Swine Genes Research Articles

Isolation, sequence identification and tissue expression profiles of 3 novel porcine genes:ASPA, NAGA, andHEXA

The complete coding sequences of 3 porcine genes - ASPA, NAGA, and HEXA - were amplified by the reverse transcriptase polymerase chain reaction (RT-PCR) based on the conserved sequence information of the mouse or other mammals and referenced pig ESTs. These 3 novel porcine genes were then deposited in the NCBI database and assigned GeneIDs: 100142661, 100142664 and 100142667. The phylogenetic tree analysis revealed that the porcine ASPA, NAGA, and HEXA all have closer genetic relationships with the ASPA, NAGA, and HEXA of cattle. Tissue expression profile analysis was also carried out and results revealed that swine ASPA, NAGA, and HEXA genes were differentially expressed in various organs, including skeletal muscle, the heart, liver, fat, kidney, lung, and small and large intestines. Our experiment is the first one to establish the foundation for further research on these 3 swine genes.

Genetic diversity of swine influenza viruses isolated from pigs during 2000 to 2005 in Thailand

Background Recent studies have revealed the existence of genetic diversity in swine influenza viruses (SIVs) in the world. In Thailand, there has been a little information on the molecular characteristics of the SIVs since the first isolation of viruses of H1N1 and H3N2 subtypes in the late 1970s. Our previous study demonstrated that Thai H1N1 SIVs possessed the classical swine H1 and avian‐like swine N1 genes (Takemae et al., Proceedings of the Options for the Control of Influenza VI.2007;350–353). Objectives In the present study, we genetically characterized 12 SIVs including those of H1N1, H1N2 and H3N2 subtypes isolated between 2000 and 2005. Methods We determined the entire nucleotide sequences of the eight gene segments of those isolates. Results Phylogenetic analysis revealed the existence of nine distinct genotypes amongst the Thai SIVs. These genotypes arose from multiple introductions of classical swine, avian‐like swine and human viruses. The existence of two distinct sublineages within classical swine H1 and NS, avian‐like swine PA and M and human H3 and N2 genes of the Thai SIVs suggested that introduction of viruses of classical swine, avian‐like swine and human origins occurred twice respectively into the Thai pig population. The predominance of avian‐like swine genes amongst the Thai SIVs was evident. In particular, three polymerase (PB1, PB2 and PA) and matrix genes of avian‐like swine origin were retained in all the Thai SIVs examined. Conclusions These observations may suggest that genes of avian‐like swine lineages have some advantages to be maintained in pigs as seen in the SIVs established through multiple introductions in other regions.

Molecular characterization and expression profile of a novel porcine gene differentially expressed in the muscle and backfat tissues from Chinese Meishan and Russian Large White pigs

The mRNA differential display technique was performed to investigate the differences of gene expression in the longissimus dorsi muscle and backfat tissues from Chinese Meishan and Russian Large White pigs. One novel gene that was differentially expressed was identified through semi-quantitative RT-PCR and the cDNA complete sequence was then obtained using the rapid amplification of cDNA ends (RACE) method. The cDNA sequence of this gene is not homologous to any of the known porcine genes. The sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 402 amino acids that contains the putative conserved transposase DDE domain and further Blast analysis revealed that this protein has 100% homology with the Tn10 transposase from Oryza sativa, Serratia marcescens, and Salmonella, and therefore, this gene can be defined as the swine Tn10 transposase gene. This novel porcine gene was finally assigned to Gene ID: 100049649. The RT-PCR analysis of the tissue expression profile was carried out using the tissue cDNAs of one Meishan pig as the templates, and the result indicated that this novel swine gene is moderately expressed in fat, and weakly expressed in small intestine, liver, kidney, and spleen but almost not expressed in heart, ovary, muscle, and lung. Our experiment established the primary foundation for further research into the biological significance of swine Tn10 transposase gene.

