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Random amplified polymorphic DNA (RAPD) markers for determination of genetic variation in wild populations of the Black Tiger prawn (Penaeus monodon) in Thailand
Abstract
Random amplified polymorphic DNA (RAPD) analysis was used to amplify the genome of black tiger prawns (Penaeus monodon) to detect DNA markers and assess the utility of the RAPD method for investigating genetic variation in wild P. monodon in Thailand. A total of 200 ten-base primers were screened, and 84 primers yielded amplification products. Six positive primers that gave highly reproducible RAPD patterns were selected for the analysis of three geographically different samples of Thai P. monodon. A total of 70 reproducible RAPD fragments ranging in size from 200 to 2000 bp were scored, and 40 fragments (57%) were polymorphic. The RAPD analysis of broodstocks from three different locales, Satun-Trang, Trat, and Angsila, revealed different levels of genetic variability among the samples. The percentages of polymorphic bands were 48% and 45% in Satun-Trang and Trat, respectively, suggesting a high genetic variability of the two samples to be used in selective breeding programs. Only 25% polymorphic bands were found in the Angsila sample, indicating the lowest polymorphic level among the three samples examined. Primer 428 detected a RAPD marker that was found only in P. monodon originating from Satun-Trang, suggesting the potential use of this marker as a population-specific marker in this species.
... Long-term and sustainable crossbreeding programs of domesticated shrimp broodstock populations may benefit to attain the stability between unceasing genetic gains and reduced risk of inbreeding depression (Zhang et al., 2010;Ríos-Pérez et al., 2017). Since last few decades, various techniques used in examining genetic diversity status of P. monodon ranged from the most traditional allozymes (Benzie et al., 1992(Benzie et al., , 1993Forbes et al., 1999;Sugama et al., 2002)), randomly amplified polymorphic DNA (Garcia and Benzie, 1995;Tassanakajon et al., 1997Tassanakajon et al., , 1998Klinbunga et al., 2001), elongation factor 1-a intron sequences (Duda and Palumbi, 1999), restriction fragment length polymorphism (RFLP) (Benzie et al., 1993Bouchon et al., 1994;Klinbunga et al., 1998Klinbunga et al., , 2001, mitochondrial DNA sequencing (Chu et al., 2002;Kumar et al., 2007;You et al., 2008;Khamnamtong et al., 2009;Waqairatu et al., 2012;Khedkar et al., 2013;Alam et al., 2016) to microsatellites (Wolfus et al., 1997;Xu et al., 1999Xu et al., , 2001Brooker et al., 2000;Supungul et al., 2000;Wuthisuthimethavee et al., 2003;Pan et al., 2004;Li et al., 2007;Dixon et al., 2008;You et al., 2008;Aziz et al., 2011;Mandal et al., 2012;Waqairatu et al., 2012). Among these techniques, microsatellite markers are promising in studying population genetic variability owing to their broad genome distribution of codominant polymorphisms, high reproducibility, convenient detection (Varshney et al., 2005;Presti and Wasko, 2014). ...
... Genetic diversity studies of P. monodon have been conducted at both microgeographic and macrogeographic levels using various molecular markers. The microgeographic scale studies were limited to one region/ country including Australia (Mulley and Latter, 1980;Benzie et al., 1992Benzie et al., , 1993Brooker et al., 2000), Thailand (Tassanakajon et al., 1997;Withyachumnarnkul et al., 1998;Klinbunga et al., 1999Klinbunga et al., , 2001Supungul et al., 2000;Khamnamtong et al., 2009), India (Kumar et al., 2007;Mandal et al., 2012;Khedkar et al., 2013), Indonesia , the Philippines (Xu et al., 2000(Xu et al., , 2001, South Africa (Forbes et al., 1999) and Malaysia (Aziz et al., 2011), while the wider scale studies involved populations distributed across major continents such as eastern Africa, Southeast Asia, Australia and South Pacific islands (Bouchon et al., 1994;Duda and Palumbi, 1999;Benzie et al., 2002;You et al., 2008;Waqairatu et al., 2012). Although genetic distinctions were reported at finer to larger geographical scales, including those driven by paleo-geographical event (Waqairatu et al., 2012), all these studies except Xu et al. (2001) were conducted on shrimp individuals collected from natural populations. ...
