A further survey of the quantitative trait loci affecting swine body size and carcass traits in five related pig populations.

Breeding for good meat quality performance while maintaining large body size and desirable carcass traits has been the major challenge for modern swine selective breeding. To address this goal, in the present work we studied five related populations produced by two commercial breeds (Berkshire and Duroc) and two Chinese breeds (Licha black pig and Lulai black pig). A single-trait GWAS performed on 20 body size and carcass traits using a self-developed China Chip-1 porcine SNP50K BeadChip identified 11 genome-wide significant QTL on nine chromosomes and 22 suggestive QTL on 15 chromosomes. For the 11 genome-wide significant QTL, eight were detected in at least two populations, and the rest were population-specific and only mapped in Shanxia black pig. Most of the genome-wide significant QTL were pleiotropic; for example, the QTL around 75.65 Mb on SSC4 was associated with four traits at genome-wide significance level. After screening the genes within 50 kb of the top SNP for each genome-wide significant QTL, NR6A1 and VRTN were chosen as candidate genes for vertebrae number; PLAG1 and BMP2 were identified as candidate genes for body size; and MC4R was the strong candidate gene for body weight. The four genes have been reported as candidates for thoracic vertebrae number, lumbar vertebrae number, carcass length and body weight respectively in previous studies. The effects of VRTN on thoracic vertebrae number, carcass length and body length have been verified in Shanxia black pig. Therefore, the VRTN genotype could be used in gene-assisted selection, and this could accelerate genetic improvement of body size and carcass traits in Shanxia black pig.

Uncovering the differentially expressed genes and pathways involved in the progression of stable coronary artery disease to acute myocardial infarction using bioinformatics analysis.

OBJECTIVE: Coronary artery disease (CAD) is the main cause of mortality worldwide. How stable coronary artery disease (SCAD) progresses to acute myocardial infarction (AMI) is not known. This study was aimed to explore the differentially expressed genes (DEGs) and pathways involved in the progression of SCAD to AMI. MATERIALS AND METHODS: Publicly available gene-expression profiles (GSE71226, GSE97320, GSE66360) were downloaded from the Gene Expression Omnibus (GEO) database and integrated to identify DEGs. The GSE59867 dataset was further used to verify the result of screened DEGs. Functional-enrichment analyses, protein-protein interaction network, microRNA-transcription factor (TF)-mRNA regulatory network, and drug-gene network were visualized. RESULTS: Sixty common DEGs (CDEGs) were screened between the SCAD-Control group and AMI-Control group in the integrated dataset. Four upregulated DEGs were selected from GSE59867. Twenty hub genes were discovered, and three significant modules were constructed in the PPI network. The intersection of functional and pathway-enrichment analyses of 60 CDEGs and the module DEGs indicated that they were mainly involved in "inflammatory response", "immune response", and "cytokine-cytokine receptor interaction". A miRNA-TF-mRNA regulatory network comprised 87 miRNAs, 16 upregulated target DEGs and 7 TFs. CONCLUSIONS: We identified several important genes and miRNAs involved in the progression of SCAD to AMI: platelet activating factor receptor (PTAFR), aquaoporin-9 (AQP9), toll-like receptor-4 (TLR4), human constitutive androstane receptor-3 (HCAR3), leucine-rich-α2 glycoprotein-1 (LRG1), mothers Against Decapentaplegic Homolog 4 (SMAD4) and miRNA-149-5p, miRNA-6778-3p, and miRNA-520a-3p. Inflammation and the immune response had important roles in the progression from SCAD to AMI.

Identification of the pivotal differentially expressed genes and pathways involved in Staphylococcus aureus-induced infective endocarditis by using bioinformatics analysis.

