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1.
Anim Genet ; 46(3): 337-9, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-25917305

RESUMO

This study was a first analysis of paternal genetic diversity for extensive Asian domestic goats using SRY gene sequences. Sequencing comparison of the SRY 3'-untranslated region among 210 Asian goats revealed four haplotypes (Y1A, Y1B, Y2A and Y2B) derived from four variable sites including a novel substitution detected in this study. In Asian goats, the predominant haplotype was Y1A (62%) and second most common was Y2B (30%). Interestingly, the Y2B was a unique East Asian Y chromosomal variant, which differentiates eastern and western Eurasian goats. The SRY geographic distribution in Myanmar and Cambodia indicated predominant the haplotype Y1A in plains areas and a high frequency of Y2B in mountain areas. The results suggest recent genetic infiltration of modern breeds into South-East Asian goats and an ancestral SRY Y2B haplotype in Asian native goats.


Assuntos
Evolução Molecular , Genes sry , Variação Genética , Cabras/genética , Animais , Camboja , DNA Mitocondrial/genética , Ásia Oriental , Haplótipos , Masculino , Mianmar , Filogeografia , Análise de Sequência de DNA , Cromossomo Y
2.
J Anim Sci ; 92(5): 1874-85, 2014 May.
Artigo em Inglês | MEDLINE | ID: mdl-24663186

RESUMO

Pooled genomic DNA has been proposed as a cost-effective approach in genomewide association studies (GWAS). However, algorithms for genotype calling of biallelic SNP are not adequate with pooled DNA samples because they assume the presence of 2 fluorescent signals, 1 for each allele, and operate under the expectation that at most 2 copies of the variant allele can be found for any given SNP and DNA sample. We adapt analytical methodology from 2-channel gene expression microarray technology to SNP genotyping of pooled DNA samples. Using 5 datasets from beef cattle and broiler chicken of varying degrees of complexity in terms of design and phenotype, continuous and dichotomous, we show that both differential hybridization (M = green minus red intensity signal) and abundance (A = average of red and green intensities) provide useful information in the prediction of SNP allele frequencies. This is predominantly true when making inference about extreme SNP that are either nearly fixed or highly polymorphic. We propose the use of model-based clustering via mixtures of bivariate normal distributions as an optimal framework to capture the relationship between hybridization intensity and allele frequency from pooled DNA samples. The range of M and A values observed here are in agreement with those reported within the context of gene expression microarray and also with those from SNP array data within the context of analytical methodology for the identification of copy number variants. In particular, we confirm that highly polymorphic SNP yield a strong signal from both channels (red and green) while lowly or nonpolymorphic SNP yield a strong signal from 1 channel only. We further confirm that when the SNP allele frequencies are known, either because the individuals in the pools or from a closely related population are themselves genotyped, a multiple regression model with linear and quadratic components can be developed with high prediction accuracy. We conclude that when these approaches are applied to the estimation of allele frequencies, the resulting estimates allow for the development of cost-effective and reliable GWAS.


Assuntos
Bovinos/genética , Galinhas/genética , DNA/genética , Genótipo , Animais , Biometria , Feminino , Masculino , Polimorfismo de Nucleotídeo Único
3.
Anim Genet ; 44(6): 636-47, 2013 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-23909810

