between SSR and leaf morphology was a little higher than that (r = 0.519) between SSR and chemical composition. This indicated that the environment had a greater impact on the chemical composition than on leaf morphology. The research findings will offer efficient techniques to cluster natural D-borneol resource plants and establish a theoretical basis for their future development and utilization.
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Affiliation(s)
- Ziqing Lu
- Bioengieering Department, Biological and Pharmaceutical College, Guangdong University of Technology, No. 100 Waihuan Xi Road, Guangzhou Higher Education Center Mega, Guangzhou, 510006, People's Republic of China
| | - Zhuolin Ma
- Bioengieering Department, Biological and Pharmaceutical College, Guangdong University of Technology, No. 100 Waihuan Xi Road, Guangzhou Higher Education Center Mega, Guangzhou, 510006, People's Republic of China
| | - Minghui Fu
- Bioengieering Department, Biological and Pharmaceutical College, Guangdong University of Technology, No. 100 Waihuan Xi Road, Guangzhou Higher Education Center Mega, Guangzhou, 510006, People's Republic of China.
| | - Jianyu Su
- School of Food Science and Engineering, South China University of Technology, No. 381, Wushan Road, Guangzhou, 510641, People's Republic of China
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Bandaranayake PCG, Naranpanawa N, Chandrasekara CHWMRB, Samarakoon H, Lokuge S, Jayasundara S, Bandaranayake AU, Pushpakumara DKNG, Wijesundara DSA. Chloroplast genome, nuclear ITS regions, mitogenome regions, and Skmer analysis resolved the genetic relationship among Cinnamomum species in Sri Lanka. PLoS One 2023; 18:e0291763. [PMID: 37729154 PMCID: PMC10511092 DOI: 10.1371/journal.pone.0291763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 09/05/2023] [Indexed: 09/22/2023] Open
Abstract
Cinnamomum species have gained worldwide attention because of their economic benefits. Among them, C. verum (synonymous with C. zeylanicum Blume), commonly known as Ceylon Cinnamon or True Cinnamon is mainly produced in Sri Lanka. In addition, Sri Lanka is home to seven endemic wild cinnamon species, C. capparu-coronde, C. citriodorum, C. dubium, C. litseifolium, C. ovalifolium, C. rivulorum and C. sinharajaense. Proper identification and genetic characterization are fundamental for the conservation and commercialization of these species. While some species can be identified based on distinct morphological or chemical traits, others cannot be identified easily morphologically or chemically. The DNA barcoding using rbcL, matK, and trnH-psbA regions could not also resolve the identification of Cinnamomum species in Sri Lanka. Therefore, we generated Illumina Hiseq data of about 20x coverage for each identified species and a C. verum sample (India) and assembled the chloroplast genome, nuclear ITS regions, and several mitochondrial genes, and conducted Skmer analysis. Chloroplast genomes of all eight species were assembled using a seed-based method.According to the Bayesian phylogenomic tree constructed with the complete chloroplast genomes, the C. verum (Sri Lanka) is sister to previously sequenced C. verum (NC_035236.1, KY635878.1), C. dubium and C. rivulorum. The C. verum sample from India is sister to C. litseifolium and C. ovalifolium. According to the ITS regions studied, C. verum (Sri Lanka) is sister to C. verum (NC_035236.1), C. dubium and C. rivulorum. Cinnamomum verum (India) shares an identical ITS region with C. ovalifolium, C. litseifolium, C. citriodorum, and C. capparu-coronde. According to the Skmer analysis C. verum (Sri Lanka) is sister to C. dubium and C. rivulorum, whereas C. verum (India) is sister to C. ovalifolium, and C. litseifolium. The chloroplast gene ycf1 was identified as a chloroplast barcode for the identification of Cinnamomum species. We identified an 18 bp indel region in the ycf1 gene, that could differentiate C. verum (India) and C. verum (Sri Lanka) samples tested.
