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Journal ArticleDOI

Genetic evidence of multiple invasions and a small number of founders of Asian Palmyra palm (Borassus flabellifer) in Thailand

12 Oct 2017-BMC Genetics (BioMed Central)-Vol. 18, Iss: 1, pp 1-8
TL;DR: It is hypothesized that there were at least two different invasive events of B. flabellifer in Thailand, which was likely brought through the Straits of Malacca to be propagated in the southern Thailand as one of the invasive events before spreading to the central Thailand.
Abstract: Borassus flabellifer or Asian Palmyra palm is an important crop for local economies in the South and Southeast Asia for its fruit and palm sugar production. Archeological and historical evidence indicated the presence of this species in Southeast Asia dating back at least 1500 years. B. flabellifer is believed to be originated in Africa, spread to South Asia and introduced into Southeast Asia through commercial routes and dissemination of cultures, however, the nature of its invasion and settlement in Thailand is unclear. Here, we analyzed genetic data of 230 B. flabellifer accessions across Thailand using 17 EST-SSR and 12 gSSR polymorphic markers. Clustering analysis revealed that the population consisted of two genetic clusters (STRUCTURE K = 2). Cluster I is found mainly in southern Thailand, while Cluster II is found mainly in the northeastern. Those found in the central are of an extensive mix between the two. These two clusters are in moderate differentiation (F ST = 0.066 and N M = 3.532) and have low genetic diversity (HO = 0.371 and 0.416; AR = 2.99 and 3.19, for the cluster I and II respectively). The minimum numbers of founders for each genetic group varies from 3 to 4 individuals, based on simulation using different allele frequency assumptions. These numbers coincide with that B. flabellifer is dioecious, and a number of seeds had to be simultaneously introduced for obtaining both male and female founders. From these data and geographical and historical evidence, we hypothesize that there were at least two different invasive events of B. flabellifer in Thailand. B. flabellifer was likely brought through the Straits of Malacca to be propagated in the southern Thailand as one of the invasive events before spreading to the central Thailand. The second event likely occurred in Khmer Empire, currently Cambodia, before spreading to the northeastern Thailand.

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Citations
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Journal ArticleDOI
TL;DR: A comparative analysis among members of the Borasseae tribe revealed that the B. flabellifer cp genome is, so far, the largest and the cp genomes of this tribe have a similar structure, gene number and gene arrangement.
Abstract: Borassus flabellifer or Asian Palmyra palm is widely distributed in South and Southeast Asia and is horticultural and economic importance for its fruit and palm sugar production. However, its population is in rapid decline, and only a few genetic data are available. We sequenced the complete chloroplast (cp) genome of B. flabellifer to provide its genetic data for further utilization. The cp genome was obtained by Illumina sequencing and manual gap fillings providing 160,021 bp in length containing a pair of inverted repeats (IRs) with 27,256 bp. These IRs divide the genome into a large single copy region 87,444 bp and a small single copy region 18,065 bp. In total, 113 unique genes, 134 SSRs and 47 large repeats were identified. This is the first complete cp genome reported in the genus Borassus. A comparative analysis among members of the Borasseae tribe revealed that the B. flabellifer cp genome is, so far, the largest and the cp genomes of this tribe have a similar structure, gene number and gene arrangement. A phylogenetic tree reconstructed based on 74 protein-coding genes from 70 monocots demonstrates short branch lengths indicating slow evolutionary rates of cp genomes in family Arecaceae.

8 citations


Cites background from "Genetic evidence of multiple invasi..."

  • ...A number of DNA markers including RAPD [11], ISSR [12], EST-SR and gSSR [13, 14] have been developed for studying the population in south and southeast Asia and demonstrated its low genetic diversity....

