Bioinformatic analysis of genomes of commercial breeds of domestic pigs for identification of breed-specific SNPs

Determining the purebredity of farm animals in a breeding system is of key importance for the entire livestock industry. Purebred breeding of plant breeds is designed to ensure the production of high-value improving breeding material for commercial livestock breeding. Determination of purebredity of pigs can be carried out using single nucleotide polymorphisms (SNP). The multiplexing technology today has reached a level that makes it possible to characterize tens and hundreds of thousands of polymorphic variants simultaneously for hundreds of animals in one run of the device. For the first time, using bioinformatics methods, an analysis of genome-wide projects was carried out for 264 individuals of the species Sus scrofa located in the Sequence Read Archive (NCBI-SRA). The in silico genotype was determined for 692 SNPs, of which 59 SNPs showed a significant potential for differentiation of four commercial breeds: large white (the most significant SNPs are Chr. 6: g.85845403T> G and Chr.16: g.74053569T> C), duroc (Chr. 4: g.55661608A> G, Chr. 14: g.107689091T> C and Chr. 14: g.107939105T> C), landrace (Chr. 5: g.99925204A> G, Chr. 18: g .40100481A> G and Chr. 18: g.7664624A> G) and pietrain (Chr. 13: g.136017764T> C and Chr.17: g.47595840A> G). For breeds of duroc and pietrain pigs, the accuracy of differentiation was at least 99%, for breeds of large white and landrace pigs - over 80%, however, the sensitivity indicator characterizing the percentage of false positive results of classification was slightly over 65%. Creation of models for molecularand-genetic studies of these breeds will allow for a genetic examination of their purebredity, which will contribute to an increase in their breeding value and preservation of the national gene pool.

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Genome-wide Association Study for Number of Vertebrae in an F2 Large White × Minzhu Population of Pigs

10.1101/016956 ◽

2015 ◽

Cited By ~ 2

Author(s):

Longchao Zhang ◽

Xin Liu ◽

Jing Liang ◽

Kebin Zhao ◽

Hua Yan ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Significant Snps ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Large White ◽

Genome Wide ◽

A Genome ◽

Mammalian Embryos ◽

Strong Candidate

Porcine carcass that is approximately 800 mm long may be expected to have one additional vertebra. Therefore, the number of vertebrae in pigs is an economically important trait. To examine the genetic basis of this trait, we genotyped 593 F2 Large White × Minzhu pigs using the Porcine SNP60K BeadChip. A genome-wide association study identified 39 significant single-nucleotide polymorphisms (SNPs) on the chromosomes SSC1 and SSC7. An 8.82-Mb region that contained all 21 significant SNPs on SSC1 harbored the gene NR6A1, previously reported to influence the number of vertebrae in pigs. The remaining 18 significant SNPs on SSC7 were concentrated in a 4.56-Mb region, which was within the quantitative trait loci interval for number of vertebrae. A haplotype sharing analysis refined the locus to a segment of ~637 Kb. The most significant SNP, SIRI0001067, was contained in this refined region on SSC7 and located in one of the introns of TGFB3. As TGFB3 influences the development of vertebrae in mammalian embryos, the gene may be another strong candidate for the number of vertebrae in pigs.

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Genome-Wide Association study Identifies a Novel Association Between a Cardiovascular Gene Polymorphism and Superior Athletic Performance

University of the Future: Re-Imagining Research and Higher Education ◽

10.29117/quarfe.2020.0111 ◽

2020 ◽

Author(s):

Mohamed Elrayess ◽

Fatima Al-Khelaifi ◽

Noha Yousri ◽

Omar Al-Bagha

Keyword(s):