RESUMO

A putative functional mutation (rs109231213) near PLAG1 (BTA14) associated with stature was studied in beef cattle. Data from 8199 Bos taurus, Bos indicus and Tropical Composite cattle were used to test the associations between rs109231213 and various phenotypes. Further, 23 496 SNPs located on BTA14 were tested for association with these phenotypes, both independently and fitted together with rs109231213. The C allele of rs109231213 significantly increased hip height, weight, net food intake, age at puberty in males and females and decreased IGF-I concentration in blood and fat depth. When rs109231213 was fitted as a fixed effect in the model, there was an overall reduction in associations between other SNPs and these traits but some SNPs remained associated (P < 10(-4) ). Frequency of the mutant C allele of rs109231213 differed among B. indicus (0.52), B. taurus (0.96) and Tropical Composite (0.68). Most chromosomes carrying the C allele had the same surrounding 10 SNP haplotype, probably because the C allele was introgressed into Brahman from B. taurus cattle. A region of reduced heterozygosity surrounds the C allele; this is small in B. taurus but 20 Mb long in Brahmans, indicating recent and strong selection for the mutant allele. Thus, the C allele appears to mark a mutation that has been selected almost to fixation in the B. taurus breeds studied here and introduced into Brahman cattle during grading up and selected to a frequency of 0.52 despite its negative effects on fertility.


Assuntos
Bovinos/genética , Proteínas de Ligação a DNA/genética , Pleiotropia Genética/genética , Fenótipo , Seleção Genética/genética , Dedos de Zinco/genética , Animais , Austrália , Bovinos/crescimento & desenvolvimento , Feminino , Estudos de Associação Genética , Genética Populacional , Genótipo , Haplótipos/genética , Desequilíbrio de Ligação , Masculino , Carne/normas , Polimorfismo de Nucleotídeo Único/genética , Especificidade da Espécie
4.
Anim Genet ; 44(1): 79-85, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-22524237

RESUMO

The domestic goat is one of the most important livestock species, but its origins and genetic diversity still remain uncertain. Multiple highly divergent maternal lineages of goat have been reported in previous studies. Although one of the mitochondrial DNA lineages, lineage B, was detected only in eastern and southern Asia, the geographic distribution of these lineages was previously unclear. Here, we examine the genetic diversity and phylogeographic structure of Asian goats by mitochondrial DNA sequences and morphological characteristics. The analyses of a total of 1661 Asian goats from 12 countries revealed a high frequency of lineage B in Southeast Asia. The frequency of this lineage tended to be higher in mountain areas than in plain areas in Southeast Asian countries, and there was a significant correlation between its frequency and morphological traits. The results suggest an original predominance of lineage B in Southeast Asia and the recent infiltration of lineage A into Southeast Asian goats.


Assuntos
DNA Mitocondrial/genética , Variação Genética , Cabras/genética , Filogeografia , Animais , Sudeste Asiático , DNA Mitocondrial/sangue , Ásia Oriental , Cabras/anatomia & histologia , Dados de Sequência Molecular , Filogenia , Reação em Cadeia da Polimerase , Análise de Sequência de DNA , Homologia de Sequência
5.
Meat Sci ; 85(2): 285-8, 2010 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-20374900

RESUMO

In Japan, Japanese Black and Holstein cattle are appreciated as popular sources of meat, and imported beef from Australia and the United States is also in demand in the meat industry. Since the BSE outbreak, the problem of false sales has arisen: imported beef has sometimes been mislabeled as domestic beef due to consumer concerns. A method is needed to correctly discriminate between Japanese and imported cattle for food safety. The objective of this study was to develop breed discrimination markers between Japanese and US cattle using a 50K SNP array. As a result, five US-specific markers (BISNP7, BISNP15, BISNP21, BISNP23, and BISNP26) were developed with allelic frequencies that ranged from 0.102 (BISNP15) to 0.250 (BISNP7) and averaged 0.184. The combined use of the five markers would permit discrimination between Japanese and US cattle with a probability of identification of 0.858. This result indicates the potential of the bovine 50K SNP array as a powerful tool for developing breed identification markers. These markers would contribute to the prevention of falsified beef displays in Japan.