Black tiger shrimp (Penaeus monodon) is one of the most important internationally traded fishery species, and the commercial success of their aquafarming primarily depends on the high quality broodstock for seed production. Therefore, identifications of genetically diverse broodstocks of P. monodon are essential to eliminate inbreeding effects, ensure sustainable seed supply, and facilitate genetic upgrading for selective breeding and restocking programs. The present study used a combination of mtDNA control region sequences and ten microsatellite markers to evaluate the genetic diversity, demographic history and population structure of P. monodon broodstocks collected from five sampling locations across the Indo-Pacific regions. The domesticated P. monodon broodstock populations were collected from Hawaii, USA (MMO), Thailand (MT) and Madagascar (MD), while the wild brood-stock populations were collected from Japan (MJ) and Malaysia (MS). Clustering analyses based on the Principle Component Analysis (PCA), Canonical Variate Analysis (CVA), STRUCTURE, and Neighbour-Joining (NJ) phylo-genetic analysis revealed that the domesticated populations were unequivocally diverged from the wild-caught populations. Haplotype networks, neutrality testing, and mismatch distribution analysis indicated a complex population expansion pattern involving Wahlund effect based on human translocation, and continental drift during the paleogeographic event in Pleistocene glacial age. Both mtDNA and microsatellite data detected relatively high levels of genetic diversity among all populations, but higher levels of nucleotide diversity in the wild populations , given that the artificial selection in aquaculture practice could reduce the genetic heterogeneity of the domesticated populations. The negative correlation of isolation by distance (IBD) results further supported the findings from neutrality test, indicating that founder stocks for genetic improvement program which were established from several geographic origins may have caused admixture in the domesticated populations. The genetic information obtained from this study could help to establish appropriate breeding strategies and genetic improvement program, and would provide essential data for genetic management and conservation of P. monodon wild populations.
... RAPDs have gained considerable attention particularly in population genetics, species and subspecies identification, phylogenetic study, linkage group identification, chromosome and genome mapping, analysis of interspecific gene flow and hybrid speciation and as a potential source for single-locus genetic fingerprints (Brown and Epifanio, 2003). These markers have been used for species identification or interspecies genetic relationship in fishes (Naish et al., 1995;Partis and Wells, 1996;Dahle et al., 1997;Das et al., 2005;Lakra et al., 2007), molluscs (Klinbunga et al., 2000), Argulus parasites (Sahoo et al., 2013) and shrimp (Shi et al., 1999;Song et al., 1999;Zhuang et al., 2001), and analysis of population structure in shrimp (Tassanakajon et al., 1997;1998;Klinbunga et al., 2001;Mishra et al., 2009), catfish and scampi (See et al., 2008;Islam et al., 2014;Mohanty et al., 2014). Sun et al. (2000) applied the techniques of RAPD and AFLP to analyze the relationships among four species of Artemia species and strains, and reported that RAPD markers successfully detected diversity and genetic differentiation among them. ...
Giant freshwater prawn, Macrobrachium rosenbergii is an important freshwater crustacean widely cultured in several countries including India. Of late, its production has come down due to slow growth rate and disease occurrences. The ICAR-Central Institute of Freshwater Aquaculture (ICAR-CIFA), Bhubaneswar in collaboration with the WorldFish, Malaysia has initiated a selective breeding programme for growth improvement of this species. In the present study, two groups of families (I. six numbers of families for growth and II. six numbers of families for disease resistance) were selected for experimentation from the families produced in the fourth generation of selection programme. Each group consisted of two extreme sub-groups of three families in each with higher and lower growth (based on weight) under group I and, susceptible and resistant families (based on larval survival following challenge with Vibrio harveyi) under group II. RAPD- PCR was used to evaluate the genetic variations between and within groups separately. Twelve selected decamer primers were used to amplify DNA fragments of three individuals of each family and data were analyzed by POPGENE version 1.31 software. In group I, a total of 102 bands were scored by the primers out of which 41 bands (40.19%) found to be polymorphic. Genetic diversity within the group varied from 0.0272 0.0965 to 0.0463 0.1316. UPGMA dendrogram of this group based on Nei’s genetic distance showed that families 5 (low growth family 2) and 6 (low growth family 3) are distantly related to high growth families. In the second group of disease resistance, 35 bands (36.46%) were found to be polymorphic out of 96 bands scored. Genetic diversity varied between 0.0301 ± 0.0957 to 0.0438 ± 0.1381 within this group. UPGMA dendrogram showed that families 1 (susceptible group 1) and 2 (susceptible group 2) are distantly related to three resistant families. Thus, the present results showed the existence of genetic variations in both growth and disease resistance traits that could be utilized in the selective breeding programme in M. rosenbergii.
