[Show abstract][Hide abstract] ABSTRACT: Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs.
PLoS ONE 09/2014; 9(9):e106780. DOI:10.1371/journal.pone.0106780 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Background: Modern breeding and artificial selection play critical roles in pig domestication and shape the genetic variation of different breeds. China has many indigenous pig breeds with various characteristics in morphology and production performance that differ from those of foreign commercial pig breeds. However, the signatures of selection on genes implying for economic traits between Chinese indigenous and commercial pigs have been poorly understood. Results: We identified footprints of positive selection at the whole genome level, comprising 44,652 SNPs genotyped in six Chinese indigenous pig breeds, one developed breed and two commercial breeds. An empirical genome-wide distribution of Fst (F-statistics) was constructed based on estimations of Fst for each SNP across these nine breeds. We detected selection at the genome level using the High-Fst outlier method and found that 81 candidate genes show high evidence of positive selection. Furthermore, the results of network analyses showed that the genes that displayed evidence of positive selection were mainly involved in the development of tissues and organs, and the immune response. In addition, we calculated the pairwise Fst between Chinese indigenous and commercial breeds (CHN VS EURO) and between Northern and Southern Chinese indigenous breeds (Northern VS Southern). The IGF1R and ESR1 genes showed evidence of positive selection in the CHN VS EURO and Northern VS Southern groups, respectively. Conclusions: In this study, we first identified the genomic regions that showed evidences of selection between Chinese indigenous and commercial pig breeds using the High-Fst outlier method. These regions were found to be involved in the development of tissues and organs, the immune response, growth and litter size. The results of this study provide new insights into understanding the genetic variation and domestication in pigs.
[Show abstract][Hide abstract] ABSTRACT: Due to the direction, intensity, duration and consistency of genetic selection, especially recent artificial selection, the production performance of domestic pigs has been greatly changed. Therefore, we reasoned that there must be footprints or selection signatures that had been left during domestication. In this study, with porcine 60K BeadChip genotyping data from both commercial Large White and local Chinese Tongcheng pigs, we calculated the extended haplotype homozygosity values of the two breeds using the long-range haplotype method to detect selection signatures. We found 34 candidate regions, including 61 known genes, from Large White pigs and 25 regions comprising 57 known genes from Tongcheng pigs. Many selection signatures were found on SSC1, SSC4, SSC7 and SSC14 regions in both populations. According to quantitative trait loci and network pathway analyses, most of the regions and genes were linked to growth, reproduction and immune responses. In addition, the average genetic differentiation coefficient F ST was 0.254, which means that there had already been a significant differentiation between the breeds. The findings from this study can contribute to further research on molecular mechanisms of pig evolution and domestication and also provide valuable references for improvement of their breeding and cultivation.
[Show abstract][Hide abstract] ABSTRACT: Modern breeding and artificial selection play critical roles in pig domestication and shape the genetic variation of different breeds. China has many indigenous pig breeds with various characteristics in morphology and production performance that differ from those of foreign commercial pig breeds. However, the signatures of selection on genes implying for economic traits between Chinese indigenous and commercial pigs have been poorly understood.
We identified footprints of positive selection at the whole genome level, comprising 44,652 SNPs genotyped in six Chinese indigenous pig breeds, one developed breed and two commercial breeds. An empirical genome-wide distribution of Fst (F-statistics) was constructed based on estimations of Fst for each SNP across these nine breeds. We detected selection at the genome level using the High-Fst outlier method and found that 81 candidate genes show high evidence of positive selection. Furthermore, the results of network analyses showed that the genes that displayed evidence of positive selection were mainly involved in the development of tissues and organs, and the immune response. In addition, we calculated the pairwise Fst between Chinese indigenous and commercial breeds (CHN VS EURO) and between Northern and Southern Chinese indigenous breeds (Northern VS Southern). The IGF1R and ESR1 genes showed evidence of positive selection in the CHN VS EURO and Northern VS Southern groups, respectively.
