Effects of SNPs using differentially expressed serum proteins at growth stages on average daily gain in pig

This study was aimed to search SNPs, which have been generated from differentially expressed proteins at growth stages, to use as molecular or biological markers accounting for variation of average daily gain (ADG). A total of 40 purebred Yorkshire pigs in half-sib pedigree were used to detect differentially expressed blood serum proteins at growth stages (12, 18, 24, and 30 weeks of age) using two-dimensional electrophoresis (2-DE). Differentially expressed spots between growth stages have been identified by MS/MS analysis resulting in nine genes (Immunoglobulin Kappa, Lambda, and Gamma, Retinol-Binding Protein, Albumin, Fibrinogen Alpha and Gamma, Antithrombin, and Alpha-1-Antitrypsin). Expression patterns by growth stages have been defined to four types depending on expression levels. PCR analysis showed 12 successful amplified products, and the sequence alignment for 270 individuals revealed 49 SNPs for the segments of SSP7107, SSP4410, SSP5112F, SSP5112R, and SSP4004. A total of 27 SNPs revealed substitutions of amino acids by SNPs in four genes (Gamma fibrinogen, Immunoglobulin G, Retinol-Binding Protein, and Immunoglobulin K), and the newly identified sequences have been submitted to GenBank with accession numbers. The genotypes from SNPs (positions at 306 of SSP4410; 280 of SSP5211F; 411 of SSP7107) were significantly associated with ADG showing additive and dominance allele effects. The identified SNPs may be helpful to understand different expression profiles of proteins at various growth stages as well as to explain genetic variations associated with ADG in pig industry.     

Comparison of stomach microRNA transcriptomes of Tibetan and Yorkshire pigs by deep sequencing

MiRNAs regulate the expression of target genes in diverse cellular processes and hence play important roles in different physiological processes, yet little is known about the stomach microRNAome (miRNAome) of the Tibetan pig. The objective of this experiment was to investigate differentially expressed stomach miRNAs participating in digestion. Firstly, we isolated total RNA by Trizol reagent from three Tibetan and three Yorkshire purebred pigs stomach samples at 90-day-old. Secondly, a comprehensive analysis of Tibetan and Yorkshire pig stomach miRNAomes was performed by small RNA sequencing in the Illumina HiSeq 2000 system. Finally, SYBR Green Real-time RT-PCR was performed to validate the differentially expressed miRNAs. We identified 318 unique miRNAs, 260 were co-expressed in both libraries, 17 and 31 miRNAs were specifically expressed in Tibetan and Yorkshire pigs respectively. Fifty six differentially expressed miRNAs were identified by the identifying differentially expressed genes 6 (IDEG6). Kyoto encyclopedia of genes and genomes analysis revealed that some of the differentially expressed miRNAs were associated with protein and fat digestion. Two differentially expressed miRNAs (miR-214-3p and ssc-un39) participating in the digestion of lipid were identified. Additionally, qRT-PCR results suggested that a higher expression of miR-214-3p in the Tibetan pig stomach could lead to relatively lower expression of calcium-dependent phospholipase A2, which is an enzyme important for the digestion of glycerol phospholipid. This study has delineated the different stomach miRNAs expression patterns of Tibetan and Yorkshire pigs, which would help explain the regulatory mechanisms of miRNAs in digestion of Tibetan pigs, and contribute to utilize a the unique digestion merits of Tibetan pig in future porcine hybridization breeding.     

Proteome Changes in Thai Indigenous Chicken Muscle during Growth Period

Proteomic profiling of the pectoralis muscle of Thai indigenous chickens during growth period was analyzed using two-dimensional gel electrophoresis (2-DE) and matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF/MS). A total of 259, 161, 120 and 107 protein spots were found to be expressed in the chicken pectoralis muscles at 0, 3, 6 and 18 weeks of age, respectively. From these expressed proteins, five distinct protein spots were significantly associated with chicken age. These protein spots were characterized and showed homology with phosphoglycerate mutase 1 (PGAM1), apolipoprotein A1 (APOA1), triosephosphate isomerase 1 (TPI1), heat shock protein 25 kDa (HSP25) and fatty acid binding protein 3 (FABP3). These five protein spots were categorized as follows: (i) the expression levels of PGAM1 and TPI1 proteins were positively correlated with chicken aging (p<0.05), (ii) the expression levels of APOA1 and FABP3 proteins were negatively correlated with chicken aging (p<0.05) and (iii) the expression levels of the HSP25 protein were up- and down-regulated during growth period. Moreover, the mRNA expression levels of the FABP3 and HSP25 genes were significantly decreased in muscle during the growth period (p<0.05), whereas no significant changes of the PGAM1, TPI1 and APOA1 gene expression from the chicken muscle was observed. The identified proteins were classified as metabolic and stress proteins. This demonstrates a difference in energy metabolism and stress proteins between age groups and shows that proteomics is a useful tool to uncover the molecular basis of physiological differences in muscle during the growth period.     