... Understanding the genetic diversity of brood stocks is essential to managing wild populations in a sustainable and efficient manner. The genetic enhancement of commercial fish and shellfish species through the adaptation of selective breeding methods will support that information (Dinesh et al. 1993;Garcia and Benzie 1995;Tassanakajon et al. 1997). Microsatellites, also known as simple sequence repeats (SSRs), are found in almost all known eukaryotic and prokaryotic organisms and have a widespread distribution throughout the genome (Waber and Wong 1993). ...
Labeo fimbriatus is a medium carp species found throughout India's peninsular river basins and is regarded as a valuable aquaculture resource alongside Indian major carps due to its taste and nutritional value. This species has recently declined dramatically due to habitat degradation and overfishing. Because of its enormous economic importance, a selective breeding programme is likely to be in place to improve performance traits. Knowledge of genetic variation among the base population from which the broodstock will be selected is an important step in this process. A diverse genetic base of broodstock is required to achieve the best response to selection for long-term aquaculture management practices. Consequently, using mitochondrial DNA (ATPase 6 and Control region) and microsatellite markers, we have made the first step toward estimating the level of genetic variation and how it is distributed among the four populations of L. fimbriatus found in peninsular rivers in India. The ATPase 6 gene analysis in four populations revealed 15 haplotypes and 51 variable sites, in contrast to the Control region, which had 60 haplotypes together with 73 variable sites and a haplotype diversity of 0.941. Twelve microsatellite loci displayed estimated allele numbers (NA) ranging from 3 to 19, observed heterozygosity (HO), and expected heterozygosity (HE), respectively, of 0.705 to 0.753 and 0.657 to 0.914. Each marker type showed a significant FST value, indicating the presence of low to moderate genetic differentiation across entire wild populations. The Godavari, Kaveri, and Mahanadi populations formed one cluster according to the UPGMA, which was based on genetic distance matrix, while the Krishna population formed a separate cluster. The comparative genetic analysis of data from different markers utilized in the current study would enable the identification of the genetic stocks of L. fimbriatus and facilitate conservation measures and selective breeding.
... While such a high-quality draft genome sequence has not been reported for P. monodon, over the past two decades, several attempts have been made to investigate the genetic architecture of this important species. BAC library construction (Wuthisuthimethavee et al., 2009), fosmid library end sequencing (Huang et al., 2011), molecular marker development (Brooker et al., 2000;Tassanakajon et al., ,1997Tassanakajon et al., , , 1998, linkage map construction (Baranski et al., 2014;Wilson et al., 2002), and transcriptome analysis Karoonuthaisiri et al., 2009;Leelatanawit et al., 2011;Lehnert et al., 1999;Pootakham et al., 2020;Sittikankaew et al., 2020;Supungul et al., 2002;Tassanakajon et al., 2006;Tong et al., 2002;Uengwetwanit et al., 2018) were successfully explored, but these attempts yielded rather limited genome information. Previous attempts to obtain genome sequence data of the black tiger shrimp relied primarily on short-read sequencing platforms. ...
To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade. However, its currently available genome assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), the highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several growth-associated genes. Our high-quality genome assembly provides an invaluable resource for genetic improvement and breeding penaeid shrimp in aquaculture. The availability of P. monodon genome enables analyses of ecological impact, environment adaptation and evolution, as well as the role of the genome to protect the ecological resources by promoting sustainable shrimp farming.
... Results suggested large nonadditive genetic effects and/or common environmental effects that could not be differentiated on the available data (Benzie, 1997;Benzie et al., 1997). RAPD was used to amplify the genome of tiger prawns by Tassanakajon et al. (1997Tassanakajon et al. ( , 1998a. Analysis of wild populations and broodstocks revealed different levels of genetic variability among them, suggesting a high genetic variability to be used in selective breeding programmes (Benzie, 2000). ...
