RESUMO
The serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 (SERPINE1) gene encodes plasminogen activator inhibitor type 1 (PAI), which is the major physiological inhibitor of tissue-type and urokinase-type plasminogen activators and plays a role in obesity and insulin resistance in women but not in men. We detected SNP FN396538:g.566G>A in intron 3 and a non-synonymous substitution NM_213910:c.612A>G in exon 3 (p.Ile159Val) and mapped the gene to position 8.4 cM on the linkage map of chromosome 3. Association analyses were conducted on the 12th-15th generation of the Meishan × Large White (MLW) cross (n = 565), with records for weight at the end of test, lifetime daily gain, test time daily gain, loin depth and backfat depth, as well as on a European wild boar × Meishan (W × M) F(2) population (n = 333) with 47 traits recorded for carcass composition and meat quality. Analyses performed across the entire MLW population or in the male animals did not show any trait significantly associated with the loci studied. In female animals, both SNPs were associated with loin depth at nominal P < 0.05 with adjusted P values equal to 0.051 (g.566) and 0.057 (c.612). Differences between homozygotes were up to 0.65 SD. In the entire W × M population and female animals, SERPINE1 was significantly associated at adjusted P < 0.05 in descending order with muscling, growth and fat accretion and in male animals with meat quality (R-value). In the studied populations, allele effects were in opposite directions, which implies that the SNPs are markers that are in linkage disequilibrium with a causative mutation.
Assuntos
Mapeamento Cromossômico , Estudos de Associação Genética , Carne/normas , Polimorfismo de Nucleotídeo Único , Serpina E2/genética , Suínos/genética , Substituição de Aminoácidos , Animais , Cromossomos de Mamíferos/genética , Clonagem Molecular , Gorduras/metabolismo , Frequência do Gene , Masculino , Fenótipo , Reação em Cadeia da Polimerase , Análise de Sequência de DNA , Suínos/crescimento & desenvolvimentoRESUMO
NAMPT encodes an enzyme catalysing the rate-limiting step in NAD biosynthesis. The extracellular form of the enzyme is known as adipokine visfatin. We detected SNP AM999341:g.669T>C (referred to as 669T>C) in intron 9 and SNP FN392209:g.358A>G (referred to as 358A>G) in the promoter of the gene. RH mapping linked the gene to microsatellite SW944. Linkage analysis placed the gene on the current USDA USMARC linkage map at position 92 cM on SSC9. Association analyses were performed in a wild boar × Meishan F2 family (W × M), with 45 traits recorded (growth and fattening, fat deposition, muscling, meat quality, stress resistance and other traits), and in a commercial Landrace × Chinese-European (LCE) synthetic population with records for 15 traits (growth, fat deposition, muscling, intramuscular fat, meat colour and backfat fatty acid content). In the W × M, SNP 669T>C was associated with muscling, fat deposition, growth and fattening, meat quality and other traits and in the LCE with muscling, meat quality and backfat fatty acid composition. In the W × M, SNP 358A>G was associated with muscling, fat deposition, growth and other traits. After correction for multiple testing, the NAMPT haplotypes were associated in the W × M with, in descending order, muscling (q = 0.0056), growth (q = 0.0056), fat deposition (q = 0.0109), fat-to-meat ratio (q = 0.0135), cooling losses (q = 0.0568) and longissimus pHU (q = 0.0695). The SNPs are hypothesized to be in linkage disequilibrium with a causative mutation affecting energy metabolism as a whole rather than fat metabolism alone.