In this study, we first identified the genomic regions that showed evidences of selection between Chinese indigenous and commercial pig breeds using the High-Fst outlier method. These regions were found to be involved in the development of tissues and organs, the immune response, growth and litter size. The results of this study provide new insights into understanding the genetic variation and domestication in pigs.
[Show abstract][Hide abstract] ABSTRACT: Interferon (IFN) is one of the major regulators of innate immunity, it also mediates the adaptive immune responses to a broad spectrum of pathogens. This study aims in identifying differences between high vs. low INF-a responders which were chosen based on serum INF-a levels at 4 hours post poly I:C treatment. A transcriptomic analysis was designed to describe the whole blood differential transcriptomal response to poly I:C by pigs with high vs. low IFN alpha levels. the capability of producing dsRNA (poly I:C)-induced serum IFN-a is highly variable in pig population. The high INF-a responders had 328 unique differentially expressed genes, suggesting that the HIGH pigs have greater responsiveness upon the dsRNA simulation. Based on the results, the interferon-dependent antiviral responsiveness through the IFN-stimulated genes (ISGs) is likely more effective in HIGH pigs. Inferring from the known organization of IFN pathways, the reason for the more IFN-a production in the HIGH pigs was likely due to the enhanced expression of IRF-7 in TLR or RIG- I/MDA5 signaling pathways. Furthermore, the larger number of the altered genes in the HIGH pigs after simulation is also possibly because of the greater number of the altered transcription factors. To our knowledge, this is the first report of comparative transcriptomic analysis to advance our understanding of whole blood immune response in pigs with different in vivo poly I:C-inducted IFN-a levels. The paper significantly expands our knowledge of how pigs respond to poly I:C which is highly relevant for understanding resistance to viral infections and also for vaccine development.
[Show abstract][Hide abstract] ABSTRACT: As important quantitative traits, the growth rate and backfat thickness are controlled by multiple genes. The aim of this investigation was to evaluate the effect of the single and multiple SNPs of four candidate genes (IGF2, JHDM1A, COPB1 and TEF-1) on growth rate and backfat thickness. The four candidate genes were mapped on the p arm of SSC 2, and there are several QTLs, such as average daily gain, backfat thickness, an imprinted QTLs affecting muscle mass and fat deposition have been reported in this region. The polymorphisms of these genes were detected using PCR-RFLP methods, mixed procedure was used to analyze the single marker association with the growth and backfat thickness traits, and the gene-gene combination was investigated using multiple-markers analysis. The single marker association analysis indicated that the IGF2 intron-3 g.3072G > A and the substitution g.93G > A of TEF-1 gene were significantly associated with the age at 100 kg (P < 0.05). The JHDM1A 3'UTR g.224C > G, the c.3096C > T polymorphism of COPB1 gene and the substitution g.93G > A of TEF-1 gene were all significantly associated with the backfat at the shoulder (P < 0.05), backfat at the last rib, backfat at the lumbar, and the average backfat thickness, respectively. The multiple-markers analysis indicated that IGF2 and TEF-1 integrated gene networks for the age at 100 kg. Therefore, we can suggest that the polymorphism of IGF2 and TEF-1 gene could be used in marker-assisted selection for the age at 100 kg in Large White pigs.
[Show abstract][Hide abstract] ABSTRACT: Caveolin-1 is the principal component of caveolae, and it is implicated in endocytosis, cholesterol homeostasis, signal transduction and tumorigenesis. MicroRNAs play key regulatory roles in many cellular processes. However, the molecular mechanism by which porcine caveolin-1 is regulated by microRNAs remains unclear. In the present study, we found that miR-124 could directly target caveolin-1 in porcine kidney epithelial cells (PK15). A luciferase reporter assay revealed that miR-124 directly bound to Cav1 mRNA. Ectopic expression of miR-124 decreased porcine Cav1 expression at both the mRNA and protein levels. Furthermore, we used transmission electron microscopy to count caveolae in the cytosolic space next to the membrane and we found that the overexpression of miR-124 in PK15 cells reduced the density of the caveolae. Our results suggested that miR-124 reduced caveolar density by targeting caveolin-1 in PK15 cells; therefore, miR-124 could play an important role in the caveolae-mediated endocytosis of pathogens and signal transduction.