... In the Philippines, P. m onod on farming started in the 1980s (Lavilla-Pitogo and de la Peña 1998) and production reached its peak in the early 1990s when the Philippines became the top P. m onod on producer in the world ( Cruz et al. 2008). Similar to the practice in other P. m onod onproducing countries (e.g., Thailand, Tassanakajon et al. 1997), P. monodon aquaculture in the Philippines still relies on broodstock caught from the wild as sources of cultured stocks. ...
The mitochondrial cytochrome oxidase I (COI) marker, widely used in phylogenetic and DNA barcoding studies, may also be informative with respect to intraspecies diversity and regional scale population structure. It is particularly useful when data reported from other studies and relevant for comparative studies were mostly generated using this marker. In this study, the COI marker was used to investigate the genetic diversity and structure of populations of the black tiger shrimp, Penaeus monodon (Fabricius, 1798), in the Philippines. Wild specimens were obtained from six locations across the Philippine archipelago. Among the 146 COI sequences observed, only 15 haplotypes were identified of which only three were found to be frequent and widely distributed and the others were either unique to a site, or found in only two sites. The COI sequences therefore indicated that the six sites did not show significant genetic differentiation based on the Chi-square test, analysis of molecular variance (AMOVA), and FST analysis. However, comparison of the data with those reported for Thailand revealed that the Philippine populations have significantly lower haplotype and nucleotide diversity. The three widely distributed haplotypes in the Philippines were also observed in Thailand; these three haplotypes appeared to be the ancestral forms as suggested by the haplotype network analysis. The Philippine haplotypes showed less sequence divergence among themselves and clustered mostly in one major lineage of the tree, although two haplotypes were found to be highly divergent and clustered with other Thai haplotypes. The genetic diversity discovered in the study represents a significant resource; it also highlights opportunities for selection of better performing stocks.
Labeo rohita, of the Cyprinidae family, is one of the most important fish species in any aquaculture system, with immense potential in terms of both commercial production and biodiversity maintenance. Accordingly, in order to find out the spatio-genetic variation and uncover any divergence in the population structure among the Labeo rohita population, partial sequencing of the 425 bp cytochrome b (mt Cytb) gene was carried out. The study revealed the presence of eleven haplotypes with nine polymorphic sites, of which 2 are singleton sites and six parsimony informative sites. It was observed that the haplotypes obtained from the same water system clustered separately, which suggests the variability due to the spatial distribution of the population in different environmental conditions. These detected high phenotypic differences between the rivers lead us to think and investigate that the divergent populations may have evolved over time and have been undergoing mutation. They may undergo micro-evolutionary processes and differentiate into genetically distinct sub-populations or stocks over time if reproductively and geographically isolated. Thus, the study signifies the presence of the huge biodiversity of Labeo rohita in the Indian River systems, which helps the species to adapt to the environmental changes and will also prove helpful for the breeding of new and better adaptable strains suitable for the climate change scenario.
The verification of authenticity and detection of food mislabeling are elements that have been of high importance for centuries. During the last few decades there has been an increasing consumer demand for the verification of food identity and the implementation of stricter controls around these matters. Fish and seafood are among the most easily adulterated foodstuffs mainly due to the significant alterations of the species' morphological characteristics that occur during the different types of processing, which render the visual identification of the animals impossible. Even simple processes, such as filleting remove very important morphological elements and suffice to prevent the visual identification of species in marketed products. Novel techniques have therefore been developed that allow identification of species, the differentiation between species and also the differentiation of individuals that belong to the same species but grow in different populations and regions. Molecular markers have been used during the last few decades to fulfill this purpose and several improvements have been implemented rendering their use applicable to a commercial scale. The reliability , accuracy, reproducibility, and time-and cost-effectiveness of these techniques allowed them to be established as routine methods in the industry and research institutes. This review article aims at presenting the most important molecular markers used for the authentication of fish and seafood. The most important techniques are described, and the results of numerous studies are outlined and discussed, allowing interested parties to easily access and compare information about several techniques and fish/seafood species.
