Expression and genomic imprinting of DCN, PON2 and PEG3 genes in porcine placenta

Imprinted genes play vital roles in the placental development and fetal growth in eutherian mammals. DCN (decorin), PON2 (paraoxonase 2) and PEG3 (paternally expressed 3) genes have been identified as imprinted genes in the mouse. Here, we detected the imprinting status of three genes in the porcine placenta on DG90 (day 90 of gestation) and the expression differences in Yorkshire and Meishan placenta on DG26, DG55 and DG90. The results indicated that the DCN and PON2 genes were not imprinted genes, while the PEG3 gene showed paternal monoallelic expression in porcine placenta. The expression of the DCN gene increased from DG26 to DG90 in both Yorkshire and Meishan pig placenta. However, this gene expression was greater in Yorkshire than Meishan pig on DG55. The expression of the PON2 gene was greater in Meishan pig than that in Yorkshire on DG26 and DG90. The PEG3 gene expression was not affected by day of pregnancy or breed. Data from the present study contribute to function genomic of porcine placental development.     

Porcine skeletal muscle differentially expressed gene CMYA1: isolation, characterization, mapping, expression and association analysis with carcass traits

To investigate the differences in gene expression between some obese and lean pig breeds, differential display of mRNA was employed in our previous research. One differentially expressed EST ( BI596262 ) was further identified as the porcine cardiomyopathy associated 1 ( CMYA1 ) gene because of its homology to the human CMYA1 gene. The full-length DNA of the porcine CMYA1 gene encompasses 9379 bp, including a complete open reading frame encoding 1839 amino acid residues, a 158-bp 5'-untranslated region and a 630-bp 3'-untranslated region. The porcine CMYA1 gene was assigned to chromosome 13 by the radiation hybrid panel (IMpRH). The porcine CMYA1 gene was expressed only in the striated muscle. Single nucleotide polymorphism (SNP) scanning in the coding region identified one synonymous mutation (c.1053C>T) and three missense mutations, c.1394A>G (p.His465Arg), c.1751A>G (p.Asp582Gly) and c.3290C>A (p.Thr1097Asp). The allele frequencies were tested among about 200 unrelated pigs from several pig breeds. Linkage mapping was further conducted with the SNP c.1751A>G (p.Asp582Gly) in a Berkshire × Yorkshire resource family and this confirmed that porcine CMYA1 is closely linked with Sw344 (distance  =  2 cM, LOD score is 129.47), an interesting region harbouring a QTL for back fat thickness. Association analysis in our experimental pig population showed that different genotypes of CMYA1 gene were associated with different back fat thicknesses ( P  <   0.05). Our results suggest that the porcine CMYA1 gene has effects on porcine back fat deposition and further investigation will be necessary to illustrate the underlying mechanisms.     

猪STCH基因的Bi-PASA遗传标记及多态性研究

微粒体应激 70蛋白三磷酸腺苷酶 (STCH)基因属于应激 70蛋白基因伴侣家族 ,在机体免疫反应和疾病抵抗力等方面起重要作用。根据人和小鼠STCH基因的保守序列设计引物 ,PCR扩增到猪STCH基因第5外显子 4 4 5bp片段。序列测定显示 ,猪STCH基因与人和小鼠STCH基因分别具有 87 13%和 80 4 5 %的同源性。通过测定和比较中国梅山猪、欧洲约克夏猪及PIC商品猪的STCH基因序列 ,发现在猪STCH基因编码区第 5外显子 10 5 0位点上存在一个单碱基突变位点。利用双向特定等位基因PCR扩增法 (Bi PASA)建立了检测猪STCH基因变异的遗传标记 ,并用该标记分析了STCH基因在中国家猪 (梅山猪、荣昌猪和金华猪 )、欧洲家猪 (约克夏猪、大白猪 )、商品猪 (PIC合成系 )以及欧洲野猪的基因频率和多态性。本研究建立的Bi PASA遗传标记和基因变异信息 ,将为进一步分析猪STCH基因变异与经济性状的相关分析提供基础资料。     

Construction of a 1.2-Mb BAC/PAC contig of the porcine gene RYR1 region on SSC 6q1.2 and comparative analysis with HSA 19q13.13

