scholarly journals Genetic structure of rainbow trout Oncorhynchus mykiss (Salmoniformes, Salmonidae) from aquaculture by DNA-markers

2021 ◽  
Vol 29 (1) ◽  
pp. 28-32
Author(s):  
О. Y. Bielikova ◽  
A. E. Mariutsa ◽  
A. I. Mruk ◽  
S. I. Tarasjuk ◽  
V. M. Romanenko
Keyword(s):  
Rainbow Trout ◽  
Genetic Structure ◽  
Dna Markers ◽  
Shannon Index ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Expected Heterozygosity ◽  
High Level ◽  
Issr Pcr ◽  
Local Stock ◽  
Simple Sequence

The rational use of valuable fish species from aquaculture is difficult to implement without knowledge of the state of the genetic structure of local stocks. Different types of DNA markers can be used to achieve the goals of selection and breeding work. The genetic structure of a local stock of rainbow trout (Oncorhynchus mykiss Walbaum, 1792) (Salmoniformes, Salmonidae) farmed in Ukraine was studied using DNA-markers: microsatellite (SSR-markers – simple-sequence repeats-markers) and intermicrosatellite (ISSR – inter-simple sequence repeat). Five fragments of trinucleotide microsatellite motifs with a single anchor nucleotide at the 3'-end were used as a primer for analysis by the ISSR-PCR method. Totally, 85 amplicons were obtained across the five loci, of which 92.9% were polymorphic. The total number of alleles ranged from 10 (marker (ACC)₆G) to 23 (marker (AGC)₆G). The following monomorphic amplicons were determined for the studied local stock of rainbow trout: according to marker (CTC)₆C – 770 and 520 bp bands, for the marker (GAG)₆C – 345, 295 and 260 bp, and for the marker (AGC)₆C – 350 bp. The average number of polymorphic bands per locus was 15.8. The selected ISSR primers had a level of polymorphic information content above the average. The most effective markers for molecular-genetic analysis of rainbow trout were (AGC)₆G and (AGC)₆C according to the percentage of polymorphic bands, marker index, effective multiplex ratio and resolving power. The selected ISSR loci allow the genetic structure of the studied local stock to be characterized using the total and the effective number of alleles per locus (Na and Ne were 1.9 and 1.4, respectively), the Shannon index (average value I was 0.4) and the unbiased expected heterozygosity (mean uHe = 0.3). Microsatellite-based analysis showed features of the genetic structure of the local stock of rainbow trout at six microsatellite loci (OMM 1032, OMM 1077, OMM 1088, Str 15, Str 60, Str 73). Allelic diversity was established and alleles with the highest frequency and most typical for the given stock were identified. The Shannon index and unbiased expected heterozygosity were determined using SSR-markers and were 1.42 and 0.79, respectively. This depicts the complexity of the population structure, a high level of genetic diversity and indicates a high level of heterozygosity of local stock. The “gene pool profile” established as a result of ISSR-PCR in the future will help to differentiate local stocks of rainbow trout in aquaculture of Ukraine. Microsatellite markers provide the ability to determine individual features of genetic variation of local populations and to conduct the management of genetic resources on fish farms.

scholarly journals ASSESSMENT OF GENETIC STRUCTURE VARIABILITY OF RAINBOW TROUT Oncorhynchus mykiss (WALBAUM, 1792) OF UKRAINIAN LOCAL STOCKS USING POLYMORPHIC BLOOD PLASMA PROTEINS

2021 ◽  
Vol 14 (2) ◽  
pp. 37-46
Author(s):  
О. Yu. Bielikova ◽  
Keyword(s):  
Rainbow Trout ◽  
Genetic Structure ◽  
Blood Plasma ◽  
Plasma Proteins ◽  
Biochemical Genetics ◽  
Allelic Variants ◽  
Relative Electrophoretic Mobility ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Blood Plasma Proteins ◽  
High Level

Rainbow trout is a valuable species of aquaculture, which is characterized by a high level of variability. Aim. The goal was to study the peculiarities of genetic variability of rainbow trout based on polymorphism of transferrin (TF), posttransferrin (PTF), esterase (EST) (EC 3.1.1.1.) and albumin (ALB) loci. Methods. Electrophoretic separation of plasma proteins of rainbow trout from three local stocks (Chernivtsi, Kharkiv and Transcarpathian) was carried out in the native polyacrylamide gel. Results. Peculiarities of the distribution and relative electrophoretic mobility of allelic variants of the studied loci of rainbow trout of Ukrainian local stocks were established.The results demonstrated the effectiveness of the analysis using methods of biochemical genetics to establish the characteristics of the genetic structure, the level of heterozygosity of local stocks and to carry out their differentiation. Conclusion. The use of selected markers would allow monitoring the dynamics of changes in the state of local stocks under the established conditions of cultivation in the future. Key words: rainbow trout, polymorphic blood plasma proteins, transferrin, posttransferrin, esterase, albumin.

