Development of SNP markers and validation 24 SNPs in darkbarbel catfish (Pelteobagrus vachelli) (original) (raw)
Related papers
Journal of Marine Science and Engineering, 2020
The striped catfish Pangasianodon hypophthalmus is an important freshwater fish cultured in many countries where the collection of wild brooders is still widely practiced. Global farming development of this species makes use of significant natural resources that pose challenges for the genetic diversity of striped catfish. Hence, this study aims to conduct a systematic genetic diversity assessment of wild and farmed catfish stocks collected from four major pangasius-farming countries, using a new genotyping by sequencing platform known as DArT-seq technology. Our population genomic analyses using 7263 single-nucleotide polymorphisms (SNPs) after high-quality-control showed that there were two distinct populations of striped catfish in the lower Mekong river: (i) wild catfish from Thailand and (ii) catfish from Cambodia and Vietnam. The genetic diversity was greatest (0.363) in the wild stock from Thailand, but it was lower in farmed and wild stocks in other countries (0.049 to 0.088...
Indonesian Aquaculture Journal
Genetic diversity is an important aspect of a selective breeding program to produce fish broodstock carrying superior traits such as fast-growing, disease resistant, and other traits. We have carried out a breeding program to produce a fast-growing striped catfish (Pangasianodon hypophthalmus) since 2010. The aim of this study was to evaluate the genetic variation of the first (G-1) and second (G-2) generations of fast-growing striped catfish using microsatellite analysis. The G-1 and G-2 populations were selected individually from populations. DNA samples were collected from 40 ind. fish of each population and analyzed using five microsatellite loci (Pg1, Pg2, Pg3, Pg13, and Pg14). The results showed that the number of alleles per loci in the G-1 and G2 populations ranged from 4 to 7 alleles, with an average of five for each generation. The average of observed heterozygosity of the G-1 population (0.420) was lower than the G-2 population (0.495). Inbreeding level showed that the G-...
Journal of Biosciences, 2001
Genetic similarity and diversity of cultured catfishSilurus asotus populations collected from two areas in western Korea were examined using randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). Out of 20 random primers tested, 5 produced 1344 RAPD bands ranging from 8.2 to 13.6 polymorphic bands per primer. The polymorphic bands in these populations ranged from 56.4% to 59.6%. Polymorphic bands per lane within populations ranged from 4.9% to 5.3%. The similarity within the Kunsan population varied from 0.39 to 0.82 with a mean (± SD) of 0.56 ± 0.08. The level of bandsharing values was 0.59 ± 007 within the catfish population from Yesan. The genetic similarity in cultured catfish populations may have been caused because individuals from two populations were reared in the same environmental conditions or by inbreeding during several generations. However, in view of bandsharing values, polymorphic bands and also the specific major bands that were inter-population-specific, significant genetic differentiation between these populations were present even if bandsharing (BS) values were somewhat numerically different. Therefore, the number of RAPD polymorphisms identified in this study may be sufficient to permit estimating genetic similarity and diversity. However, in future, additional populations, sampling sites and individuals will be necessary to make up for these weak points.
Putative SNP discovery in interspecific hybrids of catfish by comparative EST analysis
Animal Genetics, 2003
In this study, we identified putative SNP markers within genes by comparative analysis of expressed sequence tags (ESTs). Comparison of 849 ESTs from blue catfish (Ictalurus furcatus) with >11 000 ESTs from channel catfish (I. punctatus) deposited in GenBank resulted in the identification of 1020 putative SNPs within 161 genes, of which 145 were nuclear genes of known function. The observed frequency of SNPs within ESTs of the two closely related catfish species was 1.32 SNP per 100 bp. The majority of identified SNPs differed between the two species and, therefore, these SNPs are useful for mapping genes in channel catfish • blue catfish interspecific resource families. The SNPs that differed within species were also observed; these can be applied to genome scans in channel catfish resource families.
Molecular Ecology Resources, 2012
27 polymorphic EST-SSRs were used to analyze two natural populations of Clarias batrachus for population variability parameters. Allele numbers ranged from 2 to 12; and observed and expected heterozygosity values from 0.3658 and 0.6850; and 0.5668 and 0.5828, respectively. Fifteen loci showed no significant departure from HWE (p<0.05). Linkage disequilibrium test was significant for three pairs of loci. Two populations studied were found to be significantly divergent. Cross-species amplification for 7 loci was successful in two related species. These SSRs markers may be useful for the assessment of genetic variations and population differentiation studies in C. batrachus.