We screened a porcine bacterial artificial chromosome (BAC) and a P1 derived artificial chromosome (PAC) library to construct a sequence-ready approximately 1.2-Mb BAC/PAC contig of the ryanodine receptor-1 gene (RYR1) region on porcine chromosome (SSC) 6q1.2. This genomic segment is of special interest because it harbors the locus for stress susceptibility in pigs and a putative quantitative trait locus for muscle growth. Detailed physical mapping of this gene-rich region allowed us to assign to this contig 17 porcine genes orthologous to known human chromosome 19 genes. Apart from the relatively well-characterized porcine gene RYR1, the other 16 genes represent novel chromosomal assignments and 14 genes have been cloned for the first time in pig. Comparative analysis of the porcine BAC/PAC contig with the human chromosome (HSA) 19q13.13 map revealed a completely conserved gene order of this segment between pig and human. A detailed porcine-human-mouse comparative map of this region was constructed.     

Porcine granulin gene (GRN): molecular cloning, polymorphism and chromosomal localization.

GRN has been shown to have roles in multiple processes involved in cell growth, development and wound repair in rodents and humans. We have isolated the full-length cDNA of GRN gene encoding porcine granulin protein by in silico cloning, RT-PCR and RACE. The deduced amino acid indicated 71.5% identity with the corresponding human sequence and the seven and one-half granulins showed highly conservative between pig, human and murine. A single nucleotide substitution resulting in the amino acid change (ATG/Met --> TTG/Leu) was detected within exon 5. Allele frequencies in six pig breeds showed distinctive differences between those Chinese indigenous pig breeds and European pigs. Using the IMpRH panel, we mapped the porcine GRN gene to porcine chromosome 12p11-p13. Our data provide basic molecular information useful for the further investigation on the function of GRN gene.     

Cloning, transcription and chromosomal localization of the porcine whey acidic protein gene and its expression in HC11 cell line

The whey acidic protein (WAP) is the major whey protein of rodent, rabbit and camel. Recently, it was identified in the milk of swine (Simpson et al., 1998. J. Mol. Endocrinol. 20, 27-35). In this paper, the cloning of the pig WAP cDNA and of bacterial artificial chromosome (BAC) construct containing the entire porcine WAP gene is reported. The comparison of the coding sequence of the pig WAP gene to rodent or lagomorph WAP sequence already published demonstrated that only exon sequences are partially conserved. The porcine WAP gene was localized on the subtelomeric region of the chromosome 18. The estimation of the expression of the swine WAP gene in the mammary gland from lactating animals revealed a high level of expression. In order to compare the expression level of the porcine WAP gene from the large genomic fragment which contained 70 kb downstream and 50 kb upstream the pig WAP gene or the smaller one (1 kb downstream and 2.4 kb upstream), these two genomic fragments were transfected in HC11 cell line. The BAC construct was expressed 15 times higher than the plasmid when reported to the integrated copy number. This report suggests that the HC11 cell line is a useful tool to identify the regulatory sequences of milk protein genes.     

Improving the comparative map of SSC2p-q13 by sample sequencing of BAC clones

To improve the comparative map for pig chromosome 2 and increase the gene density on this chromosome, a porcine bacterial artificial chromosome (BAC) library was screened with 17 microsatellite markers and 18 genes previously assigned to pig chromosome 2. Fifty-one BAC clones located in the region of a maternally imprinted quantitative trait locus for backfat thickness (BFT) were identified. From these BACs 372 kb were sample sequenced. The average read length of a subclone was 442 basepair (bp). Contig assembly analysis showed that every bp was sequenced 1.28 times. Subsequently, sequences were compared with sequences in the nucleotide databases to identify homology with other mammalian sequences. Sequence identity was observed with sequences derived from 35 BACs. The average percentage identity with human sequences was 87.6%, with an average length of 143 bp. In total, sample sequencing of all BACs resulted in sequence identity with 29 human genes, 13 human expressed sequence tags (ESTs), 17 human genomic clones, one rat gene, one porcine gene and nine porcine ESTs. Eighteen genes located on human chromosome 11 and 19, and seven genes from other human locations, one rat gene and one porcine gene were assigned to pig chromosome 2 for the first time. The new genes were added to the radiation hybrid map at the same position as the locus from which the BAC that was sequenced was derived. In total 57 genes were placed on the radiation hybrid map of SSC2p-q13.     