scholarly journals Microsatellite-Based Analysis of Genetic Diversity and Population Structure of Rainbow Trout (Oncorhynchus mykiss) Cultured in Ukraine

2020 ◽  
Vol 5 (1) ◽  
pp. 29-39
Author(s):  
Оlena Bielikova ◽  
Serhii Тarasjuk ◽  
Antonina Mruk ◽  
Olga Zaloilo ◽  
Alexander Didenko
Keyword(s):  
Genetic Diversity ◽  
Rainbow Trout ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Principal Coordinates Analysis ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Principal Coordinates ◽  
High Level ◽  
High Degree ◽  
Simple Sequence

The genetic structure of rainbow trout farmed in Ukraine were characterized based on microsatellite loci. The selected set of SSR-markers (Simple-sequence repeatsmarkers) had a high degree of polymorphism that allowed determining the specificity of each local stock (average PIC value = 0.785 ± 0.034). The microsatellite analysis of rainbow trout from the studied stocks showed a high level of genetic diversity (uHe = 0.825 ± 0.030, PIC = 0.785 ± 0.034, I = 1.836 ± 0.127). The level of allelic diversity of the selected loci was high, where the average number of alleles per locus was 7.833, the effective number of alleles per locus was 5.687. The range of amplicon sizes of the studied loci and private alleles for each local group was determined. The cluster analysis showed the presence of three clusters. The range of genetic variability was presented in the graphical interpretation of the principal coordinates analysis (PCoA). Based on unbiased genetic distances, the Kharkiv and Transcarpathian local stocks were found to be the closest, while the Chernivtsi stock was the most distant from them.

scholarly journals GENOMIC DETERMINATION OF THE MOST IMPORTANT FATHER LINES OF SLOVAK PINZGAU COWS

AGROFOR ◽  
2016 ◽  
Vol 1 (3) ◽  
Author(s):  
Veronika KUKUČKOVÁ ◽  
Nina MORAVČÍKOVÁ ◽  
Radovan KASARDA
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
The State ◽  
Most Probable Number ◽  
Pedigree Data ◽  
Probable Number ◽  
Expected Heterozygosity ◽  
High Level ◽  
The Bayesian Approach

The aim of this study was to assess genetic structure of Slovak Pinzgau populationbased on polymorphism at molecular markers using statistical methods. Femaleoffspring of 12 most frequently used bulls in Slovak Pinzgau breeding programmewere investigated. Pinzgau cattle were found to have a high level of diversity,supported by the number of alleles observed across loci (average 5.31, range 2-11)and by the high within-breed expected heterozygosity (average 0.66, range 0.64-0.73). The state of genetic diversity is satisfying and standard for local populations.Detection of 12 possible subpopulation structures provided us with detailedinformation of the genetic structure. The Bayesian approach was applied, detectingthree, as the most probable number of clusters. The similarity of eachsubpopulation using microsatellites was confirmed also by high-throughputmolecular data. The observed inbreeding (FROH=2.3%) was higher than thatexpected based on pedigree data (FPED=0.4%) due to the limited number ofavailable generations in pedigree data. One of the most important steps indevelopment of efficient autochthonous breed protection programs ischaracterization of genetic variability and assessment of the population structure.The chosen set of microsatellites confirmed the suitability in determination of thesubpopulations of Pinzgau cattle in Slovakia. The state of genetic diversity at moredetailed level was successfully performed using bovineSNP50 BeadChip.

scholarly journals Temporal Genetic Variance and Propagule-Driven Genetic Structure Characterize Naturalized Rainbow Trout (Oncorhynchus mykiss) from a Patagonian Lake Impacted by Trout Farming

PLoS ONE ◽  
2015 ◽  
Vol 10 (11) ◽  
pp. e0142040 ◽  
Author(s):  
Javiera N. Benavente ◽  
Lisa W. Seeb ◽  
James E. Seeb ◽  
Ivan Arismendi ◽  
Cristián E. Hernández ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Genetic Structure ◽  
Oncorhynchus Mykiss ◽  
Genetic Variance ◽  
Rainbow Trout Oncorhynchus Mykiss

scholarly journals Studies on Genetic Diversity of Selected Population of Hybrid Scallop Chlamys farreri（♀）× Patinopecten yessoensis（♂） by Microsatellites Markers

2015 ◽  
Vol 5 (1) ◽  
pp. 39 ◽  
Author(s):  
Biao Wu ◽  
Aiguo Yang ◽  
Ningning Cheng ◽  
Xiujun Sun ◽  
Zhihong Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Selective Breeding ◽  
Chlamys Farreri ◽  
Patinopecten Yessoensis ◽  
Microsatellites Markers ◽  
Expected Heterozygosity ◽  
Ssr Primers ◽  
Two Populations ◽  
Simple Sequence