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Journal ArticleDOI
01 Feb 2022-Gels
TL;DR: In this article , the bioactive compounds of Borassus flabellifer L. male flower extract were determined by the Folin-Ciocalteu method and aluminum chloride colorimetric assay, respectively.
Abstract: Borassus flabellifer L. is a plant in Arecaceae family, widely distributed and cultivated in tropical Asian countries. The purpose of this study was to identify the bioactive compounds of B. flabellifer L. male flower ethanolic extract and investigate the antioxidant, anti-inflammatory, and antibacterial activities against Cutibacterium acnes. Total phenolic compounds and total flavonoids in B. flabellifer L. male flower ethanolic extract were determined by the Folin–Ciocalteu method and aluminum chloride colorimetric assay, respectively. Active substances in the extract and their quantities were analyzed by liquid chromatography and mass spectrometry (LC–MS/MS). The antioxidant evaluation was carried out using DPPH, ABTS free radical scavenging assays, and FRAP assay. C. acnes inhibitory activity was performed by the broth microdilution method. Anti-inflammatory activity was determined by the protein denaturation assay. In addition, gel containing different amounts of B. flabellifer L. male flower extract was formulated. The physical stability of the gel was observed by measuring viscosity and pH after six heating and cooling cycles, as well as 1-month storage at 4, 30, and 45 °C. The total phenolic content in the extract was 268.30 ± 12.84 mg gallic acid equivalent/g crude dry extract. The total flavonoid contents in the extract were 1886.38 ± 55.86 mg quercetin equivalent/g extract and 2884.88 ± 128.98 mg EGCG equivalent/g extract, respectively. The LC–MS/MS analysis revealed the presence of gallic acid, coumarin, and quercetin and the concentrations of quercetin, coumarin, and gallic acid in B. flabellifer male flower ethanolic extract were 0.912, 0.021, and 1.610 µg/mL, respectively. DPPH and ABTS antioxidant assays indicated that the B. flabellifer L. male flower extract had IC50 values of 31.54 ± 0.43 and 164.5 ± 14.3 µg/mL, respectively. FRAP assay revealed that the B. flabellifer male flower extract had high ferric ion reducing power. The extract was able to inhibit C. acnes bacteria with a minimum inhibitory concentration (MIC) of 250 mg/mL. At 250 and 500 µg/mL, the extract demonstrated the highest anti-inflammatory activity. The gel containing 31.25% w/w and 62.5% w/w showed good physical stability after six heating and cooling cycles, as well as 1-month storage.

8 citations

Journal ArticleDOI
TL;DR: It is proposed that, while prominent short-range pollen and seed dispersal in Benin explain most of the results, gene flux between the Central and Northern regions, as a result of animal and/or human migrations, might underlie the Savè discrepancy.
Abstract: In Sub-Saharan Africa, Borassus aethiopum Mart. (African fan palm) is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity and population structure of B. aethiopum across nine collection sites spanning the three climatic regions of Benin, West Africa, through the use of microsatellite markers. During a first phase we relied on the reported transferability of primers developed in other palm species. We find that, in disagreement with previously published results, only 22.5% of the markers tested enable amplification of B. aethiopum DNA and polymorphism detection is very low. In a second phase, we generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the de novo detection of microsatellite loci. Among the primer pairs targeting these, 11 detected polymorphisms and were further used for analyzing genetic diversity. Across the nine sites, expected heterozygosity (He) ranges from 0.263 to 0.451 with an overall average of 0.354, showing a low genetic diversity. Analysis of molecular variance (AMOVA) shows that within-site variation accounts for 53% of the genetic variation. Accordingly, the low number of migrants and positive values of the fixation index (F) in sites from both the Central (Sudano-Guinean) and the Southern (Guinean) climatic regions suggest limited gene flow between sites. The global correlation between genetic and geographic distances is weak; however, our clustering analyses indicate that B. aethiopum palms from Save (Center) are genetically more similar to those from the North than to samples from other Central sites. In the light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic diversity analyses targeting under-studied species, and suggest future applications for our molecular resources. We propose that, while prominent short-range pollen and seed dispersal in Benin explain most of our results, gene flux between the Central and Northern regions, as a result of animal and/or human migrations, might underlie the Save discrepancy.

6 citations


Cites background from "Genetic evidence of multiple invasi..."

  • ...417) [45] and for other non-timber forest products such as Khaya senegalensis (0....