Genome-Wide Gene Expression Profiles in Lung Tissues of Pig Breeds Differing in Resistance to Porcine Reproductive and Respiratory Syndrome Virus

Porcine reproductive and respiratory syndrome (PRRS) caused by PRRS virus (PRRSV) is an infectious disease characterized by severe reproductive deficiency in pregnant sows, typical respiratory symptoms in piglets, and high mortality rate of piglets. In this study, we employed an Affymetrix microarray chip to compare the gene expression profiles of lung tissue samples from Dapulian (DPL) pigs (a Chinese indigenous pig breed) and Duroc×Landrace×Yorkshire (DLY) pigs after infection with PRRSV. During infection with PRRSV, the DLY pigs exhibited a range of clinical features that typify the disease, whereas the DPL pigs showed only mild signs of the disease. Overall, the DPL group had a lower percentage of CD4⁺ cells and lower CD4⁺/CD8⁺ratios than the DLY group (p<0.05). For both IL-10 and TNF-α, the DLY pigs had significantly higher levels than the DPL pigs (p<0.01). The DLY pigs have lower serum IFN-γ levels than the DPL pigs (p<0.01). The serum IgG levels increased slightly from 0 dpi to 7 dpi, and peaked at 14 dpi (p<0.0001). Microarray data analysis revealed 16 differentially expressed (DE) genes in the lung tissue samples from the DLY and DPL pigs (q≤5%), of which LOC100516029 and LOC100523005 were up-regulated in the PRRSV-infected DPL pigs, while the other 14 genes were down-regulated in the PRRSV-infected DPL pigs compared with the PRRSV-infected DLY pigs. The mRNA expression levels of 10 out of the 16 DE genes were validated by real-time quantitative RT-PCR and their fold change was consistent with the result of microarray data analysis. We further analyzed the mRNA expression level of 8 differentially expressed genes between the DPL and DLY pigs for both uninfected and infected groups, and found that TF and USP18 genes were important in underlying porcine resistance or susceptibility to PRRSV.     

Proteomic Analysis of Fetal Ovary Reveals That Ovarian Developmental Potential Is Greater in Meishan Pigs than in Yorkshire Pigs

Time-dependent expression of functional proteins in fetal ovaries is important to understand the developmental process of the ovary. This study was carried out to enhance our understanding of the developmental process of porcine fetal ovaries and to better address the differences in fetal ovary development of local and foreign pigs. The objective of the present study is to test the expression of key proteins that regulate the growth and development of fetal ovaries in Meishan and Yorkshire porcine breeds by using proteomics technology. Six Meishan and 6 Yorkshire pregnant gilts were used in this experiment. Fetal ovaries were obtained from Yorkshire and Meishan gilts on days 55 and 90 of the gestation period. Using 2D-DIGE (two dimensional-difference in gel electrophoresis) analysis, the results showed that there are about 1551 and 1400 proteins in gilt fetal ovaries on days 55 and 90, respectively of the gestation. Using MALDI TOF-TOF MS analysis, 27 differentially expressed proteins were identified in the fetal ovaries of the 2 breeds on day 55 of gestation, and a total of 18 proteins were identified on day 90 of gestation. These differentially expressed proteins were involved in the regulation of biological processes (cell death, stress response, cytoskeletal proteins) and molecular functions (enzyme regulator activity). We also found that alpha-1-antitrypsin, actin, vimentin, and PP2A proteins promote the formation of primordial follicles in the ovaries of Yorkshire pigs on day 55 of gestation while low expression heat shock proteins and high expression alpha-fetoproteins (AFP) may promote Meishan fetal ovarian follicular development on day 90 of gestation. These findings provide a deeper understanding of how reduced expression of heat shock proteins and increased expression of AFP can significantly reduce the risk of reproductive disease in obese Meishan sows. Our study also shows how these proteins can increase the ovulation rate and may be responsible for the low reproductive efficiency reported in other obese breeds. The ovarian developmental potential was found to be greater in Meishan pigs than in Yorkshire pigs.     