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Affiliation(s)
| | - Nathasha Naranpanawa
- Faculty of Agriculture, Agricultural Biotechnology Centre, University of Peradeniya, Peradeniya, Sri Lanka
- Postgraduate Institute of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | | | - Hiruna Samarakoon
- Faculty of Agriculture, Agricultural Biotechnology Centre, University of Peradeniya, Peradeniya, Sri Lanka
| | - S. Lokuge
- Faculty of Agriculture, Agricultural Biotechnology Centre, University of Peradeniya, Peradeniya, Sri Lanka
| | - S. Jayasundara
- Faculty of Agriculture, Agricultural Biotechnology Centre, University of Peradeniya, Peradeniya, Sri Lanka
| | - Asitha U. Bandaranayake
- Faculty of Engineering, Department of Computer Engineering, University of Peradeniya, Peradeniya, Sri Lanka
| | - D. K. N. G. Pushpakumara
- Faculty of Agriculture, Department of Crop Science, University of Peradeniya, Peradeniya, Sri Lanka
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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; 11:2706. [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
| | - Zhongsheng Wang
- College of Life Sciences, Nanjing University, Nanjing 210023, China
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Cui B, Vu DD, Vu DG, Bui TTX, Rahman SU, Pham MP, Nguyen MT, Nguyen VS, Shah SNM, Tran VH. Genetic diversity and population structure of Cinnamomum balansae Lecomte inferred by microsatellites. Open Life Sci 2022; 17:323-332. [PMID: 35480486 PMCID: PMC8985697 DOI: 10.1515/biol-2022-0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 12/02/2021] [Accepted: 01/03/2022] [Indexed: 11/29/2022] Open
Abstract
Cinnamomum balansae Lecomte (Lauraceae), an economically important forest tree, is distributed in the tropical forests of central and northern Vietnam, which has been threatened in recent decades due to the destruction of its habitat and over-exploitation. The genetic diversity and population structure of the species have not been fully evaluated. We used a set of 15 microsatellites to analyze 161 adult trees from 9 different populations, representing the geographical distribution of C. balansae. Ninety-two different alleles were identified. Here our results showed a low genetic diversity level with an average Ho = 0.246 and He = 0.262, and a high level of genetic differentiation (FST = 0.601). The bottleneck tests indicated evidence of a reduction in the population size of the two populations (TC and CP). Additionally, all three clustering methods (Bayesian analysis, principal coordinate analysis, and Neighbor-joining tree) were identified in the two genetic groups. The Mantel test showed a significant positive correlation between genetic distance and geographic distance (R2 = 0.7331). This study will provide a platform for the conservation of C. balansae both in ex-situ and in-situ plans.
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Affiliation(s)
- Bei Cui
- Key Comprehensive Laboratory of Forestry, College of Forestry, Northwest A & F University , Yang Ling 712100 , China
| | - Dinh Duy Vu
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST) , 18 Hoang Quoc Viet , Cau Giay, Hanoi , Vietnam
- Institute of Tropical Ecology, Vietnam – Russia Tropical Centre, 63 Nguyen Van Huyen , Cau Giay , Hanoi , Vietnam
| | - Dinh Giap Vu
- Department of Chemical Technology – Environment, HaUI Institute of Technology, Hanoi University of Industry (HaUI) , 298 Cau Dien , Bac Tu Liem , Hanoi , Vietnam
| | - Thi Tuyet Xuan Bui
- Department of Plant Ecology, Institute of Ecology and Biological Resource, VAST, 18 Hoang Quoc Viet , Cau Giay , Hanoi , Vietnam
- Graduate University of Science and Technology, VAST, 18 Hoang Quoc Viet , Cau Giay , Hanoi , Vietnam
| | - Siddiq Ur Rahman
- Department of Computer Science & Bioinformatics, Khushal Khan Khattak University, Karak , Khyber Pakhtunkhwa , 27200 , Pakistan
| | - Mai Phuong Pham
- Institute of Tropical Ecology, Vietnam – Russia Tropical Centre, 63 Nguyen Van Huyen , Cau Giay , Hanoi , Vietnam
| | - Minh Tam Nguyen
- Department of Experimental Taxonomy and Genetic Diversity, Vietnam National Museum of Nature, VAST , 18 Hoang Quoc Viet , Cau Giay , Hanoi , Vietnam
| | - Van Sinh Nguyen
- Department of Plant Ecology, Institute of Ecology and Biological Resource, VAST, 18 Hoang Quoc Viet , Cau Giay , Hanoi , Vietnam