[Show abstract][Hide abstract] ABSTRACT: Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus that causes acute viral encephalitis in humans. Pigs are important amplifiers of JEV. The entry mechanism of JEV into porcine cells remains largely unknown. In this study, we present a study of the internalization mechanism of JEV in porcine kidney epithelial PK15 cells.
We demonstrated that the disruption of the lipid raft by cholesterol depletion with methyl-beta-cyclodextrin (MbetaCD) reduced JEV infection. We also found that the knockdown of clathrin by small interfering RNA (siRNA) significantly reduced JEV-infected cells and JEV E-glycoprotein levels, suggesting that JEV utilizes clathrin-dependent endocytosis. In contrast, the knockdown of caveolin-1, a principal component of caveolae, had only a small (although statistically significant) effect on JEV infection, however, JEV entry was not affected by genistein. These results suggested that JEV entry was independent of caveolae.
Taken together, our results demonstrate that JEV enters porcine kidney epithelial PK15 cells through cholesterol- and clathrin-mediated endocytosis.
[Show abstract][Hide abstract] ABSTRACT: MicroRNAs (miRNAs), a novel class of post-transcriptional gene regulators, have been demonstrated to be involved in several cellular processes regulating the expression of protein-coding genes. To investigate the mechanisms of miRNA-mediated regulation during the process of muscle atrophy, we performed miRNA microarray hybridization between normal differentiated C2C12 cells and dexamethasone (DEX)-treated C2C12 cells. We observed that 11 miRNAs were significantly up-regulated and six miRNAs were down-regulated in the differentiated C2C12 cells after being treated with DEX. Stem-loop real-time RT-PCR confirmed the differential expression of six selected miRNAs (miR-1, miR-147, miR-322, miR-351, and miR-503*, miR-708). miRNA potential target prediction was accomplished using TargetScan, and many target genes related to muscle growth and atrophy have been reported in previous studies. The results of the current study suggested the potential roles of these differentially expressed miRNAs in skeletal muscle atrophy.
[Show abstract][Hide abstract] ABSTRACT: Heavy pigs are used in Italy to produce fresh meat, dry-cured ham, salami and lard. Fatty acid profile determines both the dietary and organoleptic qualities of these products. The objective was to study the polymorphisms of two genes that code for enzymes of the fatty acid metabolism, namely, Stearoyl-CoA desaturase (SCD) and Fatty acid desaturase 2 (FADS2). We also investigated the polymorphism of the Sterol regulatory element binding protein gene (SREBF1) as it regulates SCD and FADS2 transcription. Significant associations of SCD were found with the ratio of oleic to stearic acid; with the concentration (g/100g of fat) of stearic and oleic acids. The concentrations of arachidonic and linoleic acids and the ratio of dihomo-gamma-linolenic to linoleic acid were significantly associated with FADS2 polymorphisms. SREBF1 polymorphism was associated with oleic acid concentrations and the ratio of arachidonic to linoleic acids. Our findings suggest that the SCD, FADS2 and SREBF1 polymorphisms are associated with dietary quality of heavy pig meat products.
[Show abstract][Hide abstract] ABSTRACT: The production performance of pigs has been significantly improved due to long-term artificial selection, and the specific variation characterizations (selection signatures) emerged from the selected genome regions. Different types of breeds are subjected to different selection intensities and had different selection signatures. Selective sweep analysis is one of major methods to detect the selection signatures. In this study, based on the 60K BeadChip genotyping data of both commercial Large White (n=45) and local Tongcheng pigs (n=45), genetic differentiation coefficient Fst was applied to detect the selection signatures. Using gPLINK software to set quality control standards, a total of 34 304 SNPs were selected for statistical analysis. Fst values between two breeds were estimated with Genepop package and the average Fst value was 0.3209. Setting Fst>0.7036 (1% of total number of Fst values) as selection threshold, 344 SNPs were obtained and SNP location annotation indicated that there were 79 candidate genes (Sus scrofa Build 9). Furthermore, network analysis was performed using Ingenuity Pathway Analysis and the preliminary results suggested that most genes were involved in growth, reproduction, and immune response, such as NCOA6, ERBB4, RUNX2, and APOB genes. The findings from this study will contribute to further identification of candidate genes and causal mutations implying for meat production and disease resistance in pig.