Athletic Performance ◽

Genome Wide Association Study ◽

Endurance Athlete ◽

Meta Analysis ◽

Significant Snps ◽

Nucleotide Polymorphisms ◽

Replication Studies ◽

Genome Wide ◽

Small Effect Size ◽

Metabolomics Analysis

Research into the genetic predisposition to superior athletic performance has been a hindered by the underpowered studies and the small effect size of identified genetic variants. The aims of this study were to investigate the association of common single-nucleotide polymorphisms (SNPs) with endurance athlete status in a large cohort of elite European athletes using GWAS approach, followed by replication studies in Russian and Japanese elite athletes and functional validation using metabolomics analysis. Results: The association of 476,728 SNPs of Illumina DrugCore Gene chip and endurance athlete status was investigated in 796 European international-level athletes (645 males, 151 females) by comparing allelic frequencies between athletes specialized in sports with high (n=662) and low/moderate (n=134) aerobic component. Validation of results was performed by comparing the frequencies of the most significant SNPs between 242 and 168 elite Russian high and low/moderate aerobic athletes, respectively, and between 60 elite Japanese endurance athletes and 406 controls. A meta-analysis has identified rs1052373 (GG homozygotes) in Myosin Binding Protein (MYBPC3; implicated in cardiac hypertrophic myopathy) gene to be associated with endurance athlete status (P=1.43E-08, odd ratio 2.2). Homozygotes carriers of rs1052373 G allele in Russian athletes had significantly greater VO2max than carriers of the AA+AG (P = 0.005). Subsequent metabolomics analysis revealed several amino acids and lipids associated with rs1052373 G allele (1.82x10-05) including the testosterone precursor androstenediol (3beta, 17beta) disulfate. Conclusion: This is the first report of genome-wide significant SNP and related metabolites associated with elite athlete status. Further investigations of the functional relevance of the identified SNPs and metabolites in relation to enhanced athletic performance are warranted.

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Genome-Wide Association Studies for the Concentration of Albumin in Colostrum and Serum in Chinese Holstein

Animals ◽

10.3390/ani10122211 ◽

2020 ◽

Vol 10 (12) ◽

pp. 2211

Author(s):

Shan Lin ◽

Zihui Wan ◽

Junnan Zhang ◽

Lingna Xu ◽

Bo Han ◽

...

Keyword(s):

Association Studies ◽

Significant Snps ◽

Albumin Concentration ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Chinese Holstein ◽

Genome Wide ◽

Chinese Holstein Cows ◽

Newborn Calves

Albumin can be of particular benefit in fighting infections for newborn calves due to its anti-inflammatory and anti-oxidative stress properties. To identify the candidate genes related to the concentration of albumin in colostrum and serum, we collected the colostrum and blood samples from 572 Chinese Holstein cows within 24 h after calving and measured the concentration of albumin in the colostrum and serum using the ELISA methods. The cows were genotyped with GeneSeek 150 K chips (containing 140,668 single nucleotide polymorphisms; SNPs). After quality control, we performed GWASs via GCTA software with 91,620 SNPs and 563 cows. Consequently, 9 and 7 genome-wide significant SNPs (false discovery rate (FDR) at 1%) were identified. Correspondingly, 42 and 206 functional genes that contained or were approximate to (±1 Mbp) the significant SNPs were acquired. Integrating the biological process of these genes and the reported QTLs for immune and inflammation traits in cattle, 3 and 12 genes were identified as candidates for the concentration of colostrum and serum albumin, respectively; these are RUNX1, CBR1, OTULIN,CDK6, SHARPIN, CYC1, EXOSC4, PARP10, NRBP2, GFUS, PYCR3, EEF1D, GSDMD, PYCR2 and CXCL12. Our findings provide important information for revealing the genetic mechanism behind albumin concentration and for molecular breeding of disease-resistance traits in dairy cattle.

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Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats

International Journal of Genomics ◽

10.1155/2020/6035694 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12

Author(s):

Y. Tilahun ◽

T. A. Gipson ◽

T. Alexander ◽

M. L. McCallum ◽

P. R. Hoyt

Keyword(s):

Association Study ◽

Candidate Genes ◽

Predictive Power ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Breeding Value ◽