- Graduate University of Science and Technology, VAST, 18 Hoang Quoc Viet , Cau Giay , Hanoi , Vietnam
| | - Syed Noor Muhammad Shah
- Department of Horticulture, Faculty of Agriculture, Gomal University , Dera Ismail Khan, 29220 , Pakistan
| | - Viet Ha Tran
- Faculty of Silviculture, Vietnam National University of Forestry , Xuan Mai , Chuong My , Hanoi , Vietnam
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Vu DD, Shah SNM, Pham MP, Bui VT, Nguyen MT, Nguyen TPT. De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics. BMC PLANT BIOLOGY 2020; 20:358. [PMID: 32727354 PMCID: PMC7391578 DOI: 10.1186/s12870-020-02571-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 07/23/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Understanding the genetic diversity in endangered species that occur inforest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. RESULTS In this study, we employed Illumina HiSeq™ 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. CONCLUSION Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.
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Affiliation(s)
- Dinh Duy Vu
- Vietnam - Russia Tropical Centre, 63 Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
- Department of Experimental Taxonomy & Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Syed Noor Muhammad Shah
- Department of Horticulture, Faculty of Agriculture, Gomal University Dera Ismail Khan, Dera Ismail Khan, Pakistan
| | - Mai Phuong Pham
- Vietnam - Russia Tropical Centre, 63 Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
| | - Van Thang Bui
- College of Forestry Biotechnology, Vietnam National University of Forestry, Xuan Mai, Hanoi, Vietnam
| | - Minh Tam Nguyen
- Department of Experimental Taxonomy & Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Thi Phuong Trang Nguyen
- Institute of Ecology and Biological Resource, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, , Cau Giay, Hanoi, Vietnam.
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Genetic Diversity and Population Genetic Structure of Cinnamomum camphora in South China Revealed by EST-SSR Markers. FORESTS 2019. [DOI: 10.3390/f10111019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cinnamomum camphora is a valuable broad-leaf tree indigenous to South China and East Asia and has been widely cultivated and utilized by humans since ancient times. However, owing to its overutilization for essential oil extraction, the Transplanting Big Trees into Cities Program, and over deforestation to make furniture, its wild populations have been detrimentally affected and are declining rapidly. In the present study, the genetic diversity and population structure of 180 trees sampled from 41 populations in South China were investigated with 22 expressed sequence tag-simple sequence repeat (EST-SSR) markers. In total, 61 alleles were harbored across 180 individuals, and medium genetic diversity level was inferred from the observed heterozygosity (Ho), expected heterozygosity (He), and Nei’ gene diversity (GD), which were 0.45, 0.44, and 0.44, respectively. Among the 41 wild populations, C. camphora had an average of 44 alleles, 2.02 effective alleles, and He ranging from 0.30 (SC) to 0.61 (HK). Analysis of molecular variance (AMOVA) showed that 17% of the variation among populations and the average pairwise genetic differentiation coefficient (FST) between populations was 0.162, indicating relatively low genetic population differentiations. Structure analysis suggested two groups for the 180 individuals, which was consistent with the principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA). Populations grouped to cluster I were nearly all distributed in Jiangxi Province (except population XS in Zhejiang Province), and cluster II mainly comprised populations from other regions, indicating a significant geographical distribution. Moreover, the Mantel test showed that this geographical distance was significantly correlated with genetic distance. The findings of this research will assist in future C. camphora conservation management and breeding programs.
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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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