scholarly journals Development of 30 SNP Markers for the Daphnia Magna based on Restriction Site-associated DNA Sequencing (RAD-seq)

2021 ◽  
Author(s):  
Shengman Zhang ◽  
Wenhui He ◽  
Haisu Zheng ◽  
Yiran Xiong ◽  
Meng Tan ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Daphnia Magna ◽  
Restriction Site ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genetics Research ◽  
Expected Heterozygosity ◽  
Water Ecosystem ◽  
Hardy Weinberg Equilibrium

Abstract Daphnia magna belongs to the Cladocera and plays an important role in the water ecosystem. With the intensification of water pollution, the wild population of D. magna has declined rapidly in recent years, and insufficient molecular markers have limited effective research and conservation of this species. In this research, 30 novel single nucleotide polymorphism (SNP) markers were developed in a cultivar of Daphnia magna and 12 wild Daphnia magna using restriction site-associated DNA sequencing (RAD-seq). The minor allele frequency, observed heterozygosity, and expected heterozygosity ranged from 0.115 to 0.721, 0.073 to 0.800, and 0.077 to 0.520, respectively. The PIC ranged from 0.071 to 0.403. Six loci showed significant deviations from the Hardy-Weinberg equilibrium after Bonferroni correction (p < 0.05).These newly developed polymorphic SNP markers for D. magna are of great significance in terms of the genetic breeding of D. magna, identification of wild and artificially domesticated species and conservation genetics research.

scholarly journals Development and characterization of 33 SNP markers in a critically endangered Hynobius amjiensis using ddRAD sequencing

2021 ◽  
Author(s):  
Xia Kan ◽  
Guoliang Wang ◽  
Lili Zhang ◽  
Xin Zhao ◽  
Shuangshuang Shan ◽  
...  
Keyword(s):  
Restriction Site ◽  
Snp Markers ◽  
Inbreeding Coefficient ◽  
Critically Endangered ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Critically Endangered Species ◽  
Expected Heterozygosity ◽  
Genetic Assessment

Abstract Hynobius amjiensis was considered as one of the 29 most threatened amphibian in China. To effectively conserve, manage and recover the population of this critically endangered species, 33 single nucleotide polymorphism (SNP) markers were developed using double digest restriction-site associated DNA (ddRAD) sequencing. The minor allele frequency per locus ranged from 0.0161 to 0.5000. The observed heterozygosity and expected heterozygosity varied from 0.0323 to 0.6667 (average 0.3303) and from 0.0317 to 0.5000 (average 0.2772), respectively. The inbreeding coefficient value ranged between − 0.3315 and 0.0000. No significant deviation from Hardy-Weinberg equlibrium (P > 0.05) were found in all loci. These novel SNPs will be helpful for the population genetic assessment and conservation of H. amjiensis.

scholarly journals Development And Identification of 131 SNP Markers In Sthenoteuthis Pteropus (Steenstrup)

2021 ◽  
Author(s):  
Yan Zhao ◽  
Congcong Wang ◽  
Bilin Liu ◽  
Gang Li ◽  
Hao Xu
Keyword(s):  
Molecular Markers ◽  
Snp Markers ◽  
Scientific Management ◽  
Sustainable Utilization ◽  
Bonferroni Correction ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Polymorphic Snps ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium

Abstract The orangeback flying squid, Sthenoteuthis pteropus, is a species of significant potential value that is widely distributed in the tropical and temperate waters of the Atlantic Ocean. There have been no reports of the population genetics and effective molecular markers for this species due to a lack of reliable information regarding its genetic structure and its many individual differences, as well as its complex and changeable life history. Therefore, the development of auxiliary molecular markers would contribute to the development, sustainable utilization, and protection of the species. In this study, 131 novel single nucleotide polymorphism (SNP) markers were developed by double digest restriction-site associated DNA sequencing (dd-RAD). The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.00 to 0.80 and 0.18 to 0.50, respectively. The polymorphism information content (PIC) value ranged from 0.18 to 0.50. None of the marker locations significantly deviated from the Hardy-Weinberg equilibrium (p >0.05) after a Bonferroni correction. These polymorphic SNPs will be important in the further analysis of the population heredity of S. pteropus and its scientific management.

scholarly journals Species-Specific Marker Discovery in Tilapia

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mochamad Syaifudin ◽  
Michaël Bekaert ◽  
John B. Taggart ◽  
Kerry L. Bartie ◽  
Stefanie Wehner ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Restriction Site ◽  
De Novo ◽  
Snp Markers ◽  
Specific Marker ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Species Analysis ◽  
Species Specific ◽  
Marker Discovery

Abstract Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations.

scholarly journals Development a Set of 46 SNP Markers for the Yellow Catfish (Tachysurus Fulvidraco)

2021 ◽  
Author(s):  
Huaxing Zhou ◽  
Tingshuang Pan ◽  
Huan Wang ◽  
He Jiang ◽  
Jun Ling ◽  
...  
Keyword(s):  
Snp Markers ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Yellow Catfish ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium ◽  
Whole Genome Resequencing ◽  
Tachysurus Fulvidraco

Abstract The whole genome resequencing was used to develop single nucleotide polymorphisms (SNP) markers for the yellow catfish (Tachysurus fulvidraco). A total of 46 SNP markers were selected from 5550676 genotyping markers which distributed on 26 chromosomes. Of the 46 SNPs analyzed, 35 SNPs conformed to Hardy-Weinberg equilibrium. The observed and expected heterozygosity of these markers ranged from 0.2519 to 0.771 and from 0.265 to 0.5018, respectively. This set of markers will be of great useful for population genetics of the yellow catfish.