[Show abstract][Hide abstract] ABSTRACT: GWAS(Genome-wide association study) strategy has been extensively used for identification of economical trait loci in livestock animals. Using Illumina's PorcineSNP60 BeadChip, a GWA study of 820 commercial pigs with reproductive traits recorded was performed. The PCA analysis showed that there was no significant population stratification. Two different statistical models Compressed Mixed Linear Model(GAPIT program package)and Bayes CPi (GenSel software) were used to implement GWAS on total number born and number born alive of the first and second parity. To compare the most significant 50 SNPs from each method, a total of 31 and 20 coincided SNPs for total number born in the first parity were identified, and there were 20 coincided SNPs for number born alive in the first parityinthe results of bothmethods. The most significant SNPs were also significant in the results of the other method. The most significantly associated regions for total number born in the first parity were located on SSC1, 2, 3, 7, 13, 16, and 18. The most significantly associated regions for number born alive in the first parity were locatedon SSC1, 3, 4, 13, and 16. There were 5 common regions significantly associated with bothtraits on SSC1, 3, 13, and 16. The most significantly associated regions forbothtotal number born and number born alive for the second parity were mainly located on six common regions on SSC7, 10, 12, 13, 14, and 16.
[Show abstract][Hide abstract] ABSTRACT: In November 2009, scientists from the US, UK, and other countries announced the complete genome sequence draft of the domestic pig. With the release of improved versions of the pig genome assembly and the increase of correctly assembled sequenced fragments over the past two years, it is particularly urgent to have the pig genes annotated at whole-genome level. This article is aimed at introducing an excellent manual annotation tool, Otterlace software, developed by Sanger institute. We used CFL1 (Cofilin 1) gene as an example to expound the usage of the three main components of Otterlace, Zmap, Blixem, and Dotter tools, and developed a practical procedure for manual annotations. We have analyzed 243 immune-related genes, among which 180 genes have been completely or partially annotated, offering novel information to the porcine functional genomics.
[Show abstract][Hide abstract] ABSTRACT: Both the CTNNBL1 (catenin, β-like1) and DGAT2 (diacylglycerol acyltransferase2) genes play important roles in adipose metabolism. In this study, we cloned these two genes in pigs. Semi-quantitative RT-PCR results showed that both genes were extensively expressed, and CTNNBL1 was at a high level in the heart and spleen, while DGAT2 was most abundant in the liver. In CTNNBL1, one synonymous mutation c.555C>T was identified in the coding region, and association analysis showed that different genotypes of CTNNBL1 were significantly associated with backfat at the shoulder and backfat at the rump (P < 0.05). In 3'-UTR of DGAT2, an A/G variation was detected by the Bcn I PCR-RFLP method, and different genotypes were significantly associated with backfat between the 6th and 7th ribs (P < 0.05). The allele frequency was tested among 188 unrelated pigs from six breeds. The results showed that for CTNNBL1, the Chinese indigenous breeds had higher frequencies of the C allele whereas the western breed had higher frequency of the T allele; and for DGAT2, allele A or G were distributed with no obvious difference in allele frequency. IMpRH was employed to localize these two genes, and CTNNBL1 was assigned to SSC17q21-23 and DGAT2 was assigned to SSC9p23-p24. The results suggest that the porcine CTNNBL1 and DGAT2 genes affect porcine fat deposition and further investigation will be necessary to illustrate the underlying mechanisms.
