Identification of a Novel Single Nucleotide Polymorphism in Porcine Beta-Defensin-1 Gene
Porcine beta-defensin-1 (PBD-1) gene plays an important role in the innate immunity of pigs. The peptide encoded by this gene is an antimicrobial peptide that has direct activity against a wide range of microbes. This peptide is involved in the co-creation of an antimicrobial barrier in the oral cav...
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| Format: | Article |
| Language: | English |
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Asian-Australasian Association of Animal Production Societies
2016-03-01
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| Series: | Asian-Australasian Journal of Animal Sciences |
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| Online Access: | http://www.ajas.info/upload/pdf/ajas-29-3-315.pdf |
| _version_ | 1818336557993558016 |
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| author | D. R. Pruthviraj A. P. Usha R. T. Venkatachalapathy |
| author_facet | D. R. Pruthviraj A. P. Usha R. T. Venkatachalapathy |
| author_sort | D. R. Pruthviraj |
| collection | DOAJ |
| description | Porcine beta-defensin-1 (PBD-1) gene plays an important role in the innate immunity of pigs. The peptide encoded by this gene is an antimicrobial peptide that has direct activity against a wide range of microbes. This peptide is involved in the co-creation of an antimicrobial barrier in the oral cavity of pigs. The objective of the present study was to detect polymorphisms, if any, in exon-1 and exon-2 regions of PBD-1 gene in Large White Yorkshire (LWY) and native Ankamali pigs of Kerala, India. Blood samples were collected from 100 pigs and genomic DNA was isolated using phenol chloroform method. The quantity of DNA was assessed in a spectrophotometer and quality by gel electrophoresis. Exon-1 and exon-2 regions of PBD-1 gene were amplified by polymerase chain reaction (PCR) and the products were subjected to single strand conformation polymorphism (SSCP) analysis. Subsequent silver staining of the polyacrylamide gels revealed three unique SSCP banding patterns in each of the two exons. The presence of single nucleotide polymorphisms (SNPs) was confirmed by nucleotide sequencing of the PCR products. A novel SNP was found in the 5′-UTR region of exon-1 and a SNP was detected in the mature peptide coding region of exon-2. In exon-1, the pooled population frequencies of GG, GT, and TT genotypes were 0.67, 0.30, and 0.03, respectively. GG genotype was predominant in both the breeds whereas TT genotype was not detected in LWY breed. Similarly, in exon-2, the pooled population frequencies of AA, AG, and GG genotypes were 0.50, 0.27, and 0.23, respectively. AA genotype was predominant in LWY pigs whereas GG genotype was predominant in native pigs. These results suggest that there exists a considerable genetic variation at PBD-1 locus and further association studies may help in development of a PCR based genotyping test to select pigs with better immunity. |
| first_indexed | 2024-12-13T14:41:13Z |
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| institution | Directory Open Access Journal |
| issn | 1011-2367 1976-5517 |
| language | English |
| last_indexed | 2024-12-13T14:41:13Z |
| publishDate | 2016-03-01 |
| publisher | Asian-Australasian Association of Animal Production Societies |
| record_format | Article |
| series | Asian-Australasian Journal of Animal Sciences |
| spelling | doaj.art-75cdea06d8df4d2e9bb8f8f1d0ed1fed2022-12-21T23:41:36ZengAsian-Australasian Association of Animal Production SocietiesAsian-Australasian Journal of Animal Sciences1011-23671976-55172016-03-0129331532010.5713/ajas.15.063823431Identification of a Novel Single Nucleotide Polymorphism in Porcine Beta-Defensin-1 GeneD. R. Pruthviraj0A. P. Usha1R. T. Venkatachalapathy2 Centre for Pig Production and Research, Kerala Veterinary and Animal Sciences University, Mannuthy, Thrissur 680651, .India Centre for Pig Production and Research, Kerala Veterinary and Animal Sciences University, Mannuthy, Thrissur 680651, .India Centre for Advanced Studies in Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Kerala Veterinary and Animal Sciences University, Mannuthy, Thrissur 680651, .IndiaPorcine beta-defensin-1 (PBD-1) gene plays an important role in the innate immunity of pigs. The peptide encoded by this gene is an antimicrobial peptide that has direct activity against a wide range of microbes. This peptide is involved in the co-creation of an antimicrobial barrier in the oral cavity of pigs. The objective of the present study was to detect polymorphisms, if any, in exon-1 and exon-2 regions of PBD-1 gene in Large White Yorkshire (LWY) and native Ankamali pigs of Kerala, India. Blood samples were collected from 100 pigs and genomic DNA was isolated using phenol chloroform method. The quantity of DNA was assessed in a spectrophotometer and quality by gel electrophoresis. Exon-1 and exon-2 regions of PBD-1 gene were amplified by polymerase chain reaction (PCR) and the products were subjected to single strand conformation polymorphism (SSCP) analysis. Subsequent silver staining of the polyacrylamide gels revealed three unique SSCP banding patterns in each of the two exons. The presence of single nucleotide polymorphisms (SNPs) was confirmed by nucleotide sequencing of the PCR products. A novel SNP was found in the 5′-UTR region of exon-1 and a SNP was detected in the mature peptide coding region of exon-2. In exon-1, the pooled population frequencies of GG, GT, and TT genotypes were 0.67, 0.30, and 0.03, respectively. GG genotype was predominant in both the breeds whereas TT genotype was not detected in LWY breed. Similarly, in exon-2, the pooled population frequencies of AA, AG, and GG genotypes were 0.50, 0.27, and 0.23, respectively. AA genotype was predominant in LWY pigs whereas GG genotype was predominant in native pigs. These results suggest that there exists a considerable genetic variation at PBD-1 locus and further association studies may help in development of a PCR based genotyping test to select pigs with better immunity.http://www.ajas.info/upload/pdf/ajas-29-3-315.pdfSelectionDisease ResistanceAntimicrobial PeptideAnkamaliLarge White YorkshirePolymerase Chain Reaction-Single Strand Conformation Polymorphism [PCR-SSCP] |
| spellingShingle | D. R. Pruthviraj A. P. Usha R. T. Venkatachalapathy Identification of a Novel Single Nucleotide Polymorphism in Porcine Beta-Defensin-1 Gene Asian-Australasian Journal of Animal Sciences Selection Disease Resistance Antimicrobial Peptide Ankamali Large White Yorkshire Polymerase Chain Reaction-Single Strand Conformation Polymorphism [PCR-SSCP] |
| title | Identification of a Novel Single Nucleotide Polymorphism in Porcine Beta-Defensin-1 Gene |
| title_full | Identification of a Novel Single Nucleotide Polymorphism in Porcine Beta-Defensin-1 Gene |
| title_fullStr | Identification of a Novel Single Nucleotide Polymorphism in Porcine Beta-Defensin-1 Gene |
| title_full_unstemmed | Identification of a Novel Single Nucleotide Polymorphism in Porcine Beta-Defensin-1 Gene |
| title_short | Identification of a Novel Single Nucleotide Polymorphism in Porcine Beta-Defensin-1 Gene |
| title_sort | identification of a novel single nucleotide polymorphism in porcine beta defensin 1 gene |
| topic | Selection Disease Resistance Antimicrobial Peptide Ankamali Large White Yorkshire Polymerase Chain Reaction-Single Strand Conformation Polymorphism [PCR-SSCP] |
| url | http://www.ajas.info/upload/pdf/ajas-29-3-315.pdf |
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