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Li G, Xiong H, Xi D, Memon S, Wang L, Liu X, Deng W. An examination of melanogenic traits and <i>TYRP1</i> polymorphism in Nanping and Romney Marsh sheep breeds. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-131-2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. The effects of mutations of the gene for tyrosinase-related
protein 1 (TYRP1) on the black muscles and coat color in Nanping
black-boned sheep were investigated. Tyrosinase activity and melanin content
in plasma were measured and compared in three random groups of sheep: Nanping
black-boned (101 heads), Nanping normal (106 heads) and Romney Marsh sheep
(82 heads, Ovis aries). Eight exons and their partial flanking
regions of the TYRP1 gene were amplified. Six intronic mutations and
six exonic polymorphisms including two non-synonymous mutations [c.203C > T
(p.A68V) and c.1202T > C (p.V401A)] were identified. Using a
bi-directional polymerase chain reaction allele-specific amplification
(bi-PASA) of the mutation c.203C > T it was shown that the frequencies of
allele C in the Nanping black-boned, Nanping normal and Romney Marsh sheep
were respectively 0.955, 0.967 and 0.744. For the mutation c.1202T > C,
the frequencies of allele T in the three populations of sheep were
respectively 0.777, 0.745 and 0.793 as measured using the single-strand
conformation polymorphism. When the data from sheep of all three populations
with the CC genotype of SNP c.203C > T were pooled, it was found that there
was significantly higher (P < 0.05) tyrosinase activity, content of
alkali-soluble melanin and ratio of eumelanin : total melanin than
in the plasma of sheep with the CT and TT genotypes. This was not so within each
of the three groups of sheep. No significant effect of the TRYP1
genotype on coat color was found. Further studies will be necessary to
determine the cause of the black traits in Nanping black-boned sheep.
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Jakubczak A, Gryzinska M, Horecka B, Kowalczyk M, Kasperek K, Gajewska K, Jezewska-Witkowska G. Single-nucleotide polymorphism of MC1R, ASIP, and TYRP2 genes in wild and farmed foxes (Vulpes vulpes). CANADIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.1139/cjas-2015-0066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA mutations within genes associated with melanogenesis can affect melanin production, leading to dyschromias. Genes that are involved in synthesis of melatonin and may affect the color of skin are melanocortin 1 receptor (MC1R), agouti locus (ASIP), and tyrosinase-related protein-2 (TYRP2). In this study, SNP identification within ASIP, MC1R, and TYRP2 gene fragments in wild and farmed foxes (Vulpes vulpes) was performed. Nine mutations in the ASIP gene which allowed us to distinguish seven SNP profiles, fourteen mutations and five SNP profiles in the MC1R gene, and seven SNP profiles based on four polymorphic nucleotides in the TYRP2 gene were detected. Analyses of obtained profiles indicate that ASIP did not undergo mutations in the wild, and significant variability of SNP profiles was found for TYRP2, with specific haplotypes noted for farm foxes and American and European wild foxes.
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Affiliation(s)
- Andrzej Jakubczak
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Magdalena Gryzinska
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Beata Horecka
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Marek Kowalczyk
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Kornel Kasperek
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Katarzyna Gajewska
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Grazyna Jezewska-Witkowska
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
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Rohrer G, Nonneman D, Miller R, Zerby H, Moeller S. Association of single nucleotide polymorphism (SNP) markers in candidate genes and QTL regions with pork quality traits in commercial pigs. Meat Sci 2012; 92:511-8. [DOI: 10.1016/j.meatsci.2012.05.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 04/10/2012] [Accepted: 05/18/2012] [Indexed: 11/28/2022]
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Jozaki K, Shinkai H, Morozumi T, Tanaka-Matsuda M, Eguchi-Ogawa T, Wada Y, Uenishi H. Cloning, expression, and polymorphisms of natural killer cell receptor NCR1 in pigs. Anim Biotechnol 2010; 21:156-63. [PMID: 20665287 DOI: 10.1080/10495391003617663] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
NCR1 (NKp46) is expressed on the surfaces of natural killer cells and recognizes hemagglutinin on the influenza virus. We cloned the NCR1 gene in pigs and found that porcine NCR1 was minimally expressed in the thymus, suggesting that NCR1 could be a useful marker of natural killer cells in pigs. We observed three nonsynonymous single nucleotide polymorphisms and one deletion of three nucleotides in the coding sequence of porcine NCR1; these may affect the function of NCR1. The polymorphisms detected here may be useful markers for breeding for influenza resistance in pigs.