Phenotypic Traits ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

Dairy Traits

This paper reports an exploratory study based on quantitative genomic analysis in dairy traits of American Alpine goats. The dairy traits are quality-determining components in goat milk, cheese, ice cream, etc. Alpine goat phenotypes for quality components have been routinely recorded for many years and deposited in the Council on Dairy Cattle Breeding (CDCB) repository. The data collected were used to conduct an exploratory genome-wide association study (GWAS) from 72 female Alpine goats originating from locations throughout the U.S. Genotypes were identified with the Illumina Goat 50K single-nucleotide polymorphisms (SNP) BeadChip. The analysis used a polygenic model where the dropping criterion was a call rate≥0.95. The initial dataset was composed of ~60,000 rows of SNPs and 21 columns of phenotypic traits and composed of 53,384 scaffolds containing other informative data points used for genomic predictive power. Phenotypic association with the 50K BeadChip revealed 26,074 reads of candidate genes. These candidate genes segregated as separate novel SNPs and were identified as statistically significant regions for genome and chromosome level trait associations. Candidate genes associated differently for each of the following phenotypic traits: test day milk yield (13,469 candidate genes), test day protein yield (25,690 candidate genes), test day fat yield (25,690 candidate genes), percentage protein (25,690 candidate genes), percentage fat (25,690 candidate genes), and percentage lactose content (25,690 candidate genes). The outcome of this study supports elucidation of novel genes that are important for livestock species in association to key phenotypic traits. Validation towards the development of marker-based selection that provides precision breeding methods will thereby increase the breeding value.

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Reduced Representation Libraries from DNA Pools Analysed with Next Generation Semiconductor Based-Sequencing to Identify SNPs in Extreme and Divergent Pigs for Back Fat Thickness

International Journal of Genomics ◽

10.1155/2015/950737 ◽

2015 ◽

Vol 2015 ◽

pp. 1-8 ◽

Cited By ~ 8

Author(s):

Samuele Bovo ◽

Francesca Bertolini ◽

Giuseppina Schiavo ◽

Gianluca Mazzoni ◽

Stefania Dall’Olio ◽

...

Keyword(s):

Frequency Estimation ◽

Breeding Value ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Large White ◽

Single Nucleotide ◽

Reduced Representation ◽

Novel Variants ◽

Dna Pools ◽

Fat Thickness

The aim of this study was to identify single nucleotide polymorphisms (SNPs) that could be associated with back fat thickness (BFT) in pigs. To achieve this goal, we evaluated the potential and limits of an experimental design that combined several methodologies. DNA samples from two groups of Italian Large White pigs with divergent estimating breeding value (EBV) for BFT were separately pooled and sequenced, after preparation of reduced representation libraries (RRLs), on the Ion Torrent technology. Taking advantage from SNAPE for SNPs calling in sequenced DNA pools, 39,165 SNPs were identified; 1/4 of them were novel variants not reported in dbSNP. Combining sequencing data with Illumina PorcineSNP60 BeadChip genotyping results on the same animals, 661 genomic positions overlapped with a good approximation of minor allele frequency estimation. A total of 54 SNPs showing enriched alleles in one or in the other RRLs might be potential markers associated with BFT. Some of these SNPs were close to genes involved in obesity related phenotypes.

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Using hapmap tools to predict oncology-related phenotypes: TPMT activity vs hapmap SNPs

Journal of Clinical Oncology ◽

10.1200/jco.2006.24.18_suppl.13035 ◽

2006 ◽

Vol 24 (18_suppl) ◽

pp. 13035-13035

Author(s):

T. Jones ◽

W. Yang ◽

W. Evans ◽

M. Relling

Keyword(s):

Cell Lines ◽

Association Studies ◽

Rank Correlation ◽

Significant Snps ◽

Positive Control ◽

Tpmt Activity ◽

International Hapmap Project ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

Thiopurine Therapy

13035 Background: Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme responsible for the S-methylation of thiopurines. There are several functional genetic polymorphisms in TPMT activity, which can lead to drug toxicities; however, among individuals with high TPMT activity, a substantial portion of enzymatic variability remains unexplained. B-lymphoblastoid CEPH cell lines have been genotyped at over 2 million single nucleotide polymorphisms (SNPs) as part of the International HapMap project. Therefore, extensive phenotype-genotype association studies can be conducted in these cell lines by systematic determination of cancer-related phenotypes. Methods: We measured the phenotype of TPMT activity in 82 CEPH cell lines. Of these, 53 had expression data available on over 8000 genes from Affymetrix Focus Array technology. We evaluated whether TPMT activity was associated with HapMap SNPs in TPMT (cis SNPs), genome-wide HapMap SNPs (trans SNPs), and level of gene expression using Kruskal-Wallis test and Spearmans rank correlation. Results: We found associations of TPMT activity with four SNPs (p < 0.05) in TPMT (± 100K bp), one of which (rs1142345, p = 0.009) is a known functional SNP responsible for TPMT deficiency. Two other significant SNPs are in linkage disequilibrium with rs1142345. Associations were also found with 1598 trans SNPs across the genome (p < 0.001). TPMT activity was associated with the expression of eight genes (p < 0.0001, FDR <20%). The only overlapping trans gene is PACSIN2, whose expression most significantly correlated with TPMT activity and also contains two significantly predictive trans SNPs. Conclusions: The CEPH cell lines were useful in that a known functional variant, rs1142345, (serving as a positive control) was associated with TPMT activity, and that additional polymorphisms in TPMT and in potentially important trans-acting factors have been identified as possible additional genomic determinants of TPMT activity. Similar experiments with other phenotypes can likewise capitalize on this publicly available resource. With further validation, these studies may lead to discovery of additional candidate polymorphisms that can lead to further optimization of thiopurine therapy in the clinic. No significant financial relationships to disclose.