Swine gene banking: A quality control perspective on collection, and analysis of samples for a national repository

The National Animal Germplasm Program (NAGP) is developing a national repository for germplasm (semen, oocytes, embryos, blood, DNA, tissue) for all agricultural species in the US. Currently, the swine collection consists of 127,479 samples from 886 boars representing 20 major, minor and composite populations. Cryopreservation per se is not an impediment to program success. Rather, the greatest difficulties encountered are in determining the quality of the samples pre- and post-thaw. Robust, broadly applicable, and cost effective quality control methodologies need to be developed and implemented. This overview of the NAGP will discuss the approaches used for cryopreserving boar semen samples, overcoming the challenges of assessing sample quality, and moving toward a quality control strategy.

In silico identification, molecular cloning and verification of a novel pig gene homologous to human<I>BCL10</I>of innate immunity and its preliminary expression profiles in pigs

We identified and characterized a novel swine gene Bcl10 with GenBank (Accession No. EU088132) which was homologous to human BCL10 (B-cell CLL/lymphoma 10) gene. The full-length cDNA of 925 bp for swine BCL10 was in silico cloned, and then its ORF of 702 bp coding 233 amino acid residues was verified by RT-PCR and DNA sequencing. NCBI BLAST assay indicated that this cDNA contained three extrons with a length of 57, 289 and 356 bp respectively, and it was located on the chromosome 4 of pig genome. Using semi-quantitative PCR, preliminary expression profiles of swine BCL10 were verified in different swine tissues. The expression of swine BCL10 was verified by GFP marker and RT-PCR assay. We found that, BCL10 expressed in high level in swine spleen, and with a modest level in thymus, brain and lymph node; low level mRNA was expressed in liver and not detectable level in kidney. The swine BCL10 gene was cloned to the GFP-containing eukaryotic expression vector pEGFP-C1 and transfected to PK-15 cell line by lipofectin. BCL10 was ex-pressed effectively in PK-15 cells. In summary, we cloned a novel swine BCL10 gene, and investigated its expression char-acters. This will be the fundament of the future research on its function.

CDNA Cloning and Tissue Expression Analyses of the Encoding Regions for Three Novel Porcine Genes- MJD1, CDC42 and NECD

The cDNAs for Machado-Joseph disease protein 1 homolog (MJD1), cell division control protein 42 homolog precursor(CDC42) and necdin (NECD) genes of pig were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) based on the conserved coding sequence information of the MJD1, CDC42, and NECD genes from mouse and other mammals and the referenced porcine EST sequence information. Tissue expression analysis showed the swine MJD1, CDC42, and NECD genes were obviously differentially expressed in different tissues including muscle, heart, liver, backfat, kidney, lung, small intestine, and large intestine. Our experiment established the primary foundation for further research on these three swine genes.

Molecular cloning, sequence identification, and tissue expression profile analysis of three novel porcine genes: SDHB, SNRPA and CRYBB1

The complete coding sequences of three porcine genes-SDHB, SNRPA and CRYBB1 were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) based on the conserved coding sequence information of the mouse or other mammals and highly homologous pig ESTs. These three genes were then deposited into GenBank database and assigned to GeneID: 100125544, 768109 and 780429. The phylogenetic tree analysis revealed that the swine SDHB and SNRPA have closer genetic relationships with the human SDHB and SNRPA, but swine CRYBB1 has a closer genetic relationship with the bovine CRYBB1.The tissue expression analysis indicated that that swine SDHB, SNRPA and CRYBB1 gene were differentially expressed in tissues including fat, lung, muscle, small intestine, kidney, large intestine, spleen and liver. Our experiment is the first to establish the primary foundation for further research on these three swine genes.

