Figure - available from: Aquaculture International
This content is subject to copyright. Terms and conditions apply.
Pterophyllum scalare wild type (a), common morphological variant (b), marble morphological variant (c), and clown morphological variant (d). Source: apiqsels.com, b and c the author, and dpixabay.com
Source publication
The objective of the present work was to develop species-specific microsatellite markers for P. scalare and to analyze the diversity and genetic structure of a wild population, from the Amazon River, and three commercial stocks (common, marble, and clown morphological variants), from farmers in Vieras-Minas Gerais. Through microsatellite-enriched g...
Citations
... It is of the utmost importance to launch management programs in order to counteract their genetic diversity. The biodiversity of any exotic species can be evaluated effectively using microsatellite-based markers (22,23)). Microsatellites markers have been the most often used approaches in literature to examine the genetic variability of C. carpio (24). Microsatellites have an unusual role in population studies because of their neutrality in selecting samples, as well as the e ciency with which conclusions based on microsatellites can be parallelized and validated in different populations (25). ...
Conservation and management of Native fauna require understanding of invasive species genetic structure and diversity. Genotyping with 10 microsatellite markers was used to evaluate 300 samples of common carp and scale carp ( Cyprinus carpio L. and Cyprinus carpio communis ) from five natural populations on River Chenab in Pakistan. These strains exhibit low to moderate level of heterozygosities. The average FIS for C. carpio was 0.507 to 0.5914 while in C. c. communis , ranged from 0.5310 to 0.6166. The FST assessments showed there was a modest degree of genetic difference between the strains. Genetic distance was largest among strains and lowest among strain populations. AMOVA showed that 90.38% of C. carpio ’s variants were from intra-population variability and 9.62% from inter-population diversity. In C. c. communis , intra-population diversity fluctuated 12.92% and inter-population diversity 87.08%. STRUCTURE Bayesian clustering analysis grouped both strains populations into 10 groups. No genetic evidence of mixing was found for pristine, original strains. A high heterozygosity relative to expected heterozygosity in common carp strain populations suggests a bottleneck. The common carp strains' directional relative migratory network showed that HT (C.c) was the core population with the most genetic exchange with the other 5 peripheral populations. Nevertheless, no C.c. communis population showed migration event except HK C.c.c. Unweighted pair group method with averages (UPGMA) dendrogram shown two clusters: common carp and scale carp. We believe our findings may strengthen exotic species management practices.
... Microsatellites, also known as simple sequence repeats (SSR), are abundant and dispersed broadly in the coding region and non-coding region of eukaryote genome and are composed of short (2-5 bp) variable tandemly repeated arrays. SSR markers are very Genes 2022, 13, 1790 2 of 12 practical genetic markers widely used in many fields, such as paternity testing, molecular marker-assisted breeding, genetic map construction, quantitative trait loci location and population genetics [4,5]. ...
... Microsatellites, also known as simple sequence repeats (SSR), are abundant and dispersed broadly in the coding region and non-coding region of eukaryote genome and are composed of short (2-5 bp) variable tandemly repeated arrays. SSR markers are very practical genetic markers widely used in many fields, such as paternity testing, molecular marker-assisted breeding, genetic map construction, quantitative trait loci location and population genetics [4,5]. ...
Hemiculter leucisculus is an invasive fish and widely distributed in the Xinjiang Tarim River. In this study, RAD-seq was used to explore the genetic diversity and population subgroup structure of H. leucisculus in the Tarim River and develop relevant Simple Sequence Repeat (SSR) markers. The study collected 40 samples distributed at four different sites of the Tarim River. A total of 7,291,260 single nucleotide polymorphisms (SNPs) were obtained. The genetic diversity results showed that the population genetic diversity level of H. leucisculus was low. The population pairwise FST values ranged from 0.231 to 0.258, indicating that there was moderate genetic differentiation among these populations. AMOVA showed that the genetic variation within populations accounted for 92.31% of the total variation. The principal component analysis (PCA) and neighbor joining (NJ) tree revealed that the four populations could be separated into two clusters (upper-middle and downstream populations) and the individuals from Taitema Lake (TTMH) showed differences and had a bigger geographic distance than the others. There is the probability that the H. leucisculus from Bosten Lake entered Taitema Lake to breed and then expanded into the Tarim River due to the water diversion projects in location. In addition, 147,705 SSRs loci were detected and 22,651 SSR primer pairs were developed. This study will contribute to providing valuable molecular data for the management of wild populations, marker-assisted selection and resource exploitation of H. leucisculus.
... More than 15-20 molecular markers are necessary to assess the genetic diversity in fish [124][125][126][127]. Polymorphic markers are often selected for subsequent studies; however, this might introduce ascertainment bias and generally overestimate genetic diversity [128,129]. ...
The Siamese fighting fish (Betta splendens) is a well-known ornamental fish and emerging model species for studying animal morphology, physiology, and behavior. A key concern of betta inbreeding is the decline in genetic diversity resulting from commercial breeding programs. Therefore, it is essential to develop markers for understanding the genetic bases of the domestication and phenotypic diversification of this species. We utilized the previously assembled genome of Siamese fighting fish to identify and characterize microsatellites and compare their genomic organization across different species. We annotated 812,134 microsatellite loci spanning 30.70 Mb, accounting for 6.57% of the Siamese fighting fish genome. We performed in silico polymorphism screening of microsatellites in the Siamese fighting fish and related species and present these sequences as candidate markers for cross-species amplification. In addition, we successfully validated two microsatellite loci using PCR-based assays in different species, which can promote further genetic characterization of diverse betta lineages. The set of polymorphic markers identified in this study may facilitate the assessment of genetic diversity and population structure and marker-assisted selection, among other applications.