Assuntos
Bovinos/genética , Marcadores Genéticos , Análise de Sequência com Séries de Oligonucleotídeos/veterinária , Polimorfismo de Nucleotídeo Único/genética , Animais , Cruzamento , Genótipo , Japão , Estados Unidos
6.
Artigo em Inglês | MEDLINE | ID: mdl-17851104

RESUMO

Stearoyl-CoA desaturase (SCD) catalyzes the synthesis of monounsaturated fatty acids (MUFAs). In cattle, the MUFAs are related to softness and flavor of meat. In order to investigate gene expression profile during bovine preadipocyte differentiation, we isolated stromal-vascular cells from perirenal adipose tissues of Japanese Black and Holstein steers. Gene expression level of adipocyte type fatty acid binding protein (FABP4), SCD, sterol regulatory element binding protein 1 (SREBP1) and CCAAT/enhancer binding protein alpha (C/EBP-alpha) were elucidated by real-time PCR assay. The levels of SCD mRNA expression were significantly increased to 10.8 and 6.3-fold in Japanese Black and Holstein, respectively, on day 1 of the culture. The difference in SCD expression between the two breeds may reflect differences in the fat development characteristics of the cattle breeds. Although transcription factors SREBP1 and C/EBP-alpha are supposed to regulate SCD expression, expression levels of the two factors were not completely consistent with that of SCD.


Assuntos
Adipócitos/enzimologia , Adipogenia , RNA Mensageiro/biossíntese , Estearoil-CoA Dessaturase/biossíntese , Adipogenia/genética , Animais , Proteína alfa Estimuladora de Ligação a CCAAT/genética , Proteína alfa Estimuladora de Ligação a CCAAT/metabolismo , Bovinos , Células Cultivadas , Indução Enzimática , Proteínas de Ligação a Ácido Graxo/genética , Proteínas de Ligação a Ácido Graxo/metabolismo , Ácidos Graxos/metabolismo , Masculino , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Estearoil-CoA Dessaturase/genética , Proteína de Ligação a Elemento Regulador de Esterol 1/genética , Proteína de Ligação a Elemento Regulador de Esterol 1/metabolismo , Fatores de Tempo
7.
Meat Sci ; 77(2): 161-6, 2007 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-22061586

RESUMO

In the meat industry, correct breed information in food labeling is required to assure meat quality. Genetic markers provide corroborating evidence to identify breed. This paper describes the development of DNA markers to discriminate between Japanese and Australian beef. Two Bos indicus-specific markers and MC1R marker were used as possible candidate markers. Amplified fragment length polymorphism method was employed to develop additional candidate markers. The 1564 primer combinations provided three markers that were converted into single nucleotide polymorphisms markers for high-throughput genotyping. In these markers, the allele frequencies in cattle from both countries were investigated for discrimination ability using PCR-RFLP. The probability of identifying Australian beef was 0.933 and probability of misjudgment was 0.017 using six selected markers. These markers could be useful for discriminating between Japanese and Australian beef and would contribute to the prevention of falsified breed labeling of meat.

8.
Anim Genet ; 37(4): 316-20, 2006 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-16879339

RESUMO

In order to develop a comparative map between chicken and quail, we identified orthologous gene markers based on chicken genomic sequences and localized them on the Japanese quail Kobe-NIBS linkage map, which had previously been constructed with amplified fragment length polymorphisms. After sequencing the intronic regions of 168 genes located on chicken chromosomes 1-8, polymorphisms among Kobe-NIBS quail family parents were detected in 51 genes. These orthologous markers were mapped on eight Japanese quail linkage groups (JQG), and they allowed the comparison of JQG to chicken macrochromosomes. The locations of the genes and their orders were quite similar between the two species except within a previously reported inversion on quail chromosome 2. Therefore, we propose that the respective quail linkage groups are macrochromosomes and designated as quail chromosomes CJA 1-8.