Comparative human-mouse-rat sequence analysis of the ICAM gene cluster on HSA 19p13.2 and a 185-kb porcine region from SSC 2q

The human intercellular adhesion molecule gene (ICAM) cluster is located in a GC-rich and gene-rich region on HSA 19p13.2. We determined the complete DNA sequence of a 185-kb porcine bacterial artificial chromosome (BAC) clone containing parts of the ICAM gene cluster. We used the porcine sequence for a detailed comparative analysis between human, pig, mouse and rat. The 185 kb of porcine sequence covered 220 kb of homologous sequence in the human genome, which adds to the growing evidence that the porcine genome is somewhat smaller than the human genome. The genomic sequences of the four species showed a high level of conserved synteny and no rearrangements in gene order were observed. During evolution, the ICAM3 gene was inactivated by mutation in the mouse and rat genome, whereas it is still present in the human and pig genome. The loss of Icam3 in rodent genomes might be relevant for rodent-specific properties of the T-cell-mediated immune response. All the other investigated genes are conserved across all four investigated sequences.     

应用ＣＡＴＳ法分离和鉴定猪ＧＦＡＰ基因的研究

根据比较锚定序列宗踪（ＣＡＴＳ）法,选择人和小鼠胶质细胞原纤维酸性蛋白（ＧＦＡＰ）基因的同源区域设计引,用ＰＣＲ方法从二花脸猪基因组中分离到４１２bp的基因片段,经与基因资料库中已训功能基因的同源性比较,该片段可鉴定为猪的ＧＦＡＰ基因,利用猪－啮齿类体细胞杂克隆板将ＧＦＡＰ基因定位于猪１２号染色体１２p11-(2/3)P13区域。     

Molecular Characterization,Polymorphism, and Association of Porcine GADD45G Gene

Growth arrest and DNA-damage-inducible gamma (GADD45G) is a reproduction related gene. In this study, the full-length cDNA sequence of porcine GADD45G gene was cloned through rapid amplification of cDNA ends (RACE) method. The porcine GADD45G gene encodes a protein of 159 amino acids that shares high homology with the GADD45G of nine species: chimpanzee (97%), sumatran orangutan (97%), white-tufted-ear marmoset (97%), northern white-cheeked gibbon (97%), cattle (97%), human (97%), rhesus monkey (97%), rat (96%), and mouse (95%). This novel porcine gene was assigned to GeneID: 100152997. Phylogenetic analysis revealed that the porcine GADD45G gene has a closer genetic relationship with the GADD45G gene of cattle. Computer-assisted analysis indicated that porcine GADD45G gene is structured in four exons and three introns. PCR-Rsa I-RFLP was established to detect an A/G mutation on the position of 294-bp of coding sequence and eight pig breeds display obvious genotype and allele frequency differences at this mutation locus. Association of this SNP with litter size traits was assessed in Large White (n = 100) and Landrace (n = 100) pig populations, and result demonstrated that this polymorphic locus was significantly associated with the litter size of all parities in Large White and Landrace sows (P < 0.01). Therefore, porcine GADD45G gene could be a useful candidate gene in selection for increasing the litter size. These data serve as a foundation for further insight into this novel porcine gene.     

Expression of beta-galactosidase and pig leptin gene in vitro by recombinant adenovirus

Adenovirus has been used in vivo and in vitro as a vector to carry a foreign gene for gene transfer. Two kinds of replication defective human recombinant adenovirus vectors were used in this study, the first containing beta-galactosidase reporter gene (AdCMVLac-Z) and the second carrying a gene for porcine leptin gene (AdCMVpLeptin). AdCMVLac-Z was tested for its ability to transfer DNA into pig kidney and pituitary cells. These cells expressed Lac-Z transiently 48 hours after the infection. In addition, when the pig kidney cells expressing the Lac-Z were replated with low density for the formation of colonies from each cell, colonies of blue cells expressing Lac-Z were observed. These results demonstrate that human recombinant adenovirus can be used as a transducing viral vector for inducing long-term expression in pig kidney cells. We also constructed a recombinant adenovirus (AdCMVpLeptin) which contained a pig leptin gene for the expression of pig leptin in vitro in the 293 human kidney cell line. 293 cells transfected with AdCMVpLeptin produced both a 15 KDa of a secretory form of porcine leptin and an 18 KDa long form containing signal peptide. Our study demonstrated that the recombinant adenovirus system offers a method for gene transfer and expression in pig cells.     