Development of microsatellite markers for use in breeding catfish, Rhamdia sp
African Journal of Biotechnology, 2015
Microsatellites markers for catfish, Rhamdia sp. were developed using Next Generation. A shotgun paired-end library was prepared according to standard protocol of Illumina Nextera DNA Library Kit with dual indexing, paired-end reads of 100 base pairs and grouped with other species. From a single race, five million readings obtained were analyzed with the program PAL_FINDER_v0.02.03. perl script was used to extract readings containing microsatellites with di-, tri-, tetra-, penta-and hexanucleotides from five million readings obtained in sequencing. Readings were grouped and used in Primer3 version 2.0.0 to design primers when GC content was greater than 30%, melting temperatures was within 58 to 65°C, with 2°C maximum difference between primers, the last 2 nucleotides in 3'extremity are G or C, and maximum poli-N of 4 nucleotides. When all criteria were met, a single pair of primers was selected according to the highest score in Primer3 and with greater amplification region of the repeated sequence. We identified 6,331 microsatellite loci potentially amplifiable (microsatellites) of which 4,755 were dinucleotide, 728 trinucleotide, 729 tetranucleotide, 117 pentanucleotídeo and 2 were hexanucleotídeo. A group of 12 loci microsatellite (including di-and tetranucleotides) has been sequenced, using Sanger's method, to obtain complete sequences for fragments between 140 and 200 pb and are currently being used to study the genetic diversity of catfish populations. The populations showed genetic variation with average number of alleles per locus of 6.14. Microsatellites acquired with Next-Generation Sequencing (NGS) are an efficient tool for obtaining highly polymorphic markers for non-model species.
Scientific reports, 2017
Single nucleotide polymorphisms (SNPs) are capable of providing the highest level of genome coverage for genomic and genetic analysis because of their abundance and relatively even distribution in the genome. Such a capacity, however, cannot be achieved without an efficient genotyping platform such as SNP arrays. In this work, we developed a high-density SNP array with 690,662 unique SNPs (herein 690 K array) that were relatively evenly distributed across the entire genome, and covered 98.6% of the reference genome sequence. Here we also report linkage mapping using the 690 K array, which allowed mapping of over 250,000 SNPs on the linkage map, the highest marker density among all the constructed linkage maps. These markers were mapped to 29 linkage groups (LGs) with 30,591 unique marker positions. This linkage map anchored 1,602 scaffolds of the reference genome sequence to LGs, accounting for over 97% of the total genome assembly. A total of 1,007 previously unmapped scaffolds wer...
Quality assessment parameters for EST-derived SNPs from catfish
BMC Genomics, 2008
Background SNPs are abundant, codominantly inherited, and sequence-tagged markers. They are highly adaptable to large-scale automated genotyping, and therefore, are most suitable for association studies and applicable to comparative genome analysis. However, discovery of SNPs requires genome sequencing efforts through whole genome sequencing or deep sequencing of reduced representation libraries. Such genome resources are not yet available for many species including catfish. A large resource of ESTs is to become available in catfish allowing identification of large number of SNPs, but reliability of EST-derived SNPs are relatively low because of sequencing errors. This project was designed to answer some of the questions relevant to quality assessment of EST-derived SNPs. Results wo factors were found to be most significant for validation of EST-derived SNPs: the contig size (number of sequences in the contig) and the minor allele sequence frequency. The larger the contigs were, the...
Freshwater habitat alteration and marine fisheries can affect anadromous fish species, and populations fluctuating in size elicit conservation concern and coordinated management. We describe the development and characterization of two sets of 96 single nucleotide polymorphism (SNP) assays for two species of anadromous alosine fishes, alewife and blueback herring (collectively known as river herring), that are native to the Atlantic coast of North America. We used data from high-throughput DNA se-quencing to discover SNPs and then developed molecular genetic assays for genotyp-ing sets of 96 individual loci in each species. The two sets of assays were validated with multiple populations that encompass both the geographic range and the known regional genetic stocks of both species. The SNP panels developed herein accurately resolved the genetic stock structure for alewife and blueback herring that was previously identified using microsatellites and assigned individuals to regional stock of origin with high accuracy. These genetic markers, which generate data that are easily shared and combined, will greatly facilitate ongoing conservation and management of river herring including genetic assignment of marine caught individuals to stock of origin.