Assuntos
Estudos de Associação Genética/métodos , Desequilíbrio de Ligação/genética , Nicotinamida Fosforribosiltransferase/genética , Polimorfismo de Nucleotídeo Único/genética , Sus scrofa/genética , Animais , Distribuição da Gordura Corporal , Mapeamento Cromossômico , Metabolismo Energético , Feminino , Haplótipos/genética , Íntrons/genética , Masculino , Carne/normas , Repetições de Microssatélites , Desenvolvimento Muscular , Regiões Promotoras Genéticas , Sus scrofa/crescimento & desenvolvimentoAssuntos
Proteínas de Ligação ao Cálcio/genética , Mapeamento Cromossômico , Proteínas da Matriz Extracelular/genética , Proteínas de Ligação ao GTP/genética , Proteínas dos Microfilamentos/genética , Músculo Esquelético/embriologia , Osteonectina/genética , Proteoglicanas/genética , Suínos/genética , Animais , Moléculas de Adesão Celular/genética , Decorina , Feminino , Feto , Fibrilinas , Idade Gestacional , Músculo Esquelético/fisiologia , Gravidez , CalponinasRESUMO
Quantitative trait loci (QTL) for fat deposition, growth and muscling traits have been previously mapped on the basis of low-density linkage maps in a wild boar x Meishan F2family to the chromosome X region flanked by SW2456 and SW1943. Improved QTL resolution was possible using data for F2 animals with a marker density of 2.7 cM distance in the SW2456 to SW1943 region, including AR, SERPINA7 and ACSL4 as candidate genes. The resolution of the QTL scan was increased substantially, as evidenced by the higher F-ratio values for all QTL. Maxima of F-ratio values for fat deposition, muscling and growth traits were 28.6, 18.2 and 16.5 respectively, and those QTL positions accounted for 7.9%, 5.0% and 4.5% of the F2 phenotypic variance (VF2) respectively. QTL for fatness and growth and for most muscling traits mapped near ACSL4, with the exception of the QTL for ham traits that mapped proximally, in the vicinity of AR. An analysis performed separately for F2 male animals showed the predominant QTL affecting fat deposition traits (up to 13.6% VF2) near AR and two QTL for muscling traits (up to 9.9% VF2) mapped close to ACSL4. In the F2 female animals, QTL affecting muscling (up to 12.1% VF2) mapped at ACSL4 and SW2456, and QTL for fat deposition (10% VF2) and growth (up to 10.5% VF2) mapped at ACSL4.
Assuntos
Distribuição da Gordura Corporal , Locos de Características Quantitativas , Suínos/genética , Cromossomo X , Animais , Mapeamento Cromossômico , Feminino , Ligação Genética , Marcadores Genéticos , Masculino , Repetições de Microssatélites , Desenvolvimento Muscular , Suínos/anatomia & histologia , Suínos/crescimento & desenvolvimentoRESUMO
DNA from 252 bovine spongiform encephalopathy (BSE) cattle and 376 non-diseased control cattle were genotyped for nine loci in the prion protein (PRNP) gene region, three loci in the neurofibromin 1 (NF1) region and four control loci on different chromosomes. The allele and genotype frequencies of the control loci were similar in BSE and control cattle. In the analysed 7.4 Mb PRNP region, the largest differences between BSE and control cattle were found for the loci REG2, R16 and R18, which are located between +300 and +5600 bp, spanning PRNP introns 1 to 2. Carriers of the REG2 genotype 128/128 were younger at BSE diagnosis than those with the other genotypes (128/140 or 140/140). The predominant haplotype REG2 128 bp-R18 173 bp occurred more frequently (P < 0.001), and the second-most frequent haplotype (REG2 140 bp-R18 175 bp) occurred less frequently (P < 0.05) in BSE than in control cattle. The largest frequency differences between BSE and control groups were observed in the Brown Swiss breed. Across all breeds, most of the same alleles and haplotypes of the PRNP region were associated with BSE. In the 23-cM NF1 region, associations with BSE incidence were found for the RM222 allele and for the DIK4009 genotype frequencies. Cattle carrying RM222 genotypes with the 127- or 129-bp alleles were about half a year older at BSE incidence than those with other genotypes. Across the breeds, different alleles and genotypes of the NF1 region were associated with BSE. The informative DNA markers were used to localize the genetic disposition to BSE and may be useful for the identification of the causative DNA variants.