Isolation, Sequence Identification and Tissue Expression Distribution of Three Novel Porcine Genes-UBC1, TRA2A and SH21A

Liu G.Y., Zhao, S.M., Song, X.L., Wang, J. and Gao, S.Z. 2008. Isolation, sequence identification and tissue expression distribution of three novel porcine genes-UBC1, TRA2A and SH21A. J. Appl. Anim. Res., 33:33–38. Ubiquitin-conjugating enzyme E2–25 kDa (UBC1), transformer-2 protein homolog TRA-2 alpha (TRA2A) and SH2 domain protein 1A (SH21A) genes are most important genes highly related or potentially related with the porcine production. The complete coding sequences of these three porcine genes were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) based on the conserved sequence information of the mouse or other mammals and referred highly homologous pig ESTs. Porcine UBC1 gene encodes a protein of 200 amino acids which contains the conserved putative UBCc domain and has high homology with the UBC1 proteins of three species-human, mouse and bovine (100%). The porcine TRA2A gene encodes a protein of 279 amino acids that contains the conserved putative RNA recognition motif (RRM) domain and has high homology with the TRA2A proteins of two species-human (99%) and mouse (97%). The porcine SH21A gene encodes a protein of 128 amino acids that contains the conserved putative src homology 2 (SH2) domain and has high homology with the SH21A proteins of two species human (92%) and mouse (86%). The tissue expression analysis indicated that the swine UBC1, TRA2A and SH21A genes were expressed in different tissues including lung, fat, small intestine, large intestine, liver, muscle, spleen and kidney. Our experiment is the first to establish the primary foundation for further research on these three swine genes.

Molecular cloning and mutation site analysis of <I>AMPD1M</I> gene in swine

Adenosine monophosphate deaminase gene (AMPD1) plays an important role in the purine nucleotide cycle.The AMPD1 gene is expressed predominantly in skeletal muscles. It related with Inosine monophosphate metabolism in muscles and carcass traits. Herein the AMPD1 gene was cloned and a CDS sequence of 2 195 bp was obtained and analyzed with PCR-SSCP. chi(2) analysis showed that the distribution of genotypes among Min pig, Yorkshire and Duroc are extremely sig-nificant different (Plt;0.01).

Cloning, sequence characterization, and tissue expression profile analysis of three novel porcine genes—RHOB, RHOG, and PRAF1

The complete coding sequences of three porcine genes—Rho-related GTP-binding proteins RHOB and RHOG and Prenylated Rab acceptor protein 1 (PRAF1) were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) based on the sequence information of the mouse or other mammals and referenced highly homologous pig ESTs. The nucleotide sequences of these three genes revealed that porcine RHOB gene encodes a protein of 196 amino acids that contains the conserved putative RhoA-like domain and has high homology with the RHOB precursor of three species—human, rat, and mouse (100%).The porcine RHOG gene encodes a protein of 191 amino acids that contains the conserved putative RhoG domain and has high homology with the RhoG precursor (RHOG) of three species—human, mouse, and Cricetus cricetus (98%). The porcine PRAF1 gene encodes a protein of 185 amino acids that contains the conserved putative PRA1 domain and has high homology with the PRAF1 of five species—dog (97%), cattle (97%), human (96%), rat (95%), and mouse (95%). The tissue expression analysis indicated swine RHOB gene was moderately expressed in lung; weakly in fat, spleen, and kidney; and almost not expressed in small intestine, large intestine, liver, and muscle. The swine RHOG gene was overexpressed in small intestine, large intestine, liver, and muscle; moderately expressed in kidney; weakly in spleen; and almost not expressed in fat and lung. The swine PRAF1 gene was overexpressed in fat and spleen, moderately in lung and kidney, weakly in small intestine and large intestine, and almost not expressed in liver and muscle. Our experiment established the primary foundation for further research on these three swine genes.

CDNA cloning, sequence identification and tissue expression distribution of three novel porcine genes: UCHL3, RIT1 and CCND3

