scholarly journals Identification of SNP markers associated with antler growth rate in sika deer (Cervus nippon)

2020 ◽  
Author(s):  
Pengfei Hu ◽  
Yongyan Deng ◽  
Hengxing Ba ◽  
chunyi li
Keyword(s):  
Growth Rate ◽  
Sika Deer ◽  
Cervus Nippon ◽  
Snp Markers ◽  
Whole Genome Sequencing Data ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Animal Genetic Resources ◽  
Antler Growth ◽  
Hardy Weinberg Equilibrium

Abstract Sika deer (Cervus nippon) constitutes one of the most valuable animal genetic resources in east Asia. The aim of this study was to identify and validate single nucleotide polymorphisms (SNPs) from antler growth-related genes of sika deer. The whole genome sequencing data of sika deer were used to identify SNP markers. Among them, 31 SNPs from antler growth-related genes exhibited significant polymorphism using genotyping by mass spectrometry. The observed and expected heterozygosities were ranged from 0.147 to 0.997 and 0.201 to 0.500, respectively. Significant deviation from the Hardy-Weinberg equilibrium was observed in 6 loci. These findings provide effective molecular detection markers for the study of variation in antler growth rate of sika deer.

scholarly journals Identification of SNP markers associated with antler growth rate in sika deer (Cervus nippon)

2020 ◽  
Author(s):  
Pengfei Hu ◽  
Yongyan Deng ◽  
Hengxing Ba ◽  
chunyi li
Keyword(s):  
Growth Rate ◽  
Sika Deer ◽  
Cervus Nippon ◽  
Snp Markers ◽  
Antler Growth

Abstract The authors have withdrawn this preprint due to author disagreement.

scholarly journals Genomic analyses provide insights into breed-of-origin effects from purebreds on three-way crossbred pigs

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8009
Author(s):  
Yu Lin ◽  
Qianzi Tang ◽  
Yan Li ◽  
Mengnan He ◽  
Long Jin ◽  
...  
Keyword(s):  
Principal Component ◽  
Snp Markers ◽  
Specific Pattern ◽  
Whole Genome Sequencing Data ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Heterozygous Snps ◽  
Specific Expression ◽  
Origin Effects ◽  
Crossbred Pigs

Crossbreeding is widely used aimed at improving crossbred performance for poultry and livestock. Alleles that are specific to different purebreds will yield a large number of heterozygous single-nucleotide polymorphisms (SNPs) in crossbred individuals, which are supposed to have the power to alter gene function or regulate gene expression. For pork production, a classic three-way crossbreeding system of Duroc × (Landrace × Yorkshire) (DLY) is generally used to produce terminal crossbred pigs with stable and prominent performance. Nonetheless, little is known about the breed-of-origin effects from purebreds on DLY pigs. In this study, we first estimated the distribution of heterozygous SNPs in three kinds of three-way crossbred pigs via whole genome sequencing data originated from three purebreds. The result suggested that DLY is a more effective strategy for three-way crossbreeding as it could yield more stably inherited heterozygous SNPs. We then sequenced a DLY pig family and identified 95, 79, 132 and 42 allele-specific expression (ASE) genes in adipose, heart, liver and skeletal muscle, respectively. Principal component analysis and unrestricted clustering analyses revealed the tissue-specific pattern of ASE genes, indicating the potential roles of ASE genes for development of DLY pigs. In summary, our findings provided a lot of candidate SNP markers and ASE genes for DLY three-way crossbreeding system, which may be valuable for pig breeding and production in the future.

scholarly journals Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1042
Author(s):  
Zhuoying Weng ◽  
Yang Yang ◽  
Xi Wang ◽  
Lina Wu ◽  
Sijie Hua ◽  
...  
Keyword(s):  
Fishery Management ◽  
Genotyping By Sequencing ◽  
Parentage Analysis ◽  
Snp Markers ◽  
Individual Identification ◽  
Pedigree Information ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Polymorphic Snps ◽  
Mixed Family

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

scholarly journals Population Genomics of American Mink Using Whole Genome Sequencing Data

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 258
Author(s):  
Karim Karimi ◽  
Duy Ngoc Do ◽  
Mehdi Sargolzaei ◽  
Younes Miar
Keyword(s):  
Population Genomics ◽  
Association Studies ◽  
American Mink ◽  
Population History ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Effective Population ◽  
Cross Validation Error

