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 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 123 SNP Markers in Neotrypaea Japonica (Ortmann 1891)

2021 ◽  
Author(s):  
Xiaoyue Sun ◽  
Jirui Zhang ◽  
Zhiwei Che
Keyword(s):  
Theoretical Basis ◽  
Species Conservation ◽  
Snp Markers ◽  
Bonferroni Correction ◽  
Frequency Range ◽  
Polymorphic Snps ◽  
Expected Heterozygosity ◽  
Minor Alleles ◽  
Hardy Weinberg Equilibrium

Abstract Neotrypaea japonica (Ortmann 1891) is a burrowing shrimp that lives in tidal flats. In this study, 123 SNP markers were isolated and characterized from N. japonica. The frequency range of minor alleles varied from 0.2500 to 0.4833, the observed heterozygosity ranged from 0.4333 to 0.9000, and the expected heterozygosity ranged from 0.4944 to 0.6503. The polymorphic parameter and inbreeding value varied from 0.3680 to 0.5651 and -0.2768 to 0.1045, respectively. Significant departures from Hardy-Weinberg equilibrium after Bonferroni correction (P < 0.05) were observed for 16 loci. The study of polymorphic SNPs will provide an important theoretical basis for further population genetic diversity analysis and species conservation of N. japonica.

scholarly journals Development and validation of 107 SNP markers in Todarodes pacificus (Ommastrephidae)

2021 ◽  
Author(s):  
Xiaoling Li ◽  
Xingxing Hu ◽  
Huajie Lu ◽  
Yang Liu ◽  
Congcong Wang
Keyword(s):  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Scientific Management ◽  
The Novel ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Todarodes Pacificus ◽  
Hardy Weinberg Equilibrium ◽  
Commercially Important ◽  
Development And Validation

Abstract Todarodes pacificus is a commercially important squid species; however, there is little information available regarding the population genetics of this species and effective molecular markers are still unavailable. In the present study, 107 novel single nucleotide polymorphism (SNP) markers were developed using Genotyping-by-Sequencing (GBS). The observed and expected heterozygosities ranged from 0.0345 to 0.5862 and 0.0339 to 0.4994, respectively. The polymorphism information content ranged from 0.0333 to 0.3747. Among these SNPs, all loci have been confirmed to fit the Hardy-Weinberg equilibrium (p > 0.05). The novel SNPs developed in this study will be helpful for the genetic conservation and scientific management of Todarodes pacificus.

scholarly journals Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2025
Author(s):  
Shyryn Almerekova ◽  
Yuliya Genievskaya ◽  
Saule Abugalieva ◽  
Kazuhiro Sato ◽  
Yerlan Turuspekov
Keyword(s):  
Population Structure ◽  
Heading Date ◽  
Snp Markers ◽  
Principal Coordinate Analysis ◽  
Neighbor Joining ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Polymorphic Snps ◽  
Ancestral Node

The genetic relationship and population structure of two-rowed barley accessions from Kazakhstan were assessed using single-nucleotide polymorphism (SNP) markers. Two different approaches were employed in the analysis: (1) the accessions from Kazakhstan were compared with barley samples from six different regions around the world using 1955 polymorphic SNPs, and (2) 94 accessions collected from six breeding programs from Kazakhstan were studied using 5636 polymorphic SNPs using a 9K Illumina Infinium assay. In the first approach, the neighbor-joining tree showed that the majority of the accessions from Kazakhstan were grouped in a separate subcluster with a common ancestral node; there was a sister subcluster that comprised mainly barley samples that originated in Europe. The Pearson’s correlation analysis suggested that Kazakh accessions were genetically close to samples from Africa and Europe. In the second approach, the application of the STRUCTURE package using 5636 polymorphic SNPs suggested that Kazakh barley samples consisted of five subclusters in three major clusters. The principal coordinate analysis plot showed that, among six breeding origins in Kazakhstan, the Krasnovodopad (KV) and Karaganda (KA) samples were the most distant groups. The assessment of the pedigrees in the KV and KA samples showed that the hybridization schemes in these breeding stations heavily used accessions from Ethiopia and Ukraine, respectively. The comparative analysis of the KV and KA samples allowed us to identify 214 SNPs with opposite allele frequencies that were tightly linked to 60 genes/gene blocks associated with plant adaptation traits, such as the heading date and plant height. The identified SNP markers can be efficiently used in studies of barley adaptation and deployed in breeding projects to develop new competitive cultivars.

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 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 Characterization of 135 SNP Markers in Chiton Acanthochitona Rubrolineatus

2021 ◽  
Author(s):  
Jirui zhang ◽  
Yunqi Song ◽  
Chenghong Wang ◽  
Shukui Zhang ◽  
Zilin Jiang ◽  
...  
Keyword(s):  
Snp Markers ◽  
Wild Populations ◽  
Effective Protection ◽  
Population Genetic Analysis ◽  
Important Species ◽  
Polymorphic Snps ◽  
Isolation And Characterization ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium

Abstract Acanthochitona rubrolineatus (Lischke, 1873) (Polyplacophora, Neoloricata, Cryptoplacidae) is an important species widely distributed in the middle and low tide zone of coastal intertidal zone along the China Sea coast. In recent years, the serious pollution of seawater has caused a sharp decline in the number of wild populations of A. rubrolineatus. Lacking of effective molecular markers limits the effective protection and management of this species. Studies for the isolation and characterization of 135 A. rubrolineatus SNPs markers were carried out. The frequency of minor allele ranges from 0.0125 to 0.5000. The observed heterozygosity and expected heterozygosity are 0.0000-0.9750, 0.0731-0.6696, respectively. The inbreeding value varies from -0.2902 to 0.9966. Among them, there are 27 sites markablely differently from Hardy-Weinberg equilibrium (P < 0.05). The study of the polymorphic SNPs will provide a therotical basis for further analysis of population genetic analysis on A. rubrolineatus.

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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