A genome-wide association study (GWAS) of the daughter pregnancy rate (DPR), cow conception (CCR), and heifer (HCR) using 1,001,374-1,194,736 first-lactation Holstein cows 75,140-75,295 SNPs identified 7567, 3798, 726 additive effects, as well 22, 27, 25 dominance effects for DPR, CCR, HCR, respectively, with log10(1/p) > 8. Most these were new some in or near genes known to affect reproduction including GNRHR, SHBG, ESR1, a gene cluster pregnancy-associated glycoproteins. The confirmed...

A genome-wide association study (GWAS) of fat percentage (FPC) using 1,231,898 first lactation cows and 75,198 SNPs confirmed a previous result that Chr14 region about 9.38 Mb in size (0.14-9.52 Mb) had significant inter-chromosome additive × (A×A) effects with all chromosomes revealed many new such effects. This divides this into two sub-regions, Chr14a at 0.14-0.88 (0.74 size) 78% Chr14b 2.21-9.52 (7.31 22% the 2761 A×A These sub-regions were separated by 1.3 gap 0.9-2.2 without The...

A genome-wide association study (GWAS) of age at first calving (AFC) using 813,114 lactation Holstein cows and 75,524 SNPs identified 2063 additive effects 29 dominance with p-values < 10−8. Three chromosomes had highly significant in the regions 7.86–8.12 Mb Chr15, 27.07–27.48 31.25–32.11 Chr19, 26.92–32.60 Chr23. Two genes those were reproductive hormone known biological functions that should be relevant to AFC, sex binding globulin (SHBG) gene, progesterone receptor (PGR) gene. The...

Abstract Background Genomic selection using single nucleotide polymorphism (SNP) markers has been widely used for genetic improvement of livestock, but most current methods genomic are based on SNP models. In this study, we investigated the prediction accuracies haplotype models fixed chromosome distances and gene boundaries compared to those phenotypic values. We also examined reasons successes failures prediction. Methods analyzed a swine population 3195 Duroc boars with records eight...

Epistasis is widely considered important, but epistasis studies lag those of SNP effects. Genome-wide association study (GWAS) using 76,109 SNPs and 294,079 first-lactation Holstein cows was conducted for testing pairwise effects five production traits three fertility traits: milk yield (MY), fat (FY), protein (PY), percentage (FPC), (PPC), daughter pregnancy rate (DPR). Among the top 50,000 each trait, had large chromosome regions with intra-chromosome epistasis. The inter-chromosome 1.9%...

A genome-wide association study of resistance to retained placenta (RETP) using 632,212 Holstein cows and 74,747 SNPs identified 200 additive effects with p-values < 10−8 on thirteen chromosomes but no dominance effect was statistically significant. The regions 87.61–88.74 Mb Chr09 about 1.13 in size had the most significant LOC112448080 other highly CCDC170 ESR1, or near RMND1 AKAP12. Four non-ESR1 genes this region were reported be involved ESR1 fusions humans. Chr23 largest number that...

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Genomic prediction using multi-allelic haplotype models improved the accuracy for all seven human phenotypes, normality transformed high density lipoproteins, low total cholesterol, triglycerides, weight, and original height body mass index without transformation. Eight SNP sets with 40,941-380,705 SNPs were evaluated. The increase in due to haplotypes was 1.86-8.12%. Haplotypes fixed chromosome distances had best four number of two gene-based lipoproteins (tied best). coding genes more...

Non-alcoholic fatty liver disease (NAFLD) is the most prevalent cause of chronic hepatic and results in non-alcoholic steatohepatitis (NASH), which progresses to fibrosis cirrhosis. Although Leptin deficient rodent models are widely used study metabolic syndrome obesity, they fail develop injuries as patients.Due high similarity with humans, we generated Leptin-deficient (Leptin-/-) pigs investigate mechanisms clinical trials obesity NAFLD caused by Leptin.The Leptin-/- showed increased body...