Characterizing the genetic structure and population history can facilitate the development of genomic breeding strategies for the American mink. In this study, we used the whole genome sequences of 100 mink from the Canadian Centre for Fur Animal Research (CCFAR) at the Dalhousie Faculty of Agriculture (Truro, NS, Canada) and Millbank Fur Farm (Rockwood, ON, Canada) to investigate their population structure, genetic diversity and linkage disequilibrium (LD) patterns. Analysis of molecular variance (AMOVA) indicated that the variation among color-types was significant (p < 0.001) and accounted for 18% of the total variation. The admixture analysis revealed that assuming three ancestral populations (K = 3) provided the lowest cross-validation error (0.49). The effective population size (Ne) at five generations ago was estimated to be 99 and 50 for CCFAR and Millbank Fur Farm, respectively. The LD patterns revealed that the average r2 reduced to <0.2 at genomic distances of >20 kb and >100 kb in CCFAR and Millbank Fur Farm suggesting that the density of 120,000 and 24,000 single nucleotide polymorphisms (SNP) would provide the adequate accuracy of genomic evaluation in these populations, respectively. These results indicated that accounting for admixture is critical for designing the SNP panels for genotype-phenotype association studies of American mink.

scholarly journals Phylogeographic Analysis Reveals Multiple International transmission Events Have Driven the Global Emergence of Escherichia coli O157:H7

2018 ◽  
Vol 69 (3) ◽  
pp. 428-437 ◽  
Author(s):  
Eelco Franz ◽  
Ovidiu Rotariu ◽  
Bruno S Lopes ◽  
Marion MacRae ◽  
James L Bono ◽  
...  
Keyword(s):  
United States ◽  
Disease Outbreaks ◽  
The United States ◽  
Human Case ◽  
Whole Genome Sequencing Data ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
E Coli ◽  
Phylogeographic Analysis ◽  
International Distribution

AbstractBackgroundShiga toxin–producing Escherchia coli (STEC) O157:H7 is a zoonotic pathogen that causes numerous food and waterborne disease outbreaks. It is globally distributed, but its origin and the temporal sequence of its geographical spread are unknown.MethodsWe analyzed whole-genome sequencing data of 757 isolates from 4 continents, and performed a pan-genome analysis to identify the core genome and, from this, extracted single-nucleotide polymorphisms. A timed phylogeographic analysis was performed on a subset of the isolates to investigate its worldwide spread.ResultsThe common ancestor of this set of isolates occurred around 1890 (1845–1925) and originated from the Netherlands. Phylogeographic analysis identified 34 major transmission events. The earliest were predominantly intercontinental, moving from Europe to Australia around 1937 (1909–1958), to the United States in 1941 (1921–1962), to Canada in 1960 (1943–1979), and from Australia to New Zealand in 1966 (1943–1982). This pre-dates the first reported human case of E. coli O157:H7, which was in 1975 from the United States.ConclusionsInter- and intra-continental transmission events have resulted in the current international distribution of E. coli O157:H7, and it is likely that these events were facilitated by animal movements (eg, Holstein Friesian cattle). These findings will inform policy on action that is crucial to reduce the further spread of E. coli O157:H7 and other (emerging) STEC strains globally.

scholarly journals Effects of Arginine Supplementation on Serum Metabolites and the Rumen Bacterial Community of Sika Deer (Cervus nippon)

2021 ◽  
Vol 8 ◽  
Author(s):  
Huazhe Si ◽  
Hanlu Liu ◽  
Weixiao Nan ◽  
Guangyu Li ◽  
Zhipeng Li ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Sika Deer ◽  
Growth Period ◽  
Cervus Nippon ◽  
Nutrient Metabolism ◽  
Antler Growth ◽  
Serum Biochemical ◽  
Relative Abundances ◽  
Biochemical Indices ◽  
Arginine Supplementation

Velvet antler is a regeneration organ of sika deer (Cervus nippon) and an important Chinese medicine, and nutrient metabolism affects its growth. Here, we investigated the effects of arginine supplementation on antler growth, serum biochemical indices, and the rumen bacterial community of sika deer during the antler growth period. Fifteen male sika deer (6 years old) were randomly assigned to three dietary groups, which were supplemented with 0 (n = 5, CON), 2.5 (n = 5, LArg), or 5.0 g/d (n = 5, HArg) L-arginine. The IGF-1, ALT and AST concentrations in the serum of LArg sika deer were significantly higher than those in the serum of CON (P &lt; 0.05) and HArg deer (P &lt; 0.05). The phyla Bacteroidetes, Firmicutes, and Proteobacteria were dominant in the rumen of sika deer among the three groups. Comparison of alpha diversities showed that the ACE and Chao1 indices significantly increased in the LArg and HArg groups compared with those in the CON group. PCoA and ANOSIM results showed that the bacterial community was significantly changed between the CON and LArg groups. Moreover, the relative abundances of Fibrobacter spp. and Prevotellaceae UCG-003 increased, but those of Clostridium sensu stricto 1 and Corynebacterium 1 decreased in the LArg and HArg groups compared with those in the CON group. Additionally, the relative abundances of 19 OTUs were significantly different between the LArg and HArg groups. These results revealed that arginine supplementation affected the sika deer rumen bacterial community and serum biochemical indices.