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Periodontal disease increases the host susceptibility to COVID-19 and its severity: a Mendelian randomization study

Journal of Translational Medicine ◽

10.1186/s12967-021-03198-2 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Yi Wang ◽

Hui Deng ◽

Yihuai Pan ◽

Lijian Jin ◽

Rongdang Hu ◽

...

Keyword(s):

Periodontal Disease ◽

Genome Wide Association Study ◽

Mendelian Randomization ◽

Host Susceptibility ◽

Sensitivity Analyses ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

Inverse Variance ◽

Weighted Median ◽

First Time

Abstract Background Emerging evidence shows that periodontal disease (PD) may increase the risk of Coronavirus disease 2019 (COVID-19) complications. Here, we undertook a two-sample Mendelian randomization (MR) study, and investigated for the first time the possible causal impact of PD on host susceptibility to COVID-19 and its severity. Methods Summary statistics of COVID-19 susceptibility and severity were retrieved from the COVID-19 Host Genetics Initiative and used as outcomes. Single nucleotide polymorphisms associated with PD in Genome-wide association study were included as exposure. Inverse-variance weighted (IVW) method was employed as the main approach to analyze the causal relationships between PD and COVID-19. Three additional methods were adopted, allowing the existence of horizontal pleiotropy, including MR-Egger regression, weighted median and weighted mode methods. Comprehensive sensitivity analyses were also conducted for estimating the robustness of the identified associations. Results The MR estimates showed that PD was significantly associated with significantly higher susceptibility to COVID-19 using IVW (OR = 1.024, P = 0.017, 95% CI 1.004–1.045) and weighted median method (OR = 1.029, P = 0.024, 95% CI 1.003–1.055). Furthermore, it revealed that PD was significantly linked to COVID-19 severity based on the comparison of hospitalization versus population controls (IVW, OR = 1.025, P = 0.039, 95% CI 1.001–1.049; weighted median, OR = 1.030, P = 0.027, 95% CI 1.003–1.058). No such association was observed in the cohort of highly severe cases confirmed versus those not hospitalized due to COVID-19. Conclusions We provide evidence on the possible causality of PD accounting for the susceptibility and severity of COVID-19, highlighting the importance of oral/periodontal healthcare for general wellbeing during the pandemic and beyond.

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Genome-wide association mapping for agronomic and quality traits in foxtail millet

10.21203/rs.2.10042/v1 ◽

2019 ◽

Author(s):

Yanhong Lou ◽

Yun Chen ◽

Zhihao Liu ◽

Mingjie Sun ◽

Fei Han ◽

...

Keyword(s):

Genome Wide Association Study ◽

Foxtail Millet ◽

Significant Snps ◽

Genomic Variation ◽

Genome Wide Association ◽

Quality Traits ◽

Nucleotide Polymorphisms ◽

High Quality ◽

Genome Wide ◽

A Genome

Abstract Background: Foxtail millet [Setaria italica (L.) P. Beauv.] is a particularly important cereal and fodder crop in arid and semi-arid regions. The genomic variation and alleles underpinning agronomic and quality traits are important for foxtail millet improvement. To better understand the diversity of foxtail millet and facilitate the genetic dissection of its agronomic and quality traits, we used high-quality single nucleotide polymorphisms (SNPs) to perform a genome-wide association study (GWAS). Results: Using genotyping-by-sequencing, 107 foxtail millet accessions were sequenced, and further analysis revealed 72,181 high-quality SNPs, of which 53 were significantly associated with 15 agronomic and quality traits. These SNPs were distributed across the nine chromosomes of foxtail millet; 44 were located in intergenic regions, whereas one and eight SNPs were located in exon and intron regions, respectively. The GWAS revealed that 28 SNPs were associated with a single trait. Conclusions: For some of the significant SNPs, favourable genotypes showed pyramiding effects for several traits. The 53 loci identified in this study will therefore be useful for breeding programs aimed at foxtail millet improvement.