MALDI-TOF/TOF-MS reveals elevated serum haptoglobin and amyloid A in Behcet's disease

Behcet's disease (BD) is a multisystemic autoimmune disease with unclear etiology and pathogenesis. To screen aberrant serum proteins in BD, serum samples were obtained from eight male BD patients with active uveitis and eight male healthy volunteers with informed consent. The serum samples from active BD patients and normal controls were pooled. Highly abundant serum proteins (albumin and IgG) were depleted from these two samples using an affinity capture based kit. The obtained samples were subjected to two-dimensional gel electrophoresis (2-DE). Protein spots were visualized with the "blue silver" staining. Differently expressed proteins were subsequently identified by matrix-assisted laser desorption /ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF-MS). Western blot and enzyme-linked immunosorbent assay (ELISA) were performed using the serum samples from 18 patients with active BD, 6 patients with inactive BD, 22 patients with Vogt-Koyanagi-Harada (VKH) syndrome, and 20 healthy volunteers to validate the results of 2-DE and MS. Proteomic profiles of the pooled samples were compared, and approximately 800 protein spots were observed in each of the gels. Expression levels of four of the protein spots in active BD were significantly higher than those in the normal controls. Mass spectrometric protein identification revealed that the four protein spots corresponded to two proteins: haptoglobin (Hp) and serum amyloid A (SAA). Western blot and ELISA showed that Hp was only overexpressed in active BD but not in inactive BD, VKH syndrome, or healthy controls. An obvious band of SAA was detected in 72.2% of the serum samples from BD patients, whereas a vague band of this protein was found in 10.0% of the tested normal samples and 9.1% of VKH samples. Our results revealed a significantly increased expression of Hp and SAA in serum of active BD patients. These two proteins may be involved in the development of BD.     

Serum differential protein identification of Xinjiang Kazakh esophageal cancer patients based on the two-dimensional liquid-phase chromatography and LTQ MS

The aim of this study was to investigate the impact of chemo-radiotherapy on serum protein expression of the esophageal cancer patients and discover potential biomarkers by detecting serum proteins mass spectrometry of the healthy Kazakh people in Xinjiang as well as the patients before and after their chemo-radiotherapy. In order to separate and compare the three serum samples (the healthy group’s, the patients’ before and after chemo-radiotherapy) with two-dimensional protein liquid chromatography system (Proteome LabTM PF-2D), then detect the differential protein spots with linear trap quadruple mass spectrometer (LTQ MS/MS). (1) The Kazakh esophageal cancer patients got 21 expressed protein spots peaks with significant difference after chemo-radiotherapy compared with before; before the treatment there were 10 different expressed protein spots compared with the healthy group, and after it there were four peaks in the expression of protein spots compared with the healthy group. (2) After LTQ mass spectrometric detection, 22 proteins were up-regulated in serum samples of the healthy group, 22 were up-regulated of the patients before medical treatment and 5 were up-regulated after chemo-radiotherapy. (3) 8 proteins including APOA1 can be served as serum markers in Kazakh esophageal cancer diagnosis, and proteins like CLU can be served as serum markers in judging the resistance and sensitivity towards chemo-radiotherapy. (4) The abnormal expressions of APOC2, APOC3, Antithrombin-III in esophageal cancer were discovered for the first time. Specific protein spots related to Xinjiang Kazakh esophageal cancer diagnosis and chemo-radiotherapy can be identified in the serum, which will probably become a maker in Kazakh esophageal cancer diagnosis and therapeutic evaluation.     

Detection and first characterization of an uncommon haptoglobin in porcine saliva of pigs with rectal prolapse by using boronic acid sample enrichment

Salivary glycoprotein profiles, obtained after boronic acid enrichment, were studied for the first time in pigs in order to search for specific overall alterations related to acute inflammatory condition. Five healthy pigs and five pigs suffering from rectal prolapse were used, and the levels of acute phase proteins were measured to determine the degree of inflammation of the animals. The enriched glycoprotein profiles, achieved by two-dimensional gel electrophoresis (2DE) were statistically evaluated and spots that appeared differentially regulated between states were subjected to MS analysis for protein identification. Spots from three unique proteins were identified: carbonic anhydrase VI (CA VI), α-1-antichymotrypsin and haptoglobin (Hp). CA VI appeared as two adjacent horizontal spot trains in the glycoprotein profile of healthy animals in its regular isoelectric points (pI). One spot of α-1-antichymotrypsin was found in saliva from pigs with rectal prolapse in an unusual basic pI, and was considered as a breakdown product. Hp was identified as several spot trains in saliva from pigs with rectal prolapse in an unusual alkaline pI and was consequently further investigated. SDS-PAGE and 2DE of paired serum and saliva samples combined with Western blot analysis showed that the unusual Hp position observed in saliva samples was absent in serum. Furthermore, N-glycans from serum and saliva Hp glycopatterns were evaluated from SDS-PAGE Hp bands and showed that the serum N-glycan distribution in Hp β-chain was comparable in quantity and quality in both groups of animals. In saliva, no Hp β-chain derived N-glycans could unambiguously be identified from this sample set, thus needing further detailed investigations in the future.     

