scholarly journals Development and characterization of 57 SNP markers in Misgurnus anguillicaudatus

2021 ◽  
Author(s):  
Guiyun Huang ◽  
Fengying Gao ◽  
Zhigang Liu ◽  
Jianmeng Cao ◽  
Gang Chen ◽  
...  
Keyword(s):  
Snp Markers ◽  
Freshwater Species ◽  
Nucleotide Polymorphisms ◽  
Misgurnus Anguillicaudatus ◽  
Population Genetic Analysis ◽  
Single Nucleotide ◽  
Natural Resource Conservation ◽  
Hardy Weinberg Equilibrium ◽  
Selection Of

Abstract The dojo loach Misgurnus anguillicaudatus is an endemic freshwater species to Asia. The effective conservation and molecular-aided selection of M. anguillicaudatus have been limited without sufficient molecular markers. In this study, 112 novel single nucleotide polymorphisms (SNPs) were screened based on 2b-RAD sequencing database, and 57 SNP markers were developed and characterized by genotyping 40 individuals using SNaPshot method. The observed heterozygosity (Ho) ranged from 0.025 to 0.675, while the expected heterozygosity (He) varied from 0.025 to 0.500. The minor allele frequency (MAF) ranged from 0.013 to 0.500. Among these SNPs, 18 loci were found to deviate significantly from the Hardy–Weinberg equilibrium after Bonferroni correction (P < 0.05). The first set of SNP markers developed from M. anguillicaudatus will provide valuable information in further population genetic analysis and natural resource conservation.

scholarly journals Development and Characterization of 177 SNP Markers in The Mud Shrimp Upogebia Major

2021 ◽  
Author(s):  
Lijun Wang ◽  
Chenghong Wang ◽  
Yunqi Song ◽  
Jirui Zhang ◽  
Donghui Sun ◽  
...  
Keyword(s):  
Polymorphic Information Content ◽  
Snp Markers ◽  
Population Genetic Analysis ◽  
Illumina Hiseq ◽  
Important Species ◽  
Natural Resource Conservation ◽  
Polymorphic Snps ◽  
Hardy Weinberg Equilibrium ◽  
Mud Shrimp

Abstract The mud shrimp Upogebia major (De Haan, 1841) (Crustacea, Decapoda, Gebiidea) is an important species widely distributed in coastal shallow waters. As an active initiation species, it has contributed significantly to the maintenance of coastal benthic biodiversity. However, there is still a lack of effective molecular markers to effectively protect and manage this species. In this study, we used the DNeasy Blood & Tissue kit to extract DNA and Illumina HiSeq 4000 sequencing technology to obtain SNP marker resources. 177 single nucleotide polymorphism (SNP) markers were developed and characterized in U. major. The minor allele frequency raged from 0.0500 to 0.5000. The observed heterozygosity and expected heterozygosity ranged from 0.0333 to 0.9000 and from 0.0966 to 0.5085, respectively. Polymorphic information content ranged from 0.0905 to 0.3750. The inbreeding coefficient values varied from − 0.2902 to 0.5968. Seventeen loci showed significant deviations from the Hardy-Weinberg equilibrium (P < 0.05). The polymorphic SNPs will be helpful for the further population genetic analysis and natural resource conservation of U. major.

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 Development and Characterization of 37 SNP Markers For The Largemouth Bass (Micropterus Salmoides) By Using PCR-RFLP Method

2021 ◽  
Author(s):  
Zhou Jiang ◽  
Jiao Cui ◽  
Jiaqi Shao ◽  
Chuanju Dong ◽  
Jinxing Du ◽  
...  
Keyword(s):  
Largemouth Bass ◽  
Polymorphic Information Content ◽  
Micropterus Salmoides ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Single Nucleotide ◽  
Important Species ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium

Abstract Largemouth bass (Micropterus salmoides) is an economically important species in China. Contrary to its rapidly increasing yield during the last decades, the domestic genetic diversity of largemouth bass has gradually declined. For further rationally excavation and utilization of largemouth bass germplasm resources, 37 single nucleotide polymorphism (SNP) markers were developed based on genotyping-by-sequencing (GBS) data and characterized by genotyping 32 individuals using the PCR-RFLP method. The effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphic information content (PIC) of these SNPs ranged from 1.168 to 1.998, 0.156 to 0.844, 0.146 to 0.507, and 0.134 to 0.375, respectively. Totally, five loci deviated significantly from Hardy-Weinberg equilibrium (p < 0.05), while there existed no linkage disequilibrium at all loci. These novel polymorphic markers will lay the foundation for future population and conservation genetics of M. salmoides.

scholarly journals Efficiency of using SNP markers in the MSTN gene in the selection of the Pushkin breed chickens