<p class="1Body">The growth superiority of hybrid scallop <em>Chlamys farreri </em>(♀) × <em>Patinopecten yessoensis </em>(♂), as the following successive generation selection have been reported. However, the data about the genetic diversity in those population remains unexplored. In this study, the genetic structure analysis of F<sub>1</sub>, F<sub>2</sub> and F<sub>3 </sub>were conducted by PCR with 10 Simple Sequence Repeats (SSR) primers. It showed that a total of 68 alleles were detected, and the number of alleles per locus ranged from 3 to 11, Polymorphism Information Content<em> </em>(<em>PIC</em>) per locus ranged from 0.4729 to 0.8429. And, the average observed heterozygosity (<em>H<sub>o</sub></em>) of the three populations were 0.6100, 0.6975 and 0.7750, while the average expected heterozygosity (<em>H<sub>e</sub></em>) were 0.7607, 0.7751 and 0.7379 respectively. <em>F<sub>st </sub></em>values among the three populations were also low (<em>F<sub>st</sub></em>&lt;0.05) which suggested low genetic differentiation between each two populations. In all, those data indicated the genetic structure challenge caused by hybridization and selection, supplying a new angle to understand artificial selective breeding.</p>

scholarly journals Genetic diversity revealed by AFLP markers in Albanian goat breeds

2012 ◽  
Vol 64 (2) ◽  
pp. 799-807 ◽  
Author(s):  
Anila Hoda ◽  
Lumturi Sena ◽  
Gentian Hykaj
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Fragment Length Polymorphism ◽  
Similarity Index ◽  
Shannon Index ◽  
Upgma Tree ◽  
Expected Heterozygosity ◽  
The Mean ◽  
High Level ◽  
Aflp Technique

The amplified fragment length polymorphism (AFLP) technique with three EcoRI/TaqI primer combinations was used in 185 unrelated individuals, representative of 6 local goat breeds of Albania, and 107 markers were generated. The mean Nei?s expected heterozygosity value for the whole population was 0.199 and the mean Shannon index was 0.249, indicating a high level of within-breed diversity. Wright?s FST index, Nei?s unbiased genetic distance and Reynolds? genetic distance were calculated. Pairwise Fst values among the populations ranged from 0.019 to 0.047. A highly significant average FST of 0.031 was estimated, showing a low level of breed subdivision. Most of the variation is accounted for by differences among individuals. Cluster analysis based on Reynolds? genetic distance between breeds and PCA were performed. An individual UPGMA tree based on Jaccard?s similarity index showed clusters with individuals from all goat breeds. Analysis of population structure points to a high level of admixture among breeds.

scholarly journals Genetic Diversity and Fine-Scale Genetic Structure in Syagrus oleracea (Mart.) Becc.: A Survivor Palm Species of the Semiarid

2019 ◽  
Vol 11 (6) ◽  
pp. 373
Author(s):  
Luciana Rodrigues de Souza ◽  
Helbert Fagundes Soares ◽  
Sara Luiza Ramos Ribeiro ◽  
Afrânio Farias de Melo Junior ◽  
Murilo Malveira Brandão ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Shannon Index ◽  
Semiarid Region ◽  
Palm Tree ◽  
Effective Number ◽  
Expected Heterozygosity ◽  
Brazilian Semiarid ◽  
Palm Species

The species Syagrus oleracea is a native palm tree, present in highly impacted environments of the Brazilian semiarid. This species is exploited for use in the manufacture of folk crafts and for human and animal feeding. The objective of this study was to characterize the diversity and genetic structure of individuals from different populations, located in anthropic regions of the Brazilian semiarid region, in the state of Minas Gerais. This information is important for species management and conservation strategies. Thus, we used ISSR molecular markers in 157 individuals in seven populations of S. oleracea. Looking at the results, one can observe that amplifications of 109 locos occurred and that an average of 18, 17 alleles were found on each primer, values that demonstrated that the ISSR technique used was highly efficient. The genetic diversity indexes were observed, showing expected heterozygosity (He) and Shannon index (I) of 0.260 and 0.383, respectively. The number of alleles observed (na) among populations was 1.954 and the effective number of alleles (ne) was 1,606. Individuals of the populations are genetically structured in groups (demes) in a random and aggregate manner. We obtained the amplification of 109 ISSR loci, with a mean of 18.2 alleles per primer. The genetic diversity indexes revealed expected heterozygosity (He) and Shannon index (I) of 0.260 and 0.383, respectively. The number of alleles observed (na) was 1.954 and the effective number of alleles (ne) was 1.606. The value of the indirect gene flow found was 1.546. Evidence of high levels of kinship in populations was found, possibly due to low migration rates and geographical barrier. In addition, we observed signs of overexploitation in the areas, which consequently leads to a low rate of gene flow, occurring inbreeding among the sampled populations of Syagrus oleracea.

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