... This high level of genetic diversity could be the result of different source populations used to supplement the current pet shop populations [44]. Other examples of genetic diversity analyses performed on commercially traded fish include studies on red and white koi carp (Cyprinus carpio L) [45], guppies (Poecilia reticulata) [46], and freshwater angelfish (Pterophyllum scalare) [47]. High levels eastern Nepal; Clade 2, Bangladesh and southern India; and Clade 3, Central Nepal (Fig. 2). ...
... Another possibility is that perhaps only a few individuals, in the already reduced population, actively breed. The mean F IS for the angelfish populations [47] were close to zero, despite being wild populations. These authors speculated that a possible explanation for this observation is overfishing at the collection site. ...
... The genetic differentiation estimates showed little to no genetic difference between the three pet shop populations from the current study. On average the SA pet shop zebrafish had higher PIC values (average PIC = 0.67) than observed in red and white koi carp (average PIC = 0.557) [45] and angelfish (average PIC = 0.587) [47]. The Ar values from the current study, ranging from 5.851 to 4.600, differed only slightly from the values reported on zebrafish by Coe et al. [14] ranging 5.478 to 1.967, with the wild population being an exception with an Ar value of 14.126. ...
Background
Zebrafish (Danio rerio), a small freshwater fish that originates from India, Bangladesh, Nepal, Bhutan and northern Myanmar, have been widely used as a model organism for studies of developmental biology and genetics. The current study aimed to determine the origin of South African pet shop stock that are currently being used to establish a laboratory population founded from diverse sources available locally.
Methods and results
Zebrafish DNA was extracted from 65 specimens housed at the University of the Free State (UFS) Department of Genetics. For phylogenetic analysis, cytb sequences were generated from all samples. A further 178 sequences were downloaded from the GenBank database, including sequences of an outgroup species (Danio kyathit). Five microsatellite markers were used to further assess the genetic diversity of the UFS zebrafish specimens. A maximum likelihood analysis was performed for the cytb data. Results of the phylogenetic analyses divided the sequences into three major genetic groups, which was congruent with a previous study on laboratory zebrafish provenance. The SA pet shop fish grouped with the lines from the northern and north-eastern regions of India. High levels of microsatellite genetic diversity were observed for the pet shop sourced population, correlating to what has previously been observed in zebrafish.
Conclusion
These results can be used to guide the future development of laboratory lines suited to the needs at the UFS.
... Another possibility is that perhaps only a few individuals, in the already reduced population, actively breed. The mean F IS for the angel sh populations(Pandol et al. 2021) were close to zero, despite being wild populations. These authors speculated that a possible explanation for this observation is over shing at the collection site. ...
Zebrafish ( Danio rerio ), a small freshwater fish that originates from India, Bangladesh, Nepal, Bhutan and northern Myanmar, have been widely used as a model organism for studies of developmental biology and genetics. The current study aimed to determine the origin of South African pet shop stock that are currently being used to establish a laboratory population founded from diverse sources available locally. Zebrafish DNA was extracted from 65 specimens housed at the University of the Free State (UFS) Department of Genetics. For phylogenetic analysis, cytb sequences were generated from all samples. A further 178 sequences were downloaded from the GenBank database, including sequences of an outgroup species ( Danio kyathit ). Five microsatellite markers were used to further assess the genetic diversity of the UFS zebrafish specimens. A maximum likelihood analysis was performed for the cytb data. Results of the phylogenetic analyses divided the sequences into three major genetic groups, which was congruent with a previous study on laboratory zebrafish provenance. The SA pet shop fish grouped with the strains from the northern and north-eastern regions of India. High levels of microsatellite genetic diversity were observed for the pet shop sourced population, correlating to what has previously been observed in zebrafish. These results can be used to guide the future development of laboratory strains suited to the needs at the UFS.
The adaptative responses and divergent evolution shown in the environments habited by the Cichlidae family allow to understand different biological properties, including fish genetic diversity and structure studies. In a zone that has been historically submitted to different anthropogenic pressures, this study assessed the genetic diversity and population structure of cichlid Caquetaia kraussii, a sedentary species with parental care that has a significant ecological role for its contribution to redistribution and maintenance of sedimentologic processes in its distribution area. This study developed de novo 16 highly polymorphic species-specific microsatellite loci that allowed the estimation of the genetic diversity and differentiation in 319 individuals from natural populations in the area influenced by the Ituango hydroelectric project in the Colombian Cauca River. Caquetaia kraussii exhibits high genetic diversity levels (Ho: 0.562–0.885; He: 0.583–0.884) in relation to the average neotropical cichlids and a three group-spatial structure: two natural groups upstream and downstream the Nechí River mouth, and one group of individuals with high relatedness degree, possibly independently formed by founder effect in the dam zone. The three genetic groups show recent bottlenecks, but only the two natural groups have effective population size that suggest their long-term permanence. The information generated is relevant not only for management programs and species conservation purposes, but also for broadening the available knowledge on the factors influencing neotropical cichlids population genetics.