2020 ◽  
Vol 23 (8) ◽  
pp. 993-998 ◽  
Author(s):  
N. V. Dementeva ◽  
A. B. Vakhrameev ◽  
T. A. Larkina ◽  
O. V. Mitrofanova
Keyword(s):  
Molecular Genetic ◽  
Live Weight ◽  
Snp Markers ◽  
Experimental Population ◽  
Adult Bird ◽  
Nucleotide Polymorphisms ◽  
Poultry Industry ◽  
Single Nucleotide ◽  
Low Efficiency ◽  
Selection Of

In the poultry industry, indicators reflecting the growth rate of young stock and the exterior characteristics of chickens are important benchmarks for breeding. Traditional selection based on phenotypic evaluation is characterized by low efficiency with a low character inheritance ratio and is difficult to apply in small groups of animals and birds bred in bioresource collections. The use of molecular genetic markers associated with economically important traits makes it possible to carry out early selection of birds. This entails an increase in the profitability of the poultry industry. Recently, single nucleotide polymorphisms (SNPs) have served as convenient markers for selection purposes. For five generations (P1–P5), an experimental selection of hens of the Pushkin breed was carried out for live weight. It was based on selection for single nucleotide polymorphism rs313744840 in the MSTN gene. As a result, a significant increase in the frequency of allele A in this gene, from 0.11 to 0.50, took place. The association of SNP markers with meat qualities in the experimental group led to changes in the exterior profile of an adult bird at 330 days of age. The individuals with the AA and AG genotypes had the greatest live weight and longest body. As a result of selection, the bird on average became larger due to an increase in the number of heterozygous individuals with long bodies and large chest girths. The depth of the chest and the width of the pelvis increased due to an increase in the frequency of allele A in the experimental population. A tendency towards an increase in these indicators with the substitution of G with A in the genotype was found. Saturation of the population with desirable alleles led to an increase in the average live weight of the chickens. Analysis of the exterior parameters of adult birds showed that this growth is achieved by increasing the depth and volume of the bird body, and not by increasing the length of the limbs. Thus, marker selection carried out for five generations in the experimental population of Pushkin breed chickens to increase body weight has reliably (p < 0.001) changed the exterior profile of adult birds.

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 Mutations in NLRP5 and NLRP9 Are Associated with Litter Size in Small Tail Han Sheep

Animals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 689 ◽  
Author(s):  
Zhuangbiao Zhang ◽  
Jishun Tang ◽  
Xiaoyun He ◽  
Ran Di ◽  
Mingxing Chu
Keyword(s):  
Genetic Analysis ◽  
Litter Size ◽  
Population Genetic ◽  
Nucleotide Polymorphisms ◽  
Population Genetic Analysis ◽  
Single Nucleotide ◽  
Sheep Breeds ◽  
Reproductive Genes ◽  
Pyrin Domain ◽  
Hardy Weinberg Equilibrium

Previous studies showed that the NLR family pyrin domain-containing 5 (NLRP5) and NLRP9 genes are two important reproductive genes; however, their effects on sheep litter size are unknown. Therefore, in this study, we first genotyped seven sheep breeds via the MassARRAY® SNP system at the loci g.60495375A > G, g.60495363G > A, and g.60499690C > A in NLRP5, and g.59030623T > C and g.59043397A > C in NLRP9. Our results revealed that each locus in most sheep breeds contained three genotypes. Then, we conducted population genetic analysis of single nucleotide polymorphisms in NLRP5 and NLRP9, and we found that the polymorphism information content value in all sheep breeds ranged from 0 to 0.36, and most sheep breeds were under Hardy–Weinberg equilibrium (p > 0.05). Furthermore, association analysis in Small Tail Han sheep indicated that two loci, g.60495363G > A in NLRP5 and g.59030623T > C in NLRP9, were highly associated with litter size. The mutation in g.60495363G > A may decrease interactions of NLRP5 with proteins, such as GDF9, whereas the mutation in g.59030623T > C may enhance the combining capacity of NLRP9 with these proteins; consequently, these mutations may influence the ovulation rate and even litter size. The findings of our study provide valuable genetic markers that can be used to improve the breeding of sheep and even other mammals.

scholarly journals Characterization of Indonesian pigmented rice (Oryza sativa) based on morphology and Single Nucleotide Polymorphisms

2019 ◽  
Vol 20 (4) ◽  
pp. 1208-1214 ◽  
Author(s):  
NUR SITI KURNIASIH ◽  
RATNA SUSANDARINI ◽  
FEBRI ADI SUSANTO ◽  
TRI RINI NURINGTYAS ◽  
GLYN JENKINS ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Single Nucleotide Polymorphisms ◽  
Morphological Characters ◽  
Snp Markers ◽  
Hybrid Vigor ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pigmented Rice ◽  
Indica And Japonica Subspecies