OBJECTIVE: Infective endocarditis (IE), particularly by Staphylococcus aureus, is an uncommon bacteremia-associated infection of the endocardium and cardiac valves. Herein, we evaluated predictive noninvasive biomarkers for IE caused by S. aureus through bioinformatics analysis. MATERIALS AND METHODS: Staphylococcus aureus-associated and IE-associated differentially expressed genes (DEGs) were identified by bioinformatics analysis of the GSE6269 and GSE29161 Gene Expression Omnibus (GEO) datasets. The DEGs were analyzed with the LIMMA package, and the coregulated genes were chosen as the intersection of DEGs between the two datasets, called common differentially expressed genes (CDEGs). The enrichment study of CDEGs was subsequently performed with the DAVID and KOBAS web resources. Finally, protein-protein interaction (PPI) network, microRNA (miRNA)-transcription factor (TF)-mRNA (messenger RNA) regulatory network, and the network of drug-genes were identified. RESULTS: From GSE6269 and GSE29161, respectively, a total of 201 and 741 DEGs were obtained. Gene Ontology (GO) analysis showed that CDEGs were primarily involved in innate immune response, extracellular exosome, as well as calcium ion binding, while the pathway analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that CDEGs were significantly enriched in the B-cell receptor, IL-17, and NF-kappa B signaling pathways. The hub genes in the PPI network included HP, S100A12, SPI1, CD14, CCR1, S100A9 and so on. In the miRNA-TF-mRNA regulatory network, SPI1 could target miR-361-5p, miR-155-5p, and miR-339-5p in the progression of IE. CONCLUSIONS: Several pivotal genes and pathways were identified in the progression of S. aureus-induced IE, which may have the potential for early detection.

A whole genome sequence association study for puberty in a large Duroc × Erhualian F2 population.

A large proportion of gilts and sows are culled from reproduction populations because of anestrus and pubertal reproductive failure. Selecting early onset of puberty gilts has a favorable effect on sows' reproductivity. However, age at puberty is hard to be routinely measured in commercial herds. With molecular genetic predictors, identifying individuals that have a propensity for early onset of puberty can be simplified. We previously performed genome scanning and a genome-wide association study for puberty in an F2 resource population using 183 microsatellites and 62 125 SNPs respectively. The detection power and resolution of identified quantitative trait loci were very low. Herein, we re-sequenced 19 founders of the F2 resource population in high coverage, and whole genome sequences of F2 individuals were imputed to perform an association study for reproductive traits. A total of 2339 SNPs associated with pubertal reproductive failure were identified in the region of 30.94-40.74 Mb on SSC7, with the top one, positioned at 33.36 Mb, explaining 16% of the phenotypic variances. We improved the magnitude of the P-value by 10E+5 to 10E+7 using the whole genome sequence rather than using low/middle density markers as in previous studies, and we narrowed down the QTL confidence interval to 5.25 Mb. Combining the annotation of gene function, RAB23 and BAK1 were perceived as the most compelling candidate genes. The identified loci may be useful in culling sows failing to show estrus by marker-assisted selection to increase reproductive efficiency of swine herds.

A genome-wide association analysis for susceptibility of pigs to enterotoxigenic Escherichia coli F41.

Enterotoxigenic Escherichia coli (ETEC) is a type of pathogenic bacteria that cause diarrhea in piglets through colonizing pig small intestine epithelial cells by their surface fimbriae. Different fimbriae type of ETEC including F4, F18, K99 and F41 have been isolated from diarrheal pigs. In this study, we performed a genome-wide association study to map the loci associated with the susceptibility of pigs to ETEC F41 using 39454 single nucleotide polymorphisms (SNPs) in 667 F2 pigs from a White Duroc×Erhualian F2 cross. The most significant SNP (ALGA0022658, P=5.59×10-13) located at 6.95 Mb on chromosome 4. ALGA0022658 was in high linkage disequilibrium (r 2>0.5) with surrounding SNPs that span a 1.21 Mb interval. Within this 1.21 Mb region, we investigated ZFAT as a positional candidate gene. We re-sequenced cDNA of ZFAT in four pigs with different susceptibility phenotypes, and identified seven coding variants. We genotyped these seven variants in 287 unrelated pigs from 15 diverse breeds that were measured with ETEC F41 susceptibility phenotype. Five variants showed nominal significant association (P<0.05) with ETEC F41 susceptibility phenotype in International commercial pigs. This study provided refined region associated with susceptibility of pigs to ETEC F41 than that reported previously. Further works are needed to uncover the underlying causal mutation(s).

Genome-wide association study identifies QTLs for EBV of backfat thickness and average daily gain in Duroc pigs.