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Deng W, Tan Y, Wang X, Xi D, He Y, Yang S, Mao H, Gao S. Molecular cloning, sequence characteristics, and polymorphism analyses of the tyrosinase-related protein 2 / DOPAchrome tautomerase gene of black-boned sheep (Ovis aries). Genome 2010; 52:1001-11. [PMID: 19953128 DOI: 10.1139/g09-078] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Tyrosinase-related protein 2 (TYRP2) plays a pivotal role in the biosynthesis of eumelanin. Black-boned sheep have excessive melanin and eumelanin, resulting in dark (black) muscles and organs. This study was designed to investigate the effects of variants of the TYRP2 gene on black traits and coat colour of black-boned sheep. Melanin traits were measured in three populations of sheep (Nanping black-boned, Nanping normal, and Romney Marsh) and compared in this study. From the TYRP2 cDNA, all 8 exons and their flanking regions were amplified and characterized. Fifteen single nucleotide polymorphisms (SNPs) were identified in the exons and their flanking regions. Five exonic polymorphic sites, including two synonymous (c.93T>G and c.1140C>T) and three non-synonymous mutations (c.163C>T (p.R55W), c.605G>A (p.R202H), and c.1141A>G (p.T381A)), were retrieved. PCR-RFLP analysis of c.605G>A showed that the frequencies of allele G in the Nanping black-boned, Nanping normal, and Romney Marsh sheep were 0.632, 0.603, and 0.886, respectively. Sheep with the GG genotype had significantly (P < 0.05) lower tyrosinase activity, alkali-soluble melanin content, and ratio of eumelanin : total melanin than sheep with GA and AA genotypes when measured across all investigated samples but not when samples within each population of sheep were compared. However, there was no association of TYRP2 genotype at a single SNP position with coat colour across populations. Nonetheless, the two breeds with higher overall tyrosinase activity did produce darker and more varied coat colours than the breed with lower tyrosinase activity.
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Affiliation(s)
- Weidong Deng
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
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Polymorphism distribution and structural conservation in RNA-sensing Toll-like receptors 3, 7, and 8 in pigs. Biochim Biophys Acta Gen Subj 2009; 1790:267-74. [PMID: 19714804 DOI: 10.1016/j.bbagen.2009.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Viral genomic RNA-both single-stranded (ss) and double-stranded (ds)-is recognized by RNA-sensing Toll-like receptors (TLRs), notably TLR3 (dsRNA), TLR7 (ssRNA), and TLR8 (ssRNA). However, our knowledge of the roles of porcine TLR3, 7, and 8 in antiviral immunity is inadequate. METHODS From information on exon-intron boundaries obtained through comparisons of the genomic and cDNA sequences, polymorphisms in the coding sequences of each gene were detected in 84 male pigs of 11 breeds. RESULTS Genomic structures are conserved between pigs and humans. The RNA-sensing TLR genes had fewer polymorphisms causing amino acid alterations than did the cell-surface TLR genes, but the alterations were distributed with a similar bias toward ectodomains. CONCLUSIONS The low level of diversity of substitutive polymorphisms in RNA-sensing TLRs than cell-surface ones implies that polymorphisms severely affecting function have been eliminated by selection pressure during longstanding pig breeding. GENERAL SIGNIFICANCE Recognition of virus-derived RNA is critical in host defense against infection. These results should provide a useful clue to analysis of the association between polymorphisms in RNA-sensing TLRs and disease resistance.