The lactase phlorizin hydrolase (LCT) gene maps to pig chromosome 15q13

A porcine 17kb genomic fragment was used as probe to map the lactase phlorizin hydrolase ( LCT ) gene to pig chromosome 15q13 by fluorescence in situ hybridization. Further, a threeallele TaqI RFLP was used to add the LCT gene to the proximal end of the chromosome 15 linkage map. Comparison of the human chromosome 2 gene map and the gene map of pig chromosome 15 indicates that the part of human chromosome 2 distal to the q13 band is homologous to pig chromosome 15.     

应用RGS双荧光替代性报告载体提高CRISPR/Cas9对猪BMP15基因的打靶效率

我国是家猪养殖和消费大国,提高母猪的繁殖力对于促进我国生猪产业的发展具有重要的作用。排卵率和产仔数是影响家畜繁殖力的关键因素,其中BMP15 (bone morphogenetic protein 15)基因已被鉴定是控制绵羊排卵数和多胎性状的一个主效基因,然而目前在家猪BMP15基因中尚未发现类似绵羊多胎品系的天然突变。基于高等哺乳动物基因功能的保守性和CRISPR/Cas9(clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9)等基因组编辑技术对动物基因组定点修饰的高效性,应用CRISPR/Cas9技术对家猪BMP15基因进行精确的遗传修饰,使家猪获得类似多胎绵羊的天然突变,对于研究该基因对家猪繁殖力的影响以及培育高繁殖力家猪新品系具有重要的意义。本研究通过CRISPR/Cas9对长白猪胎儿成纤维(porcine embryonic fibroblasts, PEF)细胞中BMP15基因进行打靶,T7E1分析显示打靶效率仅有5%。随后通过共转染RGS双荧光替代性报告载体(RFP-GFP surrogate reporter),并应用流式细胞术分选出双荧光细胞,富集到基因组被CRISPR/Cas9修饰的细胞,使基因打靶效率提高至18%。本研究结果表明,应用RGS双荧光替代性报告载体可以有效提高CRISPR/Cas9在PEF细胞中对BMP15基因的打靶效率,为今后通过体细胞核移植技术培育BMP15基因编辑猪进行了有效的探索。     

Rapid determination of perv copy number from porcine genomic DNA by real-time polymerase chain reaction

Here, we report the quantification of porcine endogenous retrovirus (PERV) copy numbers using real time PCR. After generating standard curves using plasmid DNA, copy numbers were determined for PERV pol and for a housekeeping gene, porcine estrogen receptor2 (ER2) with the same amount of genomic DNA. Using this method, we examined 6 pig breeds in Korea including two breeds of miniature pig, one domestic pig from Jeju, and imported pig breeds, Duroc, Landrace, and Yorkshire. All breeds showed PERV copy numbers ranging from 9 to 50. This method will be useful for monitoring of PERVs in a porcine xenograft.     

A Colon Cancer Related Gene-MLH1, Significantly Affecting the Pig Litter Size

MutL homolog 1, colon cancer, nonpolyposis type 2 (MLH1) is a tumor related gene. In this study, the full-length cDNA sequence of porcine MLH1 gene was cloned through rapid amplification of cDNA ends (RACE) method. The porcine MLH1 gene encodes a protein of 757 amino acids which shares high homology with the MLH1 of five species: chiru (96%), sheep (95%), cattle (93%), southern-white-rhinoceros (92%) and goat (92%). This novel porcine gene was assigned to GeneID: 100337665. Phylogenetic analysis revealed that the porcineMLH1 gene has a closer genetic relationship with theMLH1 gene of southern- white-rhinoceros. PCR-HhaI-RFLP was established to detect GU373696:c.395 G > A substitution of porcine MLH1 gene and eight pig breeds display obvious genotype and allele frequency differences at this mutation locus. Association of this SNP with litter size traits was assessed in Large White (n = 200) and Landrace (n = 200) pig populations, and result demonstrated that this polymorphic locus was significantly associated with the litter size of all parities in Large White and Landrace sows (P < 0.01). Therefore, MLH1 is also a reproduction related gene.     