Abstract. Kurniasih NS, Susandarini R, Susanto FA, Nuringtyas TR, Jenkins G, Purwestri YA. 2019. Characterization of Indonesian pigmented rice (Oryza sativa) based on morphology and Single Nucleotide Polymorphisms. Biodiversitas 20: 1208-1214. Indonesia has many cultivars of pigmented rice, but many variants have not been characterized using morphological characters and molecular markers. SNPs (Single Nucleotide polymorphisms) have been used in previous studies to identify the Indica and Japonica subspecies. Characterization of whether a line belongs to the Indica or Japonica subspecies is useful information for rice breeders, especially to generate line exhibiting the strong hybrid vigor. Morphological characters are used to determine the relationship between cultivars using cluster analysis. The SNP markers were amplified by PCR, sequenced and compared with sequences in the GenBank. Based on morphological characters, ten cultivars divide into two clusters. SNPs distinguish Indica and Japonica subspecies, and show that Hitam Lampung, Aek Sibundong, Melik, Hitam Toraja, Merah Kalimantan, and Merah Sumbawa belong to the Indica subspecies while Cempo Ireng and Pare Eja belong to Japonica. Abang Segreng and Hitam Toraja could not be clearly assigned to either the Indica or Japonica subspecies.

scholarly journals Single nucleotide polymorphism in Interleukin 1 alpha gene might be involved in the Oral Herpes recurrent episodes in Brazilian Para-Athletes

2021 ◽  
Vol 10 (16) ◽  
pp. e564101624166
Author(s):  
João Armando Brancher ◽  
Luana Mordask Bonetto ◽  
Eugenio Esteves Costa ◽  
Rodrigo Von Held ◽  
Jhenyfer da Silva Tavares ◽  
...  
Keyword(s):  
Association Studies ◽  
Interleukin 1 ◽  
Genetic Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Oral Herpes ◽  
Hardy Weinberg Equilibrium ◽  
Dna Collection ◽  
Alpha Gene

The main goal of this study was to investigate if there is an association between Oral Herpes (OH) recurrent episodes and Single Nucleotide Polymorphisms (SNPs) in IL1A, IL10, and IL1RN genes in a group of Brazilian Para-athletes. This transversal study was prepared according to the STrengthening the REporting of Genetic Association Studies (STREGA) guidelines. Oral examination and DNA collection for genotyping were performed in a non-probabilistic convenience sampling composed of Brazilian para-athletes who participated in a Brazilian selective competition. Data referring to the general characterization of sample were collected through a self-reported questionnaire. Candidate genes were chosen with the UCSC Genome Browser and SNPs in IL1A gene (rs17561, rs1304037), IL10 gene (rs1800871), and IL1RN gene (rs9005) were selected and investigated in allelic, genotypic, dominant, and recessive models. Hardy-Weinberg equilibrium was evaluated in each SNP. The sample was composed of 273 para-athletes (63 (23.4%) practice swimming, 61 (22.3%) powerlifting and 145 (63.7%) athletics). OH recurrent episodes was related by 47 (17.2%) para-athletes and the presence of T allele in the rs1304037 increased chance of OH.  These findings suggest that rs1304037 in IL1A gene is associated with OH recurrent episodes in para-athletes.

scholarly journals Heteroalleles in Common Wheat: Multiple Differences between Allelic Variants of the Gli-B1 Locus

2021 ◽  
Vol 22 (4) ◽  
pp. 1832
Author(s):  
Eugene Metakovsky ◽  
Laura Pascual ◽  
Patrizia Vaccino ◽  
Viktor Melnik ◽  
Marta Rodriguez-Quijano ◽  
...  
Keyword(s):  
Common Wheat ◽  
Dna Sequences ◽  
Fragment Length Polymorphism ◽  
Snp Markers ◽  
Group Iv ◽  
Nucleotide Polymorphisms ◽  
High Genetic Diversity ◽  
Single Nucleotide ◽  
Allelic Variants ◽  
B Genome

The Gli-B1-encoded γ-gliadins and non-coding γ-gliadin DNA sequences for 15 different alleles of common wheat have been compared using seven tests: electrophoretic mobility (EM) and molecular weight (MW) of the encoded major γ-gliadin, restriction fragment length polymorphism patterns (RFLPs) (three different markers), Gli-B1-γ-gliadin-pseudogene known SNP markers (Single nucleotide polymorphisms) and sequencing the pseudogene GAG56B. It was discovered that encoded γ-gliadins, with contrasting EM, had similar MWs. However, seven allelic variants (designated from I to VII) differed among them in the other six tests: I (alleles Gli-B1i, k, m, o), II (Gli-B1n, q, s), III (Gli-B1b), IV (Gli-B1e, f, g), V (Gli-B1h), VI (Gli-B1d) and VII (Gli-B1a). Allele Gli-B1c (variant VIII) was identical to the alleles from group IV in four of the tests. Some tests might show a fine difference between alleles belonging to the same variant. Our results attest in favor of the independent origin of at least seven variants at the Gli-B1 locus that might originate from deeply diverged genotypes of the donor(s) of the B genome in hexaploid wheat and therefore might be called “heteroallelic”. The donor’s particularities at the Gli-B1 locus might be conserved since that time and decisively contribute to the current high genetic diversity of common wheat.

Sign in / Sign up

Export Citation Format

Share Document