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1.
Kuehn LA Keele JW Bennett GL McDaneld TG Smith TP Snelling WM Sonstegard TS Thallman RM 《Journal of animal science》2011,89(6):1742-1750
Knowledge of breed composition can be useful in multiple aspects of cattle production, and can be critical for analyzing the results of whole genome-wide association studies currently being conducted around the world. We examine the feasibility and accuracy of using genotype data from the most prevalent bovine genome-wide association studies platform, the Illumina BovineSNP50 array (Illumina Inc., San Diego, CA), to estimate breed composition for individual breeds of cattle. First, allele frequencies (of Illumina-defined allele B) of SNP on the array for each of 16 beef cattle breeds were defined by genotyping a large set of more than 2,000 bulls selected in cooperation with the respective breed associations to be representative of their breed. With these breed-specific allele frequencies, the breed compositions of approximately 2,000 two-, three-, and four-way cross (of 8 breeds) cattle produced at the US Meat Animal Research Center were predicted by using a simple multiple regression technique or Mendel (http://www.genetics.ucla.edu/software/mendel) and their genotypes from the Illumina BovineSNP50 array, and were then compared with pedigree-based estimates of breed composition. The accuracy of marker-based breed composition estimates was 89% when using either estimation method for all breeds except Angus and Red Angus (averaged 79%), based on comparing estimates with pedigree-based average breed composition. Accuracy increased to approximately 88% when these 2 breeds were combined into an aggregate Angus group. Additionally, we used a subset of these markers, approximately 3,000 that populate the Illumina Bovine3K (Illumina Inc.), to see whether breed composition could be estimated with similar accuracy when using this reduced panel of SNP makers. When breed composition was estimated using only SNP in common with the Bovine 3K array, accuracy was slightly reduced to 83%. These results suggest that SNP data from these arrays could be used to estimate breed composition in most US beef cattle in situations where pedigree is not known (e.g., multiple-sire natural service matings, non-source-verified animals in feedlots or at slaughter). This approach can aid analyses that depend on knowledge of breed composition, including identification and adjustment of breed-based population stratification, when performing genome-wide association studies on populations with incomplete pedigrees. In addition, SNP-based breed composition estimates may facilitate fitting cow germplasm to the environment, managing cattle in the feedlot, and tracing disease cases back to the geographic region or farm of origin. 相似文献
2.
Karmi N Brown EA Hughes SS McLaughlin B Mellersh CS Biourge V Bannasch DL 《Journal of veterinary internal medicine / American College of Veterinary Internal Medicine》2010,24(6):1337-1342
Background: Hyperuricosuria is a condition that predisposes dogs to urate urolithiasis. A mutation that causes canine hyperuricosuria was previously identified in 3 unrelated dog breeds. The occurrence of the mutation in additional breeds was not determined. Hypothesis/Objectives: Identify additional breeds that have the hyperuricosuria mutation and estimate the mutant allele frequency in those breeds. Animals: Three thousand five hundred and thirty dogs from 127 different breeds were screened for the hyperuricosuria mutation. Methods: DNA samples were genotyped by pyrosequencing and allele‐specific polymerase chain reaction methods. Results: Mutant allele frequencies that range from 0.001 to 0.15 were identified in the American Staffordshire Terrier, Australian Shepherd, German Shepherd Dog, Giant Schnauzer, Parson (Jack) Russell Terrier, Labrador Retriever, Large Munsterlander, Pomeranian, South African Boerboel, and Weimaraner breeds. Conclusions and Clinical Importance: The hyperuricosuria mutation has been identified in several unrelated dog breeds. The mutant allele frequencies vary among breeds and can be used to determine an appropriate breeding plan for each breed. A DNA test is available and may be used by breeders to decrease the mutant allele frequency in breeds that carry the mutation. In addition, veterinarians may use the test as a diagnostic tool to identify the cause of urate urolithiasis. 相似文献
3.