Porcine SINEs: Characterization and use in species-specific amplification

A porcine repetitive DNA sequence has been isolated from an intron of the glucose phosphate isomerase gene. The copy number of this and related sequences was estimated to be approximately 10(5) copies per genome. The sequence possesses all the characteristics of short interspersed elements (SINEs) described in other mammals: The repeat is 300 bp in length, has an poly(A)stretch, and contains insertion duplication sites. Homology to seven other porcine sequences, which also have the characteristics of SINEs, has been demonstrated. Primer oligonucleotides, based on conserved regions in the SINE sequences, have been synthesized. Using these primers, PCR-mediated specific amplification of porcine sequences was demonstrated from pig x mouse and pig x hamster hybrid cell lines. Cloning and sequencing of some amplified porcine sequences verify that the sites of priming are SINE sequences.     

Rapid Determination of Perv Copy Number From Porcine Genomic DNA by Real-Time Polymerase Chain Reaction

Here, we report the quantification of porcine endogenous retrovirus (PERV) copy numbers using real time PCR. After generating standard curves using plasmid DNA, copy numbers were determined for PERV pol and for a housekeeping gene, porcine estrogen receptor2 (ER2) with the same amount of genomic DNA. Using this method, we examined 6 pig breeds in Korea including two breeds of miniature pig, one domestic pig from Jeju, and imported pig breeds, Duroc, Landrace, and Yorkshire. All breeds showed PERV copy numbers ranging from 9 to 50. This method will be useful for monitoring of PERVs in a porcine xenograft.     

Molecular cloning, characterization, and chromosomal assignment of porcine cationic amino acid transporter-1

We have cloned and characterized the gene encoding the porcine cationic amino acid transporter, member 1 (CAT-1) (HGMW-approved gene symbol SLC7A1) from porcine pulmonary artery endothelial cells. The porcine SLC7A1 encodes 629 deduced amino acid residues showing a higher degree of sequence similarity with the human counterpart (91.1%) than with the rat (87.3%) and mouse (87.6%) counterparts. Confocal microscopic examination of porcine CAT-1-GFP-expressing HEK293 cells revealed that porcine CAT-1 localizes on the plasma membrane. Amino acid uptake studies in Xenopus oocytes injected with cRNA encoding this protein demonstrated transport properties consistent with system y(+). Radiation hybrid mapping data indicate that the porcine SLC7A1 maps to the distal end of the short arm of pig chromosome 11 (SSC11). This map location is consistent with the known conservation of genome organization between human and pig and provides further confirmation that we have characterized the porcine orthologue of the human SLC7A1.     

Isolation and mapping of two porcine skeletal muscle myosin heavy chain isoforms

The present paper describes the isolation and linkage mapping of two isoforms of skeletal muscle myosin heavy chain in pig. Two partial cDNAs (pAZMY4 and pAZMY7), coding for the porcine myosin heavy chain-2B and -β respectively, have been isolated from a pig skeletal muscle cDNA library. Four RFLPs were detected with the putative porcine skeletal myosin heavy chain-2B probe (pAZMY4) and one RFLP was identified with the putative myosin heavy chain-β probe (pAZMY7). Two myosin heavy chain loci were mapped by linkage analysis performed with the five RFLPs against the PiGMaP linkage consortium ResPig database: the MYH1 locus, which identifies the fast skeletal muscle myosin heavy chain gene cluster, was located at the end of the map of porcine chromosome 12, while the MYH7 locus, which identifies the myosin heavy chain-α/-β gene cluster, was assigned to the long arm of porcine chromosome 7.