Assuntos
Encefalopatia Espongiforme Bovina/genética , Variação Genética , Neurofibromina 1/genética , Príons/genética , Animais , Bovinos , Cromossomos de Mamíferos , Frequência do Gene , Marcadores Genéticos , Haplótipos , Heterozigoto , Repetições de Microssatélites , Neurofibromina 1/química , Príons/química , Análise de Sequência de DNARESUMO
This study characterized autochthonous pig breeds of Vietnam and compared them with breeds from other regions. A total of 343 animals were considered from 5 indigenous pig breeds of Vietnam (Muong Khuong, Co, Meo, Tap Na, and Mong Cai), 2 exotic breeds kept in Vietnam (Landrace and Yorkshire), 3 European commercial breeds (German Land-race, Piétrain, and Large White), the Chinese breed Meishan, and the European Wild Boar. Each individual was genotyped for 20 selected polymorphic microsatellite loci. The Vietnamese autochthonous breeds showed higher degrees of polymorphism, allelic diversity, and heterozygosity than the other pig breeds. Also, large genetic diversity was observed across the area of distribution, with village-specific subpopulations, which led to significant inbreeding coefficients. As expected, genetic distances showed large differences among European-based, Chinese, and Vietnamese indigenous breeds and reflected the geographical distribution of breeds. In comparison with the European breeds, the Vietnamese indigenous pig breeds harbored a considerable amount of genetic diversity and, therefore, will be of significance for livestock bioconservation.
Assuntos
Cruzamento , Variação Genética/genética , Repetições de Microssatélites/genética , Suínos/classificação , Suínos/genética , Animais , Conservação dos Recursos Naturais , Europa (Continente) , Genótipo , Filogenia , Reação em Cadeia da Polimerase/veterinária , VietnãRESUMO
The lamins are components of nuclear lamina and they have a profound influence on nuclear structure and functions. They are encoded by three genes, LMNA, LMNB1 and LMNB2. A genomic fragment of the porcine LMNA gene (822 bp; from exons 7 to 9) was amplified by polymerase chain reaction and comparatively sequenced. Four single nucleotide polymorphisms (SNPs) were identified in intronic sequences: G162A, G208A, T367G and C618T. The SNPs are within the restriction sites for enzymes Bsh1236I, HpaII, AluI and Bsh1236I respectively. Allele frequencies at SNPs G208A, T367G and C618T were determined by using eight pig breeds. Linkage analysis in the Hohenheim Meishan x Piétrain family placed the LMNA gene in the chromosome 4q linkage group, between MEF2D and GBA (MEF2D - 3.0 cM - LMNA - 0.2 cM - GBA). In radiation hybrid mapping LMNA was most significantly linked to SW270 on chromosome 4 (39 cR; LOD = 7.86). The LMNA gene is located in the quantitative trait loci region for some carcass traits on chromosome 4q.
Assuntos
Cromossomos de Mamíferos/genética , Ligação Genética/genética , Lamina Tipo A/genética , Polimorfismo de Nucleotídeo Único/genética , Mapeamento de Híbridos Radioativos/veterinária , Suínos/genética , Alelos , AnimaisRESUMO
The porcine orthologues of human chromosome HSA9q22.31 genes osteoglycin (OGN) and asporin (ASPN) were mapped to porcine chromosome SSC3 using linkage analysis and a somatic cell hybrid panel. This mapping was refined to SSC3q11 using fluorescence in situ hybridization. These results confirm the existence of a small conserved synteny group between SSC3 and HSA9. Polymorphisms were revealed in both genes, including a pentanucleotide microsatellite (SCZ003) in OGN and two single nucleotide polymorphisms (AM181682.1:g.780G>T and AM181682.1:g.825T>C) in ASPN. The two genes were included in a set of markers for quantitative trait loci (QTL) mapping on SSC3 in the Hohenheim Meishan x Piétrain F2 family. Major QTL for growth and carcass traits were centred in the ASPN-SW902 region.