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Journal ArticleDOI
TL;DR: It is demonstrated that microsatellite markers efficiently assess of genetic diversity and genetic differentiation in black locust populations, and all seven populations exhibit high genetic diversity.

5 citations

References
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Journal ArticleDOI
01 Jun 2000-Genetics
TL;DR: Pritch et al. as discussed by the authors proposed a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations, which can be applied to most of the commonly used genetic markers, provided that they are not closely linked.
Abstract: We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci— e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.

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Journal ArticleDOI
TL;DR: In this paper, a simple and widely accepted multiple test procedure of the sequentially rejective type is presented, i.e. hypotheses are rejected one at a time until no further rejections can be done.
Abstract: This paper presents a simple and widely ap- plicable multiple test procedure of the sequentially rejective type, i.e. hypotheses are rejected one at a tine until no further rejections can be done. It is shown that the test has a prescribed level of significance protection against error of the first kind for any combination of true hypotheses. The power properties of the test and a number of possible applications are also discussed.

20,459 citations


"Genetic evidence of multiple invasi..." refers methods in this paper

  • ...The sequential Bonferroni correction [21] was performed according to the multiple tests....

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Journal ArticleDOI
TL;DR: It is found that in most cases the estimated ‘log probability of data’ does not provide a correct estimation of the number of clusters, K, and using an ad hoc statistic ΔK based on the rate of change in the log probability between successive K values, structure accurately detects the uppermost hierarchical level of structure for the scenarios the authors tested.
Abstract: The identification of genetically homogeneous groups of individuals is a long standing issue in population genetics. A recent Bayesian algorithm implemented in the software STRUCTURE allows the identification of such groups. However, the ability of this algorithm to detect the true number of clusters (K) in a sample of individuals when patterns of dispersal among populations are not homogeneous has not been tested. The goal of this study is to carry out such tests, using various dispersal scenarios from data generated with an individual-based model. We found that in most cases the estimated 'log probability of data' does not provide a correct estimation of the number of clusters, K. However, using an ad hoc statistic DeltaK based on the rate of change in the log probability of data between successive K values, we found that STRUCTURE accurately detects the uppermost hierarchical level of structure for the scenarios we tested. As might be expected, the results are sensitive to the type of genetic marker used (AFLP vs. microsatellite), the number of loci scored, the number of populations sampled, and the number of individuals typed in each sample.

18,572 citations


"Genetic evidence of multiple invasi..." refers methods in this paper

  • ...The best K was then inferred based on lnP(D) and delta K [25]....

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  • ...[25] was then applied and indicated the best K = 2 for a STRUCTURE clustering analysis using sampling locations based on either provinces or geographical areas (Fig....

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Journal ArticleDOI
TL;DR: Arlequin ver 3.0 as discussed by the authors is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework.
Abstract: Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.

14,271 citations

Journal Article
TL;DR: A new basis for the construction of a genetic linkage map of the human genome is described, to develop, by recombinant DNA techniques, random single-copy DNA probes capable of detecting DNA sequence polymorphisms, when hybridized to restriction digests of an individual's DNA.
Abstract: We describe a new basis for the construction of a genetic linkage map of the human genome. The basic principle of the mapping scheme is to develop, by recombinant DNA techniques, random single-copy DNA probes capable of detecting DNA sequence polymorphisms, when hybridized to restriction digests of an individual's DNA. Each of these probes will define a locus. Loci can be expanded or contracted to include more or less polymorphism by further application of recombinant DNA technology. Suitably polymorphic loci can be tested for linkage relationships in human pedigrees by established methods; and loci can be arranged into linkage groups to form a true genetic map of "DNA marker loci." Pedigrees in which inherited traits are known to be segregating can then be analyzed, making possible the mapping of the gene(s) responsible for the trait with respect to the DNA marker loci, without requiring direct access to a specified gene's DNA. For inherited diseases mapped in this way, linked DNA marker loci can be used predictively for genetic counseling.

7,853 citations


"Genetic evidence of multiple invasi..." refers methods in this paper

  • ...25 was used to determine polymorphism information content (PIC) based on Botstein et al. (1980) [23]....

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