A comparative proteomic analysis of blood serum for developmental stages in pigs

This study aimed to differentiate genes at developmental stages of pigs from 0 to 150 days of age, to build up a protein database and to find candidate genetic markers for growth traits. The analysis of two‐dimensional electrophoresis and matrix‐assisted laser‐desorption/ionization mass spectrometry separated 252 protein segments. After successfully blasting the peptide sequences, the analysis confirmed 37 differentially expressed proteins that increased from birth to 150 days of age (type A), whereas the type B proteins presented the inverse pattern. The type C proteins included proteins that were expressed continuously throughout the developmental periods. A total of 319 primer sets for 33 genes were designed to find genetic variants using pooled DNA samples of Yorkshire pigs. Amplification products for all primer sets produced approximately 20 000 clones that were sequenced, and 48 candidate SNP sites were finalized for genotyping. A total of 475 animals were used for high throughput genotyping analysis. Among these, phenotype data of all 475 animals were collected for average daily gain, backfat thickness and days to 90 kg, whereas feed conversion data were collected for 300 animals and body measurement traits (starting weight, ending weight, body length, wither height and chest depth) were collected for 209 animals. Association analysis found significant statistical differences between the animals having genotypes of 13 SNPs (g.78935883C>T, g.147629986C>T, g.98266037T>C, g.214707340G>A, g.88350299C>T, g.17180956C>T, g.17181024C>T, g.2350283A>G, g.138361311C>T, g.44996379C>T, g.44996247A>C, g.107715245C>T, g.4149631C>T) for the various measured traits. The identified genetic polymorphisms, of which one was novel (g.214707340G>A), may serve as candidate molecular markers to change population means for the targeted growth traits.     

Protein expression of lymphocytes in HLA-DR transgenic pigs by a proteomic approach

Matching donor and recipient human leucocyte antigen (HLA-II) could conquer cell-mediated rejection following transplantation. Transgenic pigs carrying HLA genes that "humanize" porcine organs, tissues, and cells were successfully generated. This study further clarifies the effect of HLA-DR transgenes on lymphocyte protein expression, via a proteomic approach. Lymphocytes were isolated from two HLA-DR transgenic pigs and three nontransgenic littermates on 157 d after birth. Soluble protein of 1x10(7) cells was separated using 2-DE. In total, 301 colloidal CBB-stained protein spots detected on all five 2-D gels were quantified. Thirty-three proteins were differentially expressed by a factor of 1.5. These proteins were subsequently identified by MALDI-TOF MS and MALDI-TOF/TOF MS/MS. These proteins were sorted into the following categories: chaperones, T-lymphocyte function, DNA/RNA processing, cytoskeleton-associated proteins, signal transduction, enzymes, and unknown. Previous studies have suggested that some of the identified proteins are associated with lymphocyte activation/proliferation. The identities of the unidentified spots and the systematic effect of these up- and down-regulated proteins on T-cell function in HLA-DR transgenic pigs require further exploration.     

Osteochondrosis in Wild Boar–Swedish Yorkshire Crossbred Pigs (F2 Generation)

Osteochondrotic lesions occur in very high frequency in growing pigs of all commercial breeds and are claimed to be associated with high growth rate, and not to occur, or to be milder, in slow-growing pigs. The present study monitored the magnitude and distribution of osteochondrotic lesions in a crossbred pig population of wild boar and Swedish Yorkshire ancestry. In this population, having a low growth rate, the distribution and extent of osteochondrotic lesions was similar to that of purebred Swedish Yorkshire pigs, and only weak relationships between the studied growth parameters and osteochondrosis could be found.     