Assuntos
Glicoproteínas/genética , Polimorfismo de Nucleotídeo Único , Proteoglicanas/genética , Locos de Características Quantitativas , Suínos/genética , Animais , Mapeamento Cromossômico , Cruzamentos Genéticos , Humanos , Peptídeos e Proteínas de Sinalização Intercelular , Repetições de Microssatélites , Suínos/crescimento & desenvolvimento , SinteniaRESUMO
Polymorphic microsatellite and open-reading frame (ORF) sites in the prion protein coding gene (PRNP) were analysed in eight sheep breeds. The three microsatellite sites S11, S15 and S24 were genotyped by fragment length analysis, and the ORF codons 136, 154 and 171 were analysed after direct sequencing. Unexpected polymerase chain reaction (PCR) products of microsatellite sites and ORF haplotypes with more than one heterozygous site were submitted to cloning and then sequenced. The microsatellite sites were polymorphic in all breeds with two to five alleles per site. On average of breeds and sites, the microsatellites had higher degrees of polymorphism than the ORF sites. The ARR/ARR ORF genotype occurred always together with the microsatellite genotypes S11 152/152, S15 179/179 and S24 144/144. As ORF and microsatellite alleles of the PRNP were observed in typical combinations, the microsatellite genotypes were significantly associated with scrapie incidences or risk classes based on the ORF genotypes. The microsatellite sites were highly polymorphic and therefore are advantageous markers for evaluation of scrapie disposition and fine mapping of effects on scrapie pathogenesis within the gene.
Assuntos
Repetições de Microssatélites/genética , Fases de Leitura Aberta/genética , Polimorfismo Genético , Príons/genética , Ovinos/genética , Animais , Sequência de Bases , Primers do DNA , Alemanha , Dados de Sequência Molecular , Alinhamento de Sequência/veterinária , Análise de Sequência de DNA/veterináriaRESUMO
A QTL analysis of multibreed experiments (i.e., crossed populations involving more than two founder breeds) offers clear advantages over classical two-breed crosses, among them increased power and a more comprehensive coverage of the total genetic variability in the species. An alternative to designed multibreed crosses is to reanalyze jointly several experiments involving different breeds. We report a multibreed, multitrait QTL analysis of SSCX that involves five different crosses, six breeds, and almost 3,000 genotyped individuals using a truly multibreed strategy to allow for any number of founder breed origins. Traits analyzed were growth, fat thickness, carcass length, and shoulder and ham weights. Generally, the joint analysis resulted in more significant QTL than the single-experiment analyses. We show that the QTL for fatness, which is highly significant (nominal P < 10(-43)), is of Asiatic origin (Meishan). The next most significant QTL (nominal P < 10(-15)) affected ham weight and seems to be segregating only between Large White and the rest of the breeds. A multitrait, multi-QTL analysis suggests that these are two distinct loci. Additionally, a locus segregating only between Iberian and Landrace affects live weight. The advantages of joint, multibreed analyses clearly outweigh their potential risks.
Assuntos
Cruzamento , Modelos Genéticos , Locos de Características Quantitativas/genética , Suínos/genética , Cromossomo X/genética , Tecido Adiposo/fisiologia , Animais , Distribuição da Gordura Corporal/veterinária , Peso Corporal/genética , Feminino , Genótipo , Funções Verossimilhança , Masculino , Suínos/crescimento & desenvolvimentoRESUMO
Kind and probability of homoplasy across allelic microsatellite fragments can be investigated using DNA of genetically diverse pig breeds. In this study, nine microsatellite loci (SW1897, SW2427, SW489, SW957, TNFB, IFNG, SW2410, SW2019 and S0215) were analysed using DNA samples of pigs from Vietnam (Indigenous breeds Co, Meo, Muong Khuong, Tap Na) and Germany (European Wild Boar, Pietrain). In a total of 39 sequences, 20 differences within isomorphic alleles were observed in comparison with the respective reference sequences. They affected five of the nine tested microsatellite loci. The majority (18) of SNPs occurred in the 5'-flanking regions of the microsatellite repeats, 10 were found in the 3'-flanking regions and only one SNP occurred within the repeat of the Wild Boar sequence of SW2427. The compound microsatellites IFNG and S0215 were unaffected by size homoplasy (SH) within our material. We conclude that the fragment length analysis of microsatellites is a reliable tool for intraspecific phylogenetic studies because SH rates within a species were low.