[Show abstract][Hide abstract] ABSTRACT: Meat quality traits are economically important traits of swine, and are controlled by multiple genes as complex quantitative traits. In the present study four genes, H-FABP (heart fatty acid-binding protein), MASTR (MEF2 activating motif and SAP domain containing transcriptional regulator), UCP3 (uncoupling protein 3) and MYOD1 (myogenic differentiation 1) were researched in Large White pigs. The polymorphisms H-FABP T/C of 5'UTR, MYOD1 g.257 A>C, UCP3 g.1406 G>A in exon 3 and MASTR c.187 C>T have been reported to be associated with meat quality traits in pigs. The aim of this study was to analyze the effect of single and multiple markers for single traits in Large White pigs. The single marker association analysis showed that the H-FABP and MASTR genes were associated with IMF (intramuscular fat content) (P < 0.05), and that the g.257 A>C of MYOD1 gene was most significantly related to muscle pH value (P < 0.01). The multiple markers for IMF were analyzed by combining the markers and quantitative trait modes into the linear regression. The results revealed that H-FABP and MASTR integrate gene networks for IMF. Thus, our study results suggested that H-FABP and MASTR polymorphisms could be used as genetic markers in the marker-assisted selection towards the improvement of IMF in Large White pigs.
[Show abstract][Hide abstract] ABSTRACT: MTPAP (mitochondrial poly(A) polymerase) gene plays a role in stabilizing the level of mitochondrial mRNAs and controlling the poly(A) length of human mitochondrial mRNAs. In this study, 2,296 bp partial cDNA sequences of the porcine MTPAP gene were obtained, which contained 1,746 bp full-length coding regions flanked by a 500 bp partial 3′-UTR. The porcine MTPAP gene was assigned to SSC10q14-q16 using the radiation hybrid (IMpRH) panel and chromosome electric location methods. Q-PCR analysis showed that MTPAP was expressed in all analyzed tissues, and has higher expression in heart, liver, skeletal muscles, and fat. One single nucleotide polymorphism g.2421T>A in intron5 of MTPAP gene was identified and detected by DdeI PCR–RFLP. Association of the genotypes with economic traits showed that different genotypes were significantly associated with juiciness, individuals with genotype AT displayed a significantly higher juiciness compared to genotype TT. The C/EBPβ transcription factors was up-regulation the expression of MTPAP by analyzing a series of MTPAP promoter reporter constructs using the dual-luciferase assay system, it indicated that MTPAP gene maybe play a critical role in fat deposition regulation which is regulated by C/EBPβ transcription factor. These findings provide an important basis for further understanding of porcine MTPAP regulation and function in swine.
[Show abstract][Hide abstract] ABSTRACT: A whole-genome association study was performed for reproductive traits in commercial sows using the PorcineSNP60 BeadChip and Bayesian statistical methods. The traits included total number born (TNB), number born alive (NBA), number of stillborn (SB), number of mummified foetuses at birth (MUM) and gestation length (GL) in each of the first three parities. We report the associations of informative QTL and the genes within the QTL for each reproductive trait in different parities. These results provide evidence of gene effects having temporal impacts on reproductive traits in different parities. Many QTL identified in this study are new for pig reproductive traits. Around 48% of total genes located in the identified QTL regions were predicted to be involved in placental functions. The genomic regions containing genes important for foetal developmental (e.g. MEF2C) and uterine functions (e.g. PLSCR4) were associated with TNB and NBA in the first two parities. Similarly, QTL in other foetal developmental (e.g. HNRNPD and AHR) and placental (e.g. RELL1 and CD96) genes were associated with SB and MUM in different parities. The QTL with genes related to utero-placental blood flow (e.g. VEGFA) and hematopoiesis (e.g. MAFB) were associated with GL differences among sows in this population. Pathway analyses using genes within QTL identified some modest underlying biological pathways, which are interesting candidates (e.g. the nucleotide metabolism pathway for SB) for pig reproductive traits in different parities. Further validation studies on large populations are warranted to improve our understanding of the complex genetic architecture for pig reproductive traits.