scholarly journals Characterization of Single Nucleotide Polymorphism Marker in the Chinese Giant Salamander Andrias davidianus

2021 ◽  
Author(s):  
Quanhe Wang ◽  
Lei Cheng ◽  
Haifeng Tian ◽  
Xiaoli Dong ◽  
Hanbing Xiao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Nutritional Value ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Andrias Davidianus ◽  
Allele Number ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium ◽  
Chinese Giant Salamander

Background: Chinese giant salamander Andrias davidianus is called “baby fish” in China. Due to its palatability and nutritional value, it was widely cultured in China. The current study was to evaluate the genetic diversity of the farmed A. davidianus. Methods: 30 salamanders were collected from farm and DNA was extracted. Thirty contigs potentially containing SNPs were selected from the previously developed RAD-seq library. The primer was designed and PCR was performed, than the products was sequenced from different direction. At last the sequences were analyzed using the vector NTI 10.Result: 5824bp high-quality sequences embodied in 16 contigs were sequenced and eighty SNP loci were identified which each SNP locus exhibited bi-alleles. The effective allele number from 1.03 to 2.00 and the minor allele frequency was 0.017 to 0.500. The expected heterozygosity was from 0.0333 to 0.5091 and the observed heterozygosity was 0.0333 to 1.0000. Sixty-six of the 80 loci significantly deviated from the Hardy-Weinberg equilibrium (P less than 0.05). The results provide useful genomic resources to evaluate the genetic diversity of A. davidianus for conservation and aquaculture.

scholarly journals Development of SNP markers derived from RAD sequencing for Atlantic salmon (Salmo salar L.) inhabiting the rivers of southern England

2021 ◽  
Author(s):  
R. Andrew King ◽  
Jamie R. Stevens
Keyword(s):  
Atlantic Salmon ◽  
Restriction Site ◽  
Snp Markers ◽  
Rad Sequencing ◽  
Effective Management ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Southern England ◽  
Target Populations ◽  
The Uk

AbstractThe rivers of the Hampshire Basin, southern England contain a genetically unique group of Atlantic salmon that have suffered dramatic declines in numbers over the last 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 94 single nucleotide polymorphism (SNP) loci for salmon from this region and investigate their applicability and variability in both target (i.e. southern English) and non-target populations. The SNP loci will be useful for population genetic and assignment studies on Atlantic salmon within the UK and beyond.

scholarly journals Development of 105 SNP markers in endangered turtle species Pelodiscus sinensis using RAD-seq

2021 ◽  
Author(s):  
Qiming Xie ◽  
Fan Liu ◽  
Jilong Zhang ◽  
Xilei Li ◽  
Tiantian Chen ◽  
...  
Keyword(s):  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
High Quality ◽  
Pelodiscus Sinensis ◽  
Single Nucleotide ◽  
Important Species ◽  
Turtle Species ◽  
Expected Heterozygosity ◽  
Genome Wide ◽  
Commercially Important

Abstract In this study, Restriction site-associated DNA sequencing (RAD-seq) was used to develop single-nucleotide polymorphism (SNP) markers for Pelodiscus sinensis, which is a commercially important species in China. We collected 15 individuals from Anhui Province and RAD-seq data of 20 individuals from NCBI: PRJNA530350 to screen high quality SNP maker through genome-wide. A total of 105 high-quality SNP markers were identified. The population genetic statistics showed that the minor allele frequency varied from 0.0571 to 0.3382, and the observed heterozygosity and expected heterozygosity ranged from 0.1143 to 0.6765 and 0.1078 to 0.4477, respectively. These novel SNP markers will serve as a valuable genetic tool for future conservation and population genetics studies in P. sinensis.

scholarly journals Developmentof 84 single nucleotide polymorphism (SNP) markers for the three-spot swimming crab (Portunus sanguinolentus) by using RAD appoach Guidong Miao1,2,3 Feng Wang1,2,3 Jihua Guo1,2,3, Pei Zhang1,2,3 Hongyu Ma4

2021 ◽  
Author(s):  
Guidong Miao ◽  
Feng Wang ◽  
Jihua Guo ◽  
Pei Zhang ◽  
Hongyu Ma
Keyword(s):  
Dna Sequences ◽  
Average Frequency ◽  
Snp Markers ◽  
Swimming Crab ◽  
Nucleotide Polymorphism ◽  
Base Pairs ◽  
Single Nucleotide ◽  
Large Size ◽  
Pcr Products ◽  
Hardy Weinberg Equilibrium

Abstract The three-spot swimming crab (Portunus sanguinolentus) is one of most important large size economic crab in China. In this study, we first isolated and characterized a set of 84 SNP loci in P. sanguinolentus. 10 pairs of primers PCR products were sequenced and a total of 3181bp high-quality DNA sequences were obtained from which 84 polymorphic SNP loci were identifed and 84 SNP loci were identified and accurated genotyped. The average frequency of SNP loci was one locus every 38 base pairs in P. sanguinolentus genome. Of these 84 SNP loci, each had bi-alleles with the minor allele frequency ranging from 0.0167 to 0.5000. The observed heterozygosity varied from 0.0333 to 0.7143, while the expected heterozygosity ranged from 0.0333 to 0.5085 per locus. 51 loci showed low variation (HO ≤ 0.3) and fourteen SNP loci showed high variation (HO ≥ 0.5). Among 84 SNP loci, 11 loci showed significant deviation from Hardy–Weinberg Equilibrium. The SNP markers developed herein will provide valuable information for elucidating population genetic diversity, population dynamics, and conservation genetics of this germplasm resource and other related crab species.

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