Assuntos
Variação Genética , Repetições de Microssatélites/genética , Modelos Genéticos , Sus scrofa/genética , Animais , Sequência de Bases , Dados de Sequência Molecular , Polimorfismo de Fragmento de Restrição , Polimorfismo de Nucleotídeo Único , Alinhamento de Sequência , Análise de Sequência de DNA , Especificidade da Espécie , VietnãRESUMO
Polymorphisms in 5'-flanking regions of milk protein encoding genes can influence the binding activity of the affected response elements and thus have an impact on the expression of the gene products. However, precise quantitative data concerning the binding properties of such variable response elements have so far not been described. In this study we present the results of a quantitative fluorescent electromobility shift assay comparing the allelic variants of a polymorphic activator protein-1 binding site in the promoter region of the bovine alphas1-casein encoding gene (CSN1S1), which is affected by an A-->G exchange at -175 bp (CSN1S1(-175bp)). A supershift assay using a commercial c-jun antibody was carried out to verify the specificity of protein binding. The gel shift analysis revealed specific and significantly reduced protein binding of oligonucleotides containing the G variant of the CSN1S1(-175bp) binding site. Further investigations comprised genotyping of the variable CSN1S1(-175bp) activator protein-1 element by an NmuCl restriction fragment length polymorphism in 62 cows of the breed Simmental and 80 cows of the breed German Holstein. Single milk proteins from at least 4 milk samples per cow were quantified by alkaline urea polyacrylamide gel electrophoresis. Homozygotes for CSN1S1(-175bp)*G were not observed, and the allele frequencies were 0.19 in Simmental and 0.05 in German Holstein. Carriers of CSN1S1(-175bp)*G showed higher content (%) as well as quantity (g/d) of alphas1-casein than CSN1S1(-175bp)*A homozygotes, independent of breed. We assume that the positive association of the CSN1S1(-175bp)*G variant with CSN1S1 expression is likely to be caused by a reduced affinity of the affected response element to a c-jun-containing CSN1S1 dimer with repressor properties.
Assuntos
Sítios de Ligação/genética , Caseínas/genética , Bovinos/genética , Proteínas do Leite/genética , Leite/metabolismo , Regiões Promotoras Genéticas , Fator de Transcrição AP-1/metabolismo , Alelos , Animais , DNA/genética , DNA/metabolismo , Ensaio de Desvio de Mobilidade Eletroforética , Feminino , Expressão Gênica , Frequência do Gene , Homozigoto , Lactação/genética , Polimorfismo Genético/genética , Polimorfismo de Fragmento de Restrição , Ligação ProteicaAssuntos
Cromossomos de Mamíferos/genética , Ligação Genética , Proteína P0 da Mielina/genética , Mapeamento de Híbridos Radioativos , Sus scrofa/genética , Animais , Sequência de Bases , Primers do DNA , Frequência do Gene , Dados de Sequência Molecular , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNAAssuntos
Receptores de Ativinas Tipo I/genética , Mapeamento Cromossômico , Mapeamento de Híbridos Radioativos , Receptores de Fatores de Crescimento Transformadores beta/genética , Sus scrofa/genética , Fator de Crescimento Transformador beta/genética , Animais , Sequência de Bases , Primers do DNA , Eletroforese em Gel de Ágar , Frequência do Gene , Dados de Sequência Molecular , Polimorfismo de Fragmento de Restrição , Polimorfismo de Nucleotídeo Único , Proteínas Serina-Treonina Quinases , Receptor do Fator de Crescimento Transformador beta Tipo I , Análise de Sequência de DNARESUMO
Twenty-four microsatellite sites with at least three repeats were found in the bovine prion protein gene (PRNP) and 23 in the ovine PRNP gene. Eight microsatellite sites were polymorphic in cattle and six in sheep with up to 10 alleles per site. In many cases allelic DNA fragments had variants in microsatellite sites and in flanking regions. Distances between microsatellite sites in eight genes from cattle and sheep occurred on average every 0.9 kb. The numerous polymorphic microsatellite sites will improve analysis of phylogenetic origin of different PRNP alleles and trait association studies for bovine spongiform encephalopathy (BSE) and scrapie.