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Genome-wide analyses reveal a strong association between LEPR gene variants and body fat reserves in ewes

10.1101/2021.11.27.470213 ◽

2021 ◽

Author(s):

Tiphaine Macé ◽

Eliel Gonzalez-Garcia ◽

Didier Foulquié ◽

Fabien Carrière ◽

Julien Pradel ◽

...

Keyword(s):

Leptin Receptor ◽

Body Condition Score ◽

Receptor Gene ◽

Strong Association ◽

Significant Snps ◽

Chromosome 1 ◽

Nucleotide Polymorphisms ◽

Fat Reserves ◽

Genome Wide ◽

Pregnancy And Lactation

Among the adaptive capacities of animals, the management of energetic body reserves (BR) through the BR mobilization and accretion processes (BR dynamics, BRD) has become an increasingly valuable attribute for livestock sustainability, allowing animals to cope with more variable environments. BRD has previously been reported to be heritable in ruminants. In the present study, we conducted genome-wide studies (GWAS) in sheep to determine genetic variants associated with BRD. BR levels and BR changes over time were obtained through body condition score measurements at eight physiological stages throughout each productive cycle in Romane ewes (n=1034) and were used as phenotypes for GWAS. After quality controls and imputation, 48,513 single nucleotide polymorphisms (SNP) were included in the GWAS. Among the QTLs identified, a major QTL associated with BR levels during pregnancy and lactation was identified on chromosome 1. In this region, several significant SNPs mapped to the leptin receptor gene (LEPR), among which one SNP mapped to the coding sequence. The point mutation induces the p.P1019S substitution in the cytoplasmic domain, close to tyrosine phosphorylation sites. The frequency of the SNP associated with increased BR levels was 32%, and the LEPR genotype explained up to 5% of the variance of the trait. These results provide strong evidence for involvement of LEPR in the regulation of BRD in sheep and highlight it as a major candidate for improving adaptive capacities.

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Genome-Wide Association Studies of Somatic Cell Count in the Assaf Breed

Animals ◽

10.3390/ani11061531 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1531

Author(s):

Yasemin Öner ◽

Malena Serrano ◽

Pilar Sarto ◽

Laura Pilar Iguácel ◽

María Piquer-Sabanza ◽

...

Keyword(s):

Somatic Cell ◽

Genome Wide Association Study ◽

Association Studies ◽

Significant Snps ◽

Genome Wide Association ◽

System Response ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

A Genome

A genome-wide association study (GWAS) was performed to identify new single nucleotide polymorphisms (SNPs) and genes associated with mastitis resistance in Assaf sheep by using the Illumina Ovine Infinium® HD SNP BeadChip (680K). In total, 6173 records from 1894 multiparous Assaf ewes with at least three test day records and aged between 2 and 7 years old were used to estimate a corrected phenotype for somatic cell score (SCS). Then, 192 ewes were selected from the top (n = 96) and bottom (n = 96) tails of the corrected SCS phenotype distribution to be used in a GWAS. Although no significant SNPs were found at the genome level, four SNPs (rs419096188, rs415580501, rs410336647, and rs424642424) were significant at the chromosome level (FDR 10%) in two different regions of OAR19. The SNP rs419096188 was located in intron 1 of the NUP210 and close to the HDAC11 genes (61 kb apart), while the other three SNPs were totally linked and located 171 kb apart from the ARPP21 gene. These three genes were related to the immune system response. These results were validated in two SNPs (rs419096188 and rs424642424) in the total population (n = 1894) by Kompetitive Allele-Specific PCR (KASP) genotyping. Furthermore, rs419096188 was also associated with lactose content.

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