Backfat thickness (BFT) and average daily gain (ADG) are two important economic traits in commercial swine production. Identifying QTLs and uncovering the molecular mechanism for BFT and ADG would greatly help to speed up the breeding progress. In current breeding program, EBV for these two traits are calculated and formulated a comprehensive breeding index, which then be used to improve pig performance. Using Illumina PorcineSNP60 BeadChip, a pilot genomewide association studies (GWAS) for BFT and ADG in 83 Duroc pigs were performed. A total of 31 genome-wise significant SN Ps were detected to be associated with BFT on SSC 4, 9, 11, 12 and 14, ten of which were coincident with previously reported QTL regions. There are two genome-wise loci prominently associated with ADG on SSC2 and SSC13, respectively. The two loci on SSC2 are well overlapped with the QTL regions previously reported. All the 31 significant SNPs associated with BFT are verified on 219 outbreed pigs, six SN Ps reach an extreme significant level and seven SNP reaches a significant level, CACNA1E and ACBD6 are chosen as positional candidate genes. Our findings not only confirmed previously findings, but also revealed a number of novel SNPs associated with BFT and ADG. Two positional candidate genes CACNA1E and ACBD6 were identified for further study. These results would facilitate the identification of causative genes for BFT and ADG.

SUSCEPTIBILITY LOCI FOR UMBILICAL HERNIA IN SWINE DETECTED BY GENOME-WIDE ASSOCIATION.

Umbilical hernia (UH) is a complex disorder caused by both genetic and environmental factors. UH brings animal welfare problems and severe economic loss to the pig industry. Until now, the genetic basis of UH is poorly understood. The high-density 60K porcine SNP array enables the rapid application of genome-wide association study (GWAS) to identify genetic loci for phenotypic traits at genome wide scale in pigs. The objective of this research was to identify susceptibility loci for swine umbilical hernia using the GWAS approach. We genotyped 478 piglets from 142 families representing three Western commercial breeds with the Illumina PorcineSNP60 BeadChip. Then significant SNPs were detected by GWAS using ROADTRIPS (Robust Association-Detection Test for Related Individuals with Population Substructure) software base on a Bonferroni corrected threshold (P = 1.67E-06) or suggestive threshold (P = 3.34E-05) and false discovery rate (FDR = 0.05). After quality control, 29,924 qualified SNPs and 472 piglets were used for GWAS. Two suggestive loci predisposing to pig UH were identified at 44.25MB on SSC2 (rs81358018, P = 3.34E-06, FDR = 0.049933) and at 45.90MB on SSC17 (rs81479278, P = 3.30E-06, FDR = 0.049933) in Duroc population, respectively. And no SNP was detected to be associated with pig UH at significant level in neither Landrace nor Large White population. Furthermore, we carried out a meta-analysis in the combined pure-breed population containing all the 472 piglets. rs81479278 (P = 1.16E-06, FDR = 0.022475) was identified to associate with pig UH at genome-wide significant level. SRC was characterized as plausible candidate gene for susceptibility to pig UH according to its genomic position and biological functions. To our knowledge, this study gives the first description of GWAS identifying susceptibility loci for umbilical hernia in pigs. Our findings provide deeper insights to the genetic architecture of umbilical hernia in pigs.

A genome scan for quantitative trait loci affecting the length of small intestine in a White Duroc x Chinese Erhualian intercross resource population.

The small intestine is a vital organ in animal gastrointestinal system, in which a large variety of nutrients are absorbed. To identify quantitative trait loci (QTL) for the length of porcine small intestine, phenotypic values were measured in 1034 individuals at 240 d from a White Duroc x Chinese Erhualian intercross F(2) population. The length of small intestine showed strong correlation with growth traits and carcass length in the F2 population. A whole-genome scan was performed based on 183 microsatellites covering the pig genome in the F(2) population. A total of 10 QTL for this trait were identified on 8 pig chromosomes (SSC), including four 1% genome-wide significant QTL on SSC2, 4, 7 and 8, one 5% genome-wide significant QTL on SSC12, and five 5% chromosome-wide significant QTL on SSC5, 7, 13 and 14. The Erhualian alleles were generally associated with shorter length of the small intestine except the alleles on SSC7 and 13. The QTL on SSC4 overlapped with the previously reported QTL for the length of small intestine. Several significant QTL on SSC2, 8, and 12 were consistent with previous reports. The significant QTL detected on SSC7 was reported for the first time. All QTL identified in this study corresponded to the known region significantly associated with growth traits, supporting the important role of the length of small intestine in pig growth.