Proteomic tracking of serum protein isoforms as screening biomarkers of ovarian cancer

Epithelial ovarian cancer is the fourth leading cause of cancer death among women. Due to the asymptomatic nature and poor survival characteristic of the disease, screening for specific biomarkers for ovarian cancer is a major health priority. Differentially expressed proteins in the serum of ovarian cancer patients have the potential to be used as cancer-specific biomarkers. In this study, proteomic methods were used to screen 24 serum samples from women with high-grade ovarian cancer and compared to a control group of 11 healthy women. Affigel-Blue treated serum samples were processed either by linear (pH 4-7) or narrow range (pH 5.5-6.7) IEF strips for the first dimension. Proteins separated in first dimension were resolved by 8-16% gradient SDS-PAGE. Protein spots were visualized by SYPRO Ruby staining, imaged by FX-imager and compared and analyzed by PDQuest software. Twenty-two protein spots were consistently differentially expressed between normal and ovarian cancer patients by resolving proteins in a linear pH strip of 4-7 for the first dimension. Six of the protein spots, significantly up-regulated in grade 3 ovarian cancer patients (p < 0.05), were identified by MALDI-TOF MS and Western blotting as the isoforms of haptoglobin precursor. When serum proteins were resolved on narrow pH range strips (5.5-6.7), 23 spots were consistently differentially expressed between normal and grade 3 ovarian cancer patients. Of these, 4 protein spots significantly down regulated in grade 3 ovarian cancer patients (p < 0.05) were identified by MALDI-TOF MS and Western blotting, as isoforms of transferrin precursor. Increased expression of serum haptoglobin and transferrin was also identified in peritoneal tumor fluid obtained from women diagnosed with grade 2/3 ovarian cancer (n = 7). Changes in the expression of haptoglobin and transferrin in the serum of women with different pathological grades of ovarian cancer was examined by one-dimensional Western blotting method. Serum samples collected from women suffering from benign, borderline, grade 1, grade 2 and grade 3 cancer (n = 4 for haptoglobin and n = 5 for transferrin in each group) were analyzed and compared to the serum of normal healthy women. The mean serum haptoglobin expression in grade 3 ovarian cancer patients was fourfold higher than in the control subjects (p < 0.05). On the other hand, transferrin expression in grade 3 ovarian cancer patients was decreased by twofold than in normal healthy women (p < 0.05). Haptoglobin expression in the serum of cancer patients (n = 7) decreased following chemotherapy (six cycles of taxol/carboplatin). Concomitant with the decrease of haptoglobin, transferrin expression remained constant in four patients, but increased in three out of seven patients included in the study. Changes in serum expression of haptoglobin correlated with the change of CA 125 levels before and after chemotherapy. In conclusion, proteomic profiling of differentially expressed proteins in the sera of normal women compared to women with ovarian cancer can greatly facilitate the discovery of a panel of biomarkers that may aid in the detection of ovarian cancer with greater specificity.     

Imputation of genotypes in Danish purebred and two-way crossbred pigs using low-density panels

Background

Genotype imputation is commonly used as an initial step in genomic selection since the accuracy of genomic selection does not decline if accurately imputed genotypes are used instead of actual genotypes but for a lower cost. Performance of imputation has rarely been investigated in crossbred animals and, in particular, in pigs. The extent and pattern of linkage disequilibrium differ in crossbred versus purebred animals, which may impact the performance of imputation. In this study, first we compared different scenarios of imputation from 5 K to 8 K single nucleotide polymorphisms (SNPs) in genotyped Danish Landrace and Yorkshire and crossbred Landrace-Yorkshire datasets and, second, we compared imputation from 8 K to 60 K SNPs in genotyped purebred and simulated crossbred datasets. All imputations were done using software Beagle version 3.3.2. Then, we investigated the reasons that could explain the differences observed.

Results

Genotype imputation performs as well in crossbred animals as in purebred animals when both parental breeds are included in the reference population. When the size of the reference population is very large, it is not necessary to use a reference population that combines the two breeds to impute the genotypes of purebred animals because a within-breed reference population can provide a very high level of imputation accuracy (correct rate ≥ 0.99, correlation ≥ 0.95). However, to ensure that similar imputation accuracies are obtained for crossbred animals, a reference population that combines both parental purebred animals is required. Imputation accuracies are higher when a larger proportion of haplotypes are shared between the reference population and the validation (imputed) populations.

Conclusions

The results from both real data and pedigree-based simulated data demonstrate that genotype imputation from low-density panels to medium-density panels is highly accurate in both purebred and crossbred pigs. In crossbred pigs, combining the parental purebred animals in the reference population is necessary to obtain high imputation accuracy.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0134-4) contains supplementary material, which is available to authorized users.