Haplotype prediction models open many possibilities to improve the accuracy of genomic selection but require more data processing and computing time than single-SNP models. To facilitate haplotype analysis for estimation using structural functional information, we developed a pipeline implement with capabilities preparation input analysis, GVCHAP, GVCHAP results. Data includes utility programs imputing; defining blocks by fixed number SNPs, distance in base pairs per block, or user defined...

Heavy chain only antibodies (HCAbs) represent a rare type of antibody that is devoid light chains and the CH1 domain have been reported in cartilaginous fish camelids.By analyzing transcript data genome sequences, we conducted comprehensive analysis Bactrian camel immunoglobulin heavy genes.Based on data, one μ gene, five γ genes, α gene ε were found.Additionally, variable region HCAbs (VHH) conventional (VH) sequences associated with γ3, γ1a/b genes amplified.Based these seven DH, six JH,...

The rapid growth in genomic selection data provides unprecedented opportunities to discover and utilize complex genetic effects for improving phenotypes, but the methodology is lacking. Epistasis are interaction effects, haplotype may contain local high-order epistasis effects. Multifactorial methods with SNP, haplotype, up third-order developed investigate contributions of global low-order phenotypic variance accuracy prediction quantitative traits. These include best linear unbiased...

Using small sets of ancestry informative markers (AIMs) constitutes a cost-effective method to accurately estimate the proportions individuals. This study aimed generate and effective number AIMs from ∼60 K single nucleotide polymorphism (SNP) data porcine three [East China pig (ECHP), South (SCHP), European commercial (EUCP)] Asian breeds domestic breeds. A total 186 samples 10 pure were divided into groups: ECHP, SCHP, EUCP. these one-vs.-rest SVM classifier, we found that using only seven...

The impact of genomic epistasis effects on the accuracy predicting phenotypic values residual feed intake (RFI) in U.S. Holstein cows was evaluated using 6215 and 78,964 SNPs. Two SNP models seven were initially evaluated. Heritability estimates RFI from 10-fold cross-validation studies identified model with additive × (A×A) (A + A×A model) to be best prediction model. Under A model, heritability 0.141, 0.263 that consisted 0.260 inter-chromosome 0.003 intra-chromosome heritability, showing...

Sheep and goat may become carriers of some zoonotic diseases. They are important livestock experimental model animals for human beings. The fast accurate identification genetic materials originating from sheep can prevent inhibit the spread diseases, monitor market product quality, maintain stability animal husbandry food industries. This study proposed a methodology identifying common specific sites genome-wide perspective. A total 150 were selected three data sources, including coding...

Abstract Background Productive life (PL) of a cow is the time remains in milking herd from first calving to exit due culling or death and an important economic trait U.S. Holstein cattle. The large samples genomic evaluation data that have become available recently provided unprecedented statistical power identify genetic factors affecting PL cows using approach genome-wide association study (GWAS). Methods GWAS analysis used 1,103,641 with phenotypic observations on genotypes 75,282 single...

The accuracy of predicting seven human phenotypes 3657–7564 individuals using global epistasis effects was evaluated and compared to the haplotype genomic prediction 380,705 SNPs 10-fold cross-validation studies. were normality transformed high density lipoproteins (HDL), low (LDL), total cholesterol (TC), triglycerides (TG), weight (WT), original phenotypic observations height (HTo) body mass index (BMIo). Fourth-order virtually had no contribution variances, third-order did not affect...

Abstract Liver fibrosis occurs during chronic liver disease. Advanced results in cirrhosis, failure and often requires transplantation. However, due to the lack of human models, mechanisms underlining pathogenesis remain unclear. Recent studies implicated a central role deranged lipid metabolism its pathogenesis. In this study, we generated LEPTIN-deficient ( LEPTIN -/- ) pigs using zinc finger nuclease technology investigate associated with obesity. The showed increased body fat significant...

ABSTRACT The rapid growth in genomic selection data provides unprecedented opportunities to discover and utilize complex genetic effects for improving phenotypes but methodology is lacking. Epistasis are interaction haplotype may contain local high-order epistasis effects. Multifactorial methods with SNP, up the third-order developed investigate contributions of global low-order phenotypic variance accuracy gnomic prediction quantitative traits. These include best linear unbiased (GBLUP)...