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 GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yu Wan ◽  
Ryan R. Wick ◽  
Justin Zobel ◽  
Danielle J. Ingle ◽  
Michael Inouye ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Level ◽  
R Package ◽  
Whole Genome Sequencing Data ◽  
Nucleotide Polymorphisms ◽  
Network Approach ◽  
Sequencing Data ◽  
Association Tests ◽  
Novel Approach ◽  
Antimicrobial Resistance Genes

Abstract Background Horizontal gene transfer contributes to bacterial evolution through mobilising genes across various taxonomical boundaries. It is frequently mediated by mobile genetic elements (MGEs), which may capture, maintain, and rearrange mobile genes and co-mobilise them between bacteria, causing horizontal gene co-transfer (HGcoT). This physical linkage between mobile genes poses a great threat to public health as it facilitates dissemination and co-selection of clinically important genes amongst bacteria. Although rapid accumulation of bacterial whole-genome sequencing data since the 2000s enables study of HGcoT at the population level, results based on genetic co-occurrence counts and simple association tests are usually confounded by bacterial population structure when sampled bacteria belong to the same species, leading to spurious conclusions. Results We have developed a network approach to explore WGS data for evidence of intraspecies HGcoT and have implemented it in R package GeneMates (github.com/wanyuac/GeneMates). The package takes as input an allelic presence-absence matrix of interested genes and a matrix of core-genome single-nucleotide polymorphisms, performs association tests with linear mixed models controlled for population structure, produces a network of significantly associated alleles, and identifies clusters within the network as plausible co-transferred alleles. GeneMates users may choose to score consistency of allelic physical distances measured in genome assemblies using a novel approach we have developed and overlay scores to the network for further evidence of HGcoT. Validation studies of GeneMates on known acquired antimicrobial resistance genes in Escherichia coli and Salmonella Typhimurium show advantages of our network approach over simple association analysis: (1) distinguishing between allelic co-occurrence driven by HGcoT and that driven by clonal reproduction, (2) evaluating effects of population structure on allelic co-occurrence, and (3) direct links between allele clusters in the network and MGEs when physical distances are incorporated. Conclusion GeneMates offers an effective approach to detection of intraspecies HGcoT using WGS data.

scholarly journals An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Lidia de los Ríos-Pérez ◽  
Julien A. Nguinkal ◽  
Marieke Verleih ◽  
Alexander Rebl ◽  
Ronald M. Brunner ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genome Assembly ◽  
Large Scale ◽  
High Density ◽  
Whole Genome Sequencing Data ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Sander Lucioperca ◽  
Economic Significance ◽  
Marker Distance

AbstractPikeperch (Sander lucioperca) is a fish species with growing economic significance in the aquaculture industry. However, successful positioning of pikeperch in large-scale aquaculture requires advances in our understanding of its genome organization. In this study, an ultra-high density linkage map for pikeperch comprising 24 linkage groups and 1,023,625 single nucleotide polymorphisms markers was constructed after genotyping whole-genome sequencing data from 11 broodstock and 363 progeny, belonging to 6 full-sib families. The sex-specific linkage maps spanned a total of 2985.16 cM in females and 2540.47 cM in males with an average inter-marker distance of 0.0030 and 0.0026 cM, respectively. The sex-averaged map spanned a total of 2725.53 cM with an average inter-marker distance of 0.0028 cM. Furthermore, the sex-averaged map was used for improving the contiguity and accuracy of the current pikeperch genome assembly. Based on 723,360 markers, 706 contigs were anchored and oriented into 24 pseudomolecules, covering a total of 896.48 Mb and accounting for 99.47% of the assembled genome size. The overall contiguity of the assembly improved with a scaffold N50 length of 41.06 Mb. Finally, an updated annotation of protein-coding genes and repetitive elements of the enhanced genome assembly is provided at NCBI.

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