The complete CDS sequences of three porcine genes: UCHL3, RIT1 and CCND3 were amplified using RT-PCR based on the sequence information of the mouse or other mammals and referenced highly homologous pig ESTs. Sequence analysis of these three genes revealed that the porcine UCHL3 gene encodes a protein of 230 amino acids and has high homology with the ubiquitin carboxyl-terminal hydrolase isozyme L3 (UCHL3) of four species-bovine (97%), human (96%), mouse (95%) and rat (94%). The porcine RIT1 gene encodes a protein of 219 amino acids and has high homology with the GTP-binding protein Rit1 (RIT1) of two species-human (97%), mouse (97%). The porcine CCND3 gene encodes a protein of 292 amino acids and has high homology with the G1/S-specific cyclin-D3 (CCND3) of four species-bovine (98%), human (97%), mouse (93%) and rat (92%). The phylogenetic tree analysis revealed that the swine UCHL3 has a closer genetic relationship with the UCHL3 of bovine, and the swine RIT1 has closer genetic relationships with the RIT1 of human, but the swine CCND3 has a closer genetic relationship with the CCND3 of bovine. The RT-PCR gene expression analysis indicated that the swine UCHL3, RIT1 and CCND3 genes were differentially expressed in tissues including small intestine, large intestine, liver, muscle, fat, lung, spleen and kidney. Our experiment established the primary foundation for further research on these three swine genes.

Molecular characterization and expression profile of a novel porcine gene differentially expressed in the muscle tissues from Meishan, Large White and their hybrids

In order to detect the molecular mechanism of heterosis in pigs, the mRNA differential display technique was performed to investigate the differences in gene expression in the longissimus dorsi muscle tissues from Meishan, Meishan x Large White cross and Large White pigs. One novel gene that was differentially expressed was identified using semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR) and its full-length cDNA sequence was obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the gene is not homologous to any of the known porcine genes. Sequence analysis revealed that open reading frame of this gene encoding a protein of 105 amid acids and this protein showed 100% homology to bovine and ovine CYCS, and therefore, this gene can be defined as the swine CYCS gene. The genomic sequence of swine CYCS gene was finally amplified and result revealed that the swine CYCS gene contains no introns. Tissue expression profile analysis revealed that swine CYCS gene was highly expressed in muscle, fat and lung, moderately expressed in ovary, kidney, and liver, and weekly expressed in heart, spleen and small intestine. Our results established the primary foundation for further research into the biological significance of swine CYCS gene.

Molecular characterization of the encoding regions and tissue expression analyses for three novel porcine genes––HNRPA1, YIPF5 and UB2D2

The complete encoding regions of three porcine genes--heterogeneous nuclear ribonucleoprotein A1 (HNRPA1), YIP1 family member 5 (YIPF5) and ubiquitin-conjugating enzyme E2 D2 (UB2D2) were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) based on the conserved encoding region information of the mouse or other mammals and the referenced highly homologous pig ESTs of these conserved encoding regions. These three novel porcine genes were assigned to GeneID: 768103, 768112, and 780418. The phylogenetic tree analysis revealed that the swine HNRPA1 has closer genetic relationships with the HNRPA1 of mouse and rhesus monkey, but the swine YIPF5 has a closer genetic relationship with the YIPF5 of cattle and the swine UB2D2 shows an evolutional model different with the UB2D2 of other five species. The tissue expression analysis indicated that the swine HNRPA1 gene was moderately expressed in fat, spleen and kidney, weakly expressed in muscle and lung, and hardly expressed in small intestine, large intestine and liver. The swine YIPF5 gene was moderately expressed in fat and spleen, and hardly expressed in small intestine, large intestine, liver, lung, muscle and kidney. The swine UB2D2 gene was weakly expressed in lung, and hardly expressed in small intestine, large intestine, liver, muscle, fat, spleen and kidney. Our experiment established the primary foundation for further research on these three swine genes.

Isolation, sequence identification and tissue expression distribution of three novel porcine genes—RAB14, S35A3 and ITM2A