Allais S Journaux L Levéziel H Payet-Duprat N Raynaud P Hocquette JF Lepetit J Rousset S Denoyelle C Bernard-Capel C Renand G 《Journal of animal science》2011,89(1):1-11
The objectives of the study were to evaluate allelic frequencies and to test the association of polymorphisms in the calpastatin (CAST) and μ-calpain (CAPN1) genes with meat tenderness in 3 French beef breeds. A total of 1,114 Charolais, 1,254 Limousin, and 981 Blonde d'Aquitaine purebred young bulls were genotyped for 3 SNP in the CAST gene and 4 SNP in the CAPN1 gene. Two of these markers, 1 in each gene, can be found in Australian or American commercial genetic tests. Others have previously been reported in American studies or are newly evidenced SNP. The quantitative traits studied were Warner-Bratzler shear force and a tenderness score evaluated by trained sensory panels. All the SNP were informative in the 3 breeds. Associations of individual markers or haplotypes with traits were analyzed. The results differed in the 3 breeds. The G allele of a CAST marker (position 97574679 on Btau4.0) was found to exert a significant effect on the shear force (+0.18 phenotypic SD; RSD) and tenderness score (-0.22 RSD) in the Blonde d'Aquitaine breed. In the same breed, this marker was associated with another CAST SNP (position 97576054 on Btau4.0) such that the GA haplotype appeared to be associated with tougher meat. Two CAPN1 markers (positions 45221250 and 45241089 on Btau4.0) had a significant effect on both traits in the Charolais breed (from |0.11| to |0.25| RSD). In the same breed, these markers were associated with another CAPN1 SNP (position 45219395 on Btau4.0) such that the ACA and AGG haplotypes appeared to be associated with a tender meat and a tougher meat, respectively. Consequently, the present results indicate that the effects of the markers studied are breed-specific and cannot be extended to all Bos taurus breeds. Further studies are also required to identify other more appropriate markers for French beef breeds. 相似文献
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5.
Ciampolini R Cetica V Ciani E Mazzanti E Fosella X Marroni F Biagetti M Sebastiani C Papa P Filippini G Cianci D Presciuttini S 《Journal of animal science》2006,84(1):11-19
Assignment tests based on multilocus genotypes are becoming increasingly important to certify quality and origin of livestock products and assure food safety and authenticity. The purpose of this study was to determine the potential of microsatellites (STR) for determining the breed origin of beef products among cattle breeds present in the market. We typed 19 STR in 269 animals from 4 cattle breeds. Based on Wright's F-statistics, 4 loci were discarded, and the remaining 15 loci (FIT = 0.101, FST = 0.089, and FIS = 0.013) were used to compute the likelihood that each multilocus genotype of the total sample was drawn from its true breed instead of another breed. To avoid occurrence of zero likelihood when one or more alleles were missing from a tested breed, sample allele frequencies were estimated assuming uniform prior distributions. Log-likelihood ratio [log(LR)] distributions of the individual assignments were determined for all possible breed contrasts, and their means and SD were used to infer the true-positive and false-positive rates at several values of the log(LR). The posterior probability that the animals of a presumed breed were actually drawn from that breed instead of any another breed was then calculated. Given an observed value of log(LR) > 0 and assuming equal priors, these probabilities were > 99.5% in 10 of 12 possible breed contrasts. For the 2 most closely related breeds (FST = 0.041), this probability was 96.3%, and the probability of excluding the origin of an animal from an alleged breed when it was actually derived from another breed was similar. 相似文献
6.