Assuntos
Galinhas/genética , Cromossomos , Coturnix/genética , Animais , Mapeamento Cromossômico , Análise Mutacional de DNA , Genes , Ligação Genética , Marcadores Genéticos , Polimorfismo Genético , Homologia de Sequência do Ácido Nucleico
9.
Anim Genet ; 36(3): 227-31, 2005 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-15932402

RESUMO

The Japanese quail (Coturnix japonica) is a notably valuable egg and meat producer but has also been used as a laboratory animal. In the present study, we constructed a Japanese quail linkage map with 1735 polymorphic amplified fragment length polymorphisms markers, and nine chicken microsatellite (MS) markers, as well as sex and phenotypes of two genetic diseases; a muscular disorder (LWC) and neurofilament-deficient mutant (Quv). Linkage analysis revealed 578 independent loci. The resulting linkage map contained 44 multipoint linkage groups covering 2597.8 cM and an additional 218.2 cM was contained in 21 two-point linkage groups. The total map was 2816 cM in length with an average marker interval of 5.5 cM. The Quv locus was located on linkage group 5, but linkage was not found between the LWC locus and any of the markers. Comparative mapping with chicken using orthologous markers revealed chromosomal assignments of the quail linkage group 1 to chicken chromosome 2 (GGA2), 5 to GGA22, 2 to GGA5, 8 to GGA7, 27 to GGA11, 29 to GGA1 and 45 to GGA4.


Assuntos
Doenças das Aves/genética , Mapeamento Cromossômico , Coturnix/genética , Doenças Musculares/veterinária , Proteínas de Neurofilamentos/genética , Animais , Primers do DNA , Eletroforese em Gel de Poliacrilamida , Repetições de Microssatélites/genética , Doenças Musculares/genética , Mutação/genética , Técnicas de Amplificação de Ácido Nucleico , Polimorfismo de Fragmento de Restrição
10.
Anim Genet ; 35(1): 40-3, 2004 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-14731228

RESUMO

Using amplified fragment length polymorphism (AFLP) fingerprinting, selective genotyping was performed to determine if this method was effective for selecting superior breeding stock. Forty-eight cows with extreme genetic merit for beef marbling score (BMS) were selected from a population of Japanese Black cattle (n = 4462), including 25 with the highest for predicted breeding value (PBV) and 23 with the lowest. Sixteen AFLP fragments were selected for further analysis based on fragment frequency differences between the high and low groups. A linear discriminant analysis using these AFLP fragments was applied in order to derive a discriminant function that classified the cows into high and low groups. Seven of the 16 fragments were included in the resulting function and the discriminant scores (general genetic values, GGV) of the 48 cows were calculated using the function. These cows were clearly separated into high and low groups by GGV with a correlation ratio of 0.91 (discriminative error of 2.1%). The same function was then applied to 121 additional cows that were randomly selected from the original population. A significant regression coefficient of GGV on BMS-PBV (R2 = 0.45) was obtained, which indicates that the GGV can be used as a selection criterion for BMS in this population. These results suggest that AFLP fingerprinting can be used for animal breeding without identifying the underlying genes affecting the trait of interest.


Assuntos
Cruzamento/métodos , Bovinos/genética , Polimorfismo de Fragmento de Restrição , Agricultura/métodos , Animais , Constituição Corporal , Primers do DNA , Análise Discriminante , Análise de Regressão
11.
Meat Sci ; 67(2): 275-80, 2004 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-22061324

RESUMO

In the meat industry, correct breed information in food labeling is required to assure meat quality. Genetic markers provide corroborating evidence to identify breed. This paper describes the development of DNA markers to discriminate between Japanese Black and F1 (Japanese Black×Holstein) breeds. Amplified fragment length polymorphism method was employed to detect candidate markers absent in Japanese Black but present in Holstein. The 500 primer combinations yielded six selected markers that were converted into single nucleotide polymorphisms markers for high-throughput genotyping. The allele frequencies in both breeds were investigated for discrimination ability using PCR-RFLP. The probability of identifying F1 was 0.882 and probability of misjudgment was 0.0198. The markers could be useful for discriminating between Japanese Black and F1 and would contribute to the elimination of falsified breed labeling of meat.

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