The complete coding sequences of three porcine genes--RAB14, S35A3 and ITM2A were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) based on the conserved sequence information of the mouse or other mammals. The nucleotide sequence analysis of these three genes revealed that porcine RAB14 gene encodes a protein of 215 amino acids that contains the conserved putative Ras-related protein Rab-14 domain and has high homology with the Ras-related protein Rab-14 (RAB14) of four species--human and mouse (99%) and rat (100%), dictyostelium discoideum (71%). The porcine S35A3 gene encodes a protein of 325 amino acids that contains the conserved putative nucleotide-sugar transporter domain and has high homology with the UDP-N-acetylglucosamine transporter (S35A3) of five species--cattle (98%), dog (97%), human (96%), mouse (95%) and rat (94%). The porcine ITM2A gene encodes a protein of 254 amino acids that contains the conserved putative BRICHOS domain and has high homology with the integral membrane protein 2A (ITM2A) of two species--human (89%), and mouse (88%). The tissue expression analysis indicated that the swine RAB14 gene was over-expressed in fat, lung, spleen, and kidney, moderately in large intestine, weakly in small intestine, and hardly expressed in muscle and liver. The swine S35A3 gene was moderately expressed in large intestine, fat, and spleen, weakly in liver and lung, and almost not expressed in muscle, small intestine, and liver. The swine ITM2A gene was over-expressed in fat and spleen, moderately in lung, weakly in muscle, and hardly expressed in liver, small intestine, large intestine, and kidney. Our experiment established the primary foundation for further research on these three swine genes.

Isolation, sequence identification and tissue expression profile of three novel porcine genes – ARL1, ARL3 and ARL4A

The complete coding sequences of three porcine genes – ADP-ribosylation factor-like protein 1 (ARL1), ADP-ribosylation factor-like protein 3 (ARL3) and ADP-ribosylation factor-like protein 4A (ARL4A) were amplified using reverse transcriptase polymerase chain reaction (RT-PCR) based on the conserve sequence information of human or other mammals. These three novel genes were assigned to GeneID: 595113, 595114, and 595121. Gene expression profile analysis was carried out in several tissues and results revealed that swine ARL1 gene was highly expressed in fat, lung, spleen, moderately expressed in large intestine, weakly expressed in liver, muscle, and very weakly expressed in small intestine and kidney. The swine ARL3 gene was weakly expressed in lung, spleen, and kidney, hardly expressed in small intestine, large intestine, liver, muscle and fat. The swine ARL4A gene was moderately expressed in fat and lung, weakly in large intestine, liver, and spleen, and not expressed in small intestine, muscle, and kidney. Our experiment is the first to establish the primary foundation for further research on these three porcine genes.

Isolation, sequence analysis and expression profile of a novel porcine gene, NIP7, differentially expressed in the Longissimus dorsi muscle tissues from Meishan, Meishan × Large White cross and Large White pigs

In order to detect the molecular mechanism of heterosis in pigs, the mRNA differential display technique was performed to investigate the differences in gene expression in the Longissimus dorsi muscle tissues from Meishan, Meishan x Large White cross and Large White pigs. One novel gene that was differentially expressed was identified using semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR) and its complete cDNA sequence was obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the gene is not homologous to any of the known porcine genes. The sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 180 amino acids that contains the conserved putative RNA-binding domain in PseudoUridine synthase and Archaeosine transglycosylase (PUA) and has high homology with the 60S ribosome subunit biogenesis protein NIP7 homolog of three species--human (98%), mouse (97%) and rat (96%)--so that it can be defined as swine 60S ribosome subunit biogenesis protein NIP7 homolog (NIP7). The tissue expression analysis indicated that the swine NIP7 gene is over expressed in muscle, heart, liver, fat, kidney, and lung, but weakly expressed in small intestine, ovary, and spleen. The genomic DNA sequence of swine NIP7 gene was finally amplified and result revealed that the swine NIP7 gene contains five exons and four introns. Our experiment is the first to establish the primary foundation for further research on the swine NIP7 gene.

Oviduct-specific Glycoprotein 1 Locus is Associated with Litter Size and Weight of Ovaries in Pigs

Oviduct-specific glycoprotein 1 (OVGP1) is implicated in playing a role in fertilization and early embryo development. In this study, we have obtained the sequence of intron 9 of OVGP1 gene in swine. Comparative sequencing of Meishan (a native Chinese breed) and Large White pig breeds revealed an A/T substitution at position 943. A PCR-EcoRI-RFLP assay was developed to detect this mutation. Polymorphism analysis in Qingping animals showed that pigs with BB genotype had lower number of piglets born alive (NBA) in multiple parities than pigs with AA (p<0.05) and AB genotype (p<0.01). In Large White×Meishan (LW×M) F2 offspring, the weight of both ovaries (OW) of the BB genotype was significantly lighter than that of AB (p = 0.05) and AA (p<0.01) genotypes. Analysis of the data also revealed that the mutation locus affected these two traits mostly by additive effects. These studies indicated that the polymorphism was associated with NBA and OW in two distinct populations and further investigations in more purebreds or crossbreds are needed to confirm these results. (Asian-Aust. J. Anim. Sci. 2006. Vol 19, No. 5 : 632-637)