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Kojima-Shibata C, Shinkai H, Morozumi T, Jozaki K, Toki D, Matsumoto T, Kadowaki H, Suzuki E, Uenishi H. Differences in distribution of single nucleotide polymorphisms among intracellular pattern recognition receptors in pigs. Immunogenetics 2008; 61:153-60. [PMID: 19099299 DOI: 10.1007/s00251-008-0350-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Accepted: 12/04/2008] [Indexed: 12/20/2022]
Abstract
Pathogens localized extracellularly or incorporated into endosomes are recognized mainly by Toll-like receptors, whereas pathogens and pathogen-derived molecules that invade into the cytoplasm of host cells typically are recognized by intracellular pattern recognition receptors (PRRs), such as retinoic acid-inducible gene (RIG)-like helicases (RLHs) and nucleotide-binding oligmerization domain (NOD)-like receptors (NLRs). RIG-I and melanoma differentiation-associated gene 5 (MDA5), which belong to the RLH family, recognize viral genomic RNA, whereas NOD2, a member of the NLR family, responds to microbial peptidoglycans. These receptors may play an important role in pig opportunistic infectious diseases, such as pneumonia and diarrhea, which markedly impair livestock productivity, such that polymorphisms of these receptor genes are potential targets of pig breeding to increase disease resistance. Here, we report single nucleotide polymorphisms (SNPs) in porcine DDX58, IFIH1, and NOD2, which encode RIG-I, MDA5, and NOD2, respectively. Interestingly, compared with DDX58 and IFIH1, NOD2 abounded in nonsynonymous SNPs both throughout the coding sequence and in sequences encoding domains important for ligand recognition, such as helicase domains for RIG-I and MDA5 and leucine-rich repeats in NOD2. These differences in the distribution of SNPs in intracellular PRRs may parallel the diversity of their ligands, which include nucleic acids and peptidoglycans.
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Affiliation(s)
- Chihiro Kojima-Shibata
- Miyagi Livestock Experimental Station, Miyagi Prefecture, 1 Hiwatashi, Minamisawa, Iwadeyama, Osaki, Miyagi, Japan
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Kaminski S, Help H, Brym P, Rusc A, Wójcik E. SNiPORK - a microarray of SNPs in candidate genes potentially associated with pork yield and quality - development and validation in commercial breeds. Anim Biotechnol 2008; 19:43-69. [PMID: 18228175 DOI: 10.1080/10495390701880946] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
SNiPORK is an oligonucleotide microarray based on the arrayed primer extension (APEX) technique, allowing genotyping of single nucleotide polymorphisms (SNPs) in genes of interest for pork yield and quality traits. APEX consists of a sequencing reaction primed by an oligonucleotide anchored with its 5' end to a glass slide and terminating one nucleotide before the polymorphic site. Extension with one fluorescently labeled dideoxynucleotide complementary to the template reveals the polymorphism. Ninety SNPs were selected from those associated directly or potentially with pork traits. Of the 90 SNPs, 5 did not produce a positive signal. For 85 SNPs, 100% repeatiblity was proved by double genotyping of 13 randomly chosen boars. In addition, the accuracy of genotyping was verified in 2 sib-families by a Mendelian inheritance of 49-50 homozygous genotypes from sire to sons. Three genotype discrepancies were found (97% accuracy rate). All inaccurities were confirmed by an alternative method (sequencing and PCR-RFLP assays). Moreover, the exclusion power of the chip was evalueted by an SNP inheritance analysis of unrelated boars within each sib-family. In the validation step, 88 boars (13 Pietrain, 31 Landrace, 16 Large White, 8 Duroc, 7 Hampshire x Pietrain crosses, and 13 other hybrid lines) were screened to validate SNPs. Among the 85 selected SNPs, 12 were found to be monoallelic, the rest showing at least two genotypes for the entire population under study. The primary application of the SNiPORK chip is the simultaneous genotyping of dozens of SNPs to study gene interaction and consequently better understand the genetic background of pork yield and quality. The chip may prospectively be used for evolutionary studies, evaluation of genetic distances between wild and domestic pig breeds, traceability tests, as well as the starting point for developing a platform for identification and paternity analysis.
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Affiliation(s)
- Stanisław Kaminski
- Department of Animal Genetics, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.
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OKUMURA N, HAMASIMA N, SUZUKI K, AWATA T. Genomic organization of the porcine dopachrome tautomerase (DCT) gene. Anim Sci J 2008. [DOI: 10.1111/j.1740-0929.2008.00515.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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