A genome-wide scan reveals candidate susceptibility loci for pig hernias in an intercross between White Duroc and Erhualian.

Pig scrotal/inguinal and umbilical hernias are the most prevalent congenital disorders in pigs and often cause animal welfare problems and economic loss. To identify susceptibility loci for these traits, a genome-wide scan with 194 microsatellite markers covering the pig genome was performed in a White Duroc x Erhualian resource population with 23 scrotal/inguinal F(2) animals, 50 umbilical F(2) animals, and their unaffected siblings. A sex-average linkage map with a total length of 2,350.3 cM and an average marker interval of 12.84 cM was constructed. Both nonparametric genome-wide linkage (NPL) analysis and transmission disequilibrium test (TDT) were implemented to detect closely linked markers. The NPL analysis revealed 11 chromosomal regions on SSC1, 2, 3, 6, 7, 8, 10, and 11 for umbilical hernia and 5 regions on SSC2, 4, 8, 13, and 16 for scrotal/inguinal hernia, whereas the TDT test identified susceptibility loci for umbilical hernia on SSC1, 2, 4, 7, 10, 13, 14, and 15 and for scrotal/inguinal hernias on SSC2, 8, 10, and 18. The most promising loci were SWR1928 on SSC7 and SW830 on SSC10 for umbilical hernia, and SW933 on SSC8 for scrotal hernia, which were consistently detected by both NPL and TDT. Several previously reported chromosomal regions for scrotal/inguinal hernia were confirmed, and new evidence for linkage with this pig defect was found. Moreover, susceptibility loci for pig umbilical hernia were detected for the first time.

Immobilization of the cell-adhesive peptide Arg-Gly-Asp-Cys (RGDC) on titanium surfaces by covalent chemical attachment.

Surface modification of acid-pretreated titanium with 3-aminopropyltriethoxylsilane (APTES) in dry toluene resulted in covalently bonded siloxane films with surface coverage that was relatively controllable by regulating the reaction conditions. A hetero-bifunctional cross-linker, N-succinimidyl-3-maleimidopropionate (SMP), reacted with the terminal amino groups, forming the exposed maleimide groups. Finally, a model cell-binding peptide, Arg-Gly-Asp-Cys (RGDC), was immobilized on the surface through covalent addition of the cysteine thiol groups to the maleimide groups. X-ray photoelectron spectroscopy, radiolabelling techniques, and ellipsometry were used to quantify and characterize the modified surfaces.

The nerve gap dilemma: a comparison of nerves repaired end to end under tension with nerve grafts in a primate model.

The objective of this study was to compare, in a clinically relevant primate model, axon regeneration after epineurial repair under tension (15 mm gap) with interfascicular nerve grafts with the use of either standard microsuture techniques or a new interfascicular nerve graft technique termed fascicular tubulization that uses a hypoantigenic collagen membrane formed into a tube to approximate nerve ends. Electrophysiologic analysis demonstrated that the percentage of proximal axons that conducted across the repair site was greater in those nerves repaired under tension with epineurially placed sutures than in either of the tensionless repairs involving interfascicular graft techniques. The mean diameters of the regenerated axons repaired under tension with epineurial sutures were greater than those of the nerves repaired with interfascicular grafts, although the difference was not statistically significant. Interfascicular nerve grafting with tubulization using the current collagen tube resulted in regeneration equal to the sutured interfascicular nerve grafts. For modest defects (perhaps up to 3 to 4 cm in the adult), it seems advantageous to accept the modest tension associated with an epineurial repair rather than to use an autograft (or artificial graft) to achieve a tension-free repair.

A comparison of suture and tubulization nerve repair techniques in a primate.

This study compared standard methods of nerve repair, epineurial or perineurial sutures with a technique termed fascicular tubulization using a biodegradable polyglycolic acid tube in a nonhuman primate model. Electrophysiologic analysis demonstrated that the percentage of proximal axons that conducted across the repair site did not significantly differ among the three techniques while epineurial suture repairs were associated with significantly longer conduction delays across the repair site compared with the other two techniques. Even though fascicular tubulization using the current polyglycolic acid tube resulted in regeneration equal to the currently perceived best suture repair technique, associated technical problems with the current tube design indicate that this fascicular tubulization technique cannot, at present, be considered as an alternative to present clinically used nerve suture techniques.