Isolation, Sequence Analysis and Expression Profile of a Novel Swine Gene Differentially Expressed in the Longissimus Dorsi Muscle Tissues from Landrace&amp;times;Large White Cross-combination

The mRNA differential display technique was performed to investigate the differences in gene expression in the Longissimus dorsi muscle tissues from LandracexLarge White cross-combination. One novel gene that was differentially expressed was identified using semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) and its complete cDNA sequence was obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the gene is not homologous to any of the known porcine genes. The sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 260 amino acids that contains the putative conserved domain of the carbonic anhydrase, and this protein has high homology with the carbonic anhydrase III (CA-III) of four species mouse (91%), horse (91%), rat (89%) and human (86%)-so that it can be defined as swine carbonic anhydrase III. The phylogenetic tree analysis revealed that the swine CA-III has a closer genetic relationship with the horse CA-III than with those of mouse, rat and human. The tissue expression analysis indicated that the swine CA-III gene is generally expressed in most tissues. Our experiment is the first to establish the primary foundation for further research on the swine CA-III gene.

Isolation, Sequence Analysis and Expression Profile of a Novel Swine Gene Differentially Expressed in the Longissimus Dorsi Muscle Tissues from LandracexLarge White Cross-combination

The mRNA differential display technique was performed to investigate the differences in gene expression in the Longissimus dorsi muscle tissues from LandracexLarge White cross-combination. One novel gene that was differentially expressed was identified using semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) and its complete cDNA sequence was obtained using the rapid amplification of cDNA ends (RACE) method. The nucleotide sequence of the gene is not homologous to any of the known porcine genes. The sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 260 amino acids that contains the putative conserved domain of the carbonic anhydrase,and this protein has high homology with the carbonic anhydrase Ⅲ (CA-Ⅲ) of four species-mouse (91%),horse (91%), rat (89%) and human (86%)-so that it can be defined as swine carbonic anhydrase Ⅲ. The phylogenetic tree analysis revealed that the swine CA-Ⅲ has a closer genetic relationship with the horse CA-Ⅲ than with those of mouse, rat and human. The tissue expression analysis indicated that the swine CA-Ⅲ gene is generally expressed in most tissues. Our experiment is the first to establish the primary foundation for further research on the swine CA-Ⅲ gene.

Mapping and association studies of diabetes related genes in the pig

The mitogen-activated protein kinase 8 (MAPK8), resistin (RETN), 11 beta hydroxysteroid dehydrogenase isoform 1 (HSD11B1) and protein kinase B Akt2 (AKT2) genes are all genes known to affect insulin signalling and have been implicated in the progression of obesity and type 2 diabetes in humans. In this study, polymorphisms in the porcine diabetes related MAPK8, RETN, HSD11B1 and AKT2 genes were identified, mapped and their associations with phenotypic measurements in swine were analysed. Polymorphisms detected in the MAPK8, RETN and HSD11B1 loci were used to genotype a Berkshire-Yorkshire pig breed reference family. Using linkage analysis, RETN, HSD11B1 and MAPK8 genes were mapped to pig chromosomes 2, 9 and 14, respectively, while the AKT2 gene was physically mapped to pig chromosome 6q21. Results presented here suggest associations between the polymorphisms in the MAPK8, RETN and HSD11B1 genes with several phenotypic measurements, including fat deposition traits in the pig. Because these genes have been implicated in obesity and diabetes in humans, and this study suggests associations with fat related traits, further research on these genes in swine may provide useful information on genetic factors underlying lean pork production.