The diacylglycerol O-acyltransferase (DGAT1) is a microsomal enzyme that catalyzes the final step of triglyceride synthesis. Recent work have evidenced a significant association between lysine at amino acid position 232 with elevated milk fat content, while an alanine at this position is associated with lowered milk fat content. The aim of the present work was to develop a simple and inexpensive PCR-SSCP assay in order to discriminate the CG/AA alleles in exon 8 of the DGAT1 gene. In addition, this method was used to analyze the polymorphism of the DGAT1 through PCR-SSCP methods in 14 populations of cattle from Argentine, Bolivia and Uruguay. The PCR primers were designed from GenBank reported sequences. In this study, we found three PCR-SSCP variants, which were denominated from "A" to "C". However, DNA sequencing analysis showed that "A" variant corresponded with the A allele, while both "B" and "C" observed pattern have the motif AA at positions 10,433-10,434 (K allele), being two alternative conformations of the same DNA sequence. Both variants were detected within each breed with the exception of Hereford, and the heterozygosity varied between 0.000 and 0.524. The gene frequency analysis evidenced significant differences among the studied breeds (F(ST) = 0.325, p = 0.000). European Bos taurus breeds, with the exception of Jersey breed, showed the lowest frequency of the K allele, while highest K allele frequencies were harboured by Bos indicus type cattle. In addition, unselected South American Creole cattle breeds and the synthetic Brangus breed had intermediate allele frequencies. 相似文献
7.
PrP genotype frequencies of Quebec sheep breeds determined by real-time PCR and molecular beacons 
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下载免费PDF全文 Yvan L'Homme Anne Leboeuf Johanne Cameron 《Canadian journal of veterinary research》2008,72(4):320-324
The allele and genotype frequencies of the prion protein gene (PrP), known to have an impact on scrapie susceptibility, were determined by real-time PCR for 500 Quebec purebred rams. Molecular beacons were very efficient in discriminating the 5 alleles investigated. Polymorphisms at coding positions 136, 154, and 171 of the PrP gene were analyzed using 3 separate real-time PCR reactions and a total of 7 molecular beacons. A total of 4 different alleles (ARQ, ARR, AHR, and VRQ) were observed at different frequencies among the 7 breeds of sheep investigated. Results show that more than 50% of the rams in every breed carried at least one ARR allele, which is considered the most resistant to scrapie. The susceptibility ARQ allele was also present in every breed and together with the ARR allele, they were the most frequent alleles found in Quebec rams. The VRQ allele associated with the highest susceptibility to scrapie occurred in 5 of the 7 breeds, although at low frequencies. Overall, the results indicate that the frequencies of PrP alleles and genotypes in common breeds of sheep in Quebec make it feasible to reduce scrapie risk by selective breeding. 相似文献
8.
Susceptibility to clinical scrapie is associated with polymorphisms in the prion protein (PrP) gene. The ARR allele reduces susceptibility to clinical disease caused by all known strains of the transmissible spongiform encephalopathy (TSE) agents. For the economically important German breeds of sheep the PrP allele frequencies are well known, but this paper presents representative genotyping results for 1526 sheep from two smaller milk sheep breeds and 2446 sheep from 14 mostly indigenous land sheep breeds. The ARR allele was detected in each breed but the breed-specific ARR frequencies varied between 1 and 63 per cent. In small populations with a very low ARR frequency the ARR allele could be lost by genetic drift. A simulation study was therefore made to examine the effects of different breeding schemes in populations of different sizes on attempts to select for the ARR allele in an endangered population. In breeds in which no homozygous rams are available the breeding strategy would depend on the number of heterozygous rams, and the genotyping and selection of suitable breeding ewes would reduce the time required to achieve a highly resistant population. In general, in all the breeds a selection programme to achieve 99 per cent ARR homozygous genotypes would be feasible in six to nine generations, depending on the initial allele frequencies. In small populations the inbreeding rate may increase if no specific mating plans are developed by the breeding organisations. 相似文献
9.
选用来源于牛和绵羊的27个微卫星DNA标记,对山东省4个地方山羊品种进行遗传多样性分析,通过计算等位基因频率、多态信息含量、不同标记的平均杂和度、总群体杂合度、亚群体杂合度、群体杂合度、基因分化系数、不同群体的F-统计量、基因流动数、不同群体间的基因流动个数和遗传距离并进行聚类分析,评估其种内变异和种间变异的关系,以群体平均杂合度、F-统计量和遗传分化系数为基础,结合四个山羊种群的实际生存状况,提出避免近交和种群间杂交符合山东山羊种群实际状况的保种模式。研究结果可为山东地方种质特性研究提供基础数据,为山东地方山羊种群的合理保护利用提供科学依据。 相似文献
10.
L J Kennedy S D Carter A Barnes S Bell D Bennett B Ollier W Thomson 《Veterinary immunology and immunopathology》1999,69(2-4):101-111
Although 36 DLA-DRB1 and 10 DLA-DQA1 allele sequences have been published to date, no data on individual allele frequencies exists, either for specific breeds or cross breeds, and the full extent of the polymorphism at each of these loci is still not known. We have used sequence-specific oligonucleotide probing (SSOP) to characterise a series of 367 dogs for their DRB1 and DQA1 alleles. These included individual animals from over 60 different breeds, with numbers per breed ranging from 1 to 39. DLA types were generated from 218 dogs for DRB1 and from 330 dogs for DQA1, while 181 dogs were characterised for both these loci. The frequency of individual DRB1 and DQA1 alleles showed considerable interbreed variation, e.g. 83% of West Highland White Terriers were DRB1*01 as opposed to 9% of Collies. No breed had >9 of the 22 DRB1 types defined in this study; several breeds had only two DRB1 types. DLA-DQA1 showed less variation in allele numbers per breed, but also showed considerable interbreed frequency variation. Haplotype analysis revealed over 44 different DRB1/DQA1 combinations. Of these, 25 were in a number of animals, and also in an animal that was homozygous for one or both of these loci. Some DRB1 alleles could be found in combination with several different DQA1 alleles, while others were only present in one haplotypic combination. DLA allele frequency data in normal dogs will be critical for disease association studies. It may also be possible to use haplotype data to establish the genetic relationships between different dog breeds. 相似文献
11.
MyoD基因在不同猪种中的分布及群体遗传结构分析 总被引：1，自引：0，他引：1
利用RFLP法检测了MyoD基因在10个中外猪种及部分杂交群体中的分布情况,分析了各群体内MyoD基因的遗传分布、遗传变异、群体杂合性等群体遗传信息,并进一步以各群体基因频率为基础,计算出群体间遗传距离和进化距离,根据进化距离对群体进行聚类,重建了系统发生树。结果表明:MyoD基因内含子1的DdeI酶切位点上不同基因型的分布在多数群体中都服从Hardy-Weinberg平衡,但在杜洛克和DLY群体中发生偏离。总体上讲,各试验群体的遗传多样性较丰富,群体遗传变异性较高,进化过程中受到自然选择压的作用,选择潜力较大。在系统发生树上,10个群体被分为4个分枝。分别是长白猪血缘、原始地方品种、杜洛克血缘和高原藏猪分枝。这一结果与各猪种的育种过程有较高的吻合性。说明部分功能基因的RFLP数据可用于近缘物种间的遗传分化研究。 相似文献
12.
Naohiko OKUMURA Toshimi MATSUMOTO Noriyuki HAMASIMA Takashi AWATA 《Animal Science Journal》2008,79(3):303-313
Here, we report the variability in the KIT tyrosine kinase receptor and its ligand KITLG genes by determining single nucleotide polymorphisms (SNPs) in 384 individuals including 11 pig breeds, two synthetic-line cross pigs, two cross breeds, and one Japanese wild boar. SNPs and indels within the coding sequence regions of KITLG and KIT and their 5'-flanking regions were detected by aligning sequences from eight pigs, and subsequently the SNPs were genotyped using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF-MS). Principal component analysis using allele frequencies in the SNP locus showed a distant relationship between Asian and Euro-American pig groups, except for Berkshire and Tokyo X breeds. These breeds were located within the mid-portion of the distribution in the first principal component. The Hampshire breed was distant from the other pig groups on the axis of the second principal component. Haplotype frequencies that were deduced using non-synonymous substitutions of the KIT gene revealed the uniqueness of Landrace, Large White, Middle White, and three-way cross pigs (LWD) and of the Hampshire breed. On the other hand, the haplotypes of KITLG and KIT detected in the Berkshire breed were prevalent in Asian pig groups. This tendency is different from that observed in other Euro-American pig breeds. 相似文献
13.
Hidetoshi NARA Miho INOUE-MURAYAMA Akiko KOSHIMURA Akinori SUGIYAMA Yuichi MURAYAMA Masami MAEJIMA Yuko UEDA Hideyuki ITO Ettore RANDI Heui-Soo KIM Ji-Hong HA Hitoshi KITAGAWA Yukari TAKEUCHI Yuji MORI Toshiroh IWASAKI Mitsuo MORITA Katuaki ÔTA Shin'ichi ITO 《Animal Science Journal》2005,76(1):81-86
Various dog breeds are remarkably different from each other not only in their sizes and shapes but also in behavioral traits, suggesting that some of these characteristics are under genetic control. However, little is known about genes related to behavioral traits in canine species. In humans, it has been reported that the dopamine receptor D4 gene (DRD4) includes polymorphism at several regions that relate to personality or psychiatric disorders. In an earlier study by the authors of the present study, the polymorphisms in canine DRD4 exon III and exon I regions were reported. In the present study, a novel polymorphism in canine DRD4 intron II was found based on a 17 base pair insertion/deletion, and the two alleles detected were named P (shorter allele) and Q (longer allele). The allelic distribution in 28 breeds of dog, including a total of 1114 unrelated individuals, were then investigated. Both P and Q alleles were detected in most of the breeds investigated; however, the frequencies of P and Q differed greatly between breeds. With respect to classification based on breed origin, P and Q alleles were frequent in Occidental and Oriental breeds, respectively. Furthermore, two subspecies of wolves, the ancestors of dogs, were analyzed for the comparison of allele frequencies with dogs, and the P allele was predominant in both European and Chinese wolves. 相似文献
14.
Naoto WATANABE Takahisa YAMADA Sachiyo YOSHIOKA Masayuki ITOH Youichi SATOH Masako FURUTA Shigeki KOMATSU Yoshihiko SUMIO Tatsuo FUJITA Yoshiyuki SASAKI 《Animal Science Journal》2010,81(1):142-144
Our previous study detected a single nucleotide polymorphism (SNP), g.1471620G > T , in the 5' flanking region of the endothelial differentiation sphingolipid G-protein-coupled receptor 1 ( EDG1 ) gene, which has been considered as a positional functional candidate for the gene responsible for marbling, and showed association of the g.1471620G > T SNP with marbling in Japanese Black beef cattle. In the present study, we investigated the allele frequency distribution of the g.1471620G > T SNP among the 5 cattle breeds, Japanese Black, Japanese Brown, Japanese Short Horn, Holstein, and Brown Swiss breeds. The T allele at the g.1471620G > T SNP associated with high marbling was found at high frequency in Japanese Black breed that has been subjected to a strong selection for high marbling, while the allele was absent or at very low frequencies in the other breeds that have not been strongly selected for high marbling. Based on this finding, we hypothesized that the pressure of the strong selection for high marbling in Japanese Black breed has increased the frequency of the T allele at the g.1471620G > T SNP in the EDG1 . 相似文献
15.
以AA白鸡、广西鸡、E1矮小鸡品系为试验材料,采用PCR-SSCP技术对鸡细胞外脂肪酸结合蛋白基因(EX-FABP)的2个片段进行PCR扩增,分析了EX-FABP基因在3个鸡品系的多态性。结果表明:EX-FABP基因在2对引物扩增片段中均存在PCR-SSCP多态性。对于引物1扩增片段,3个鸡品系均检测到BB基因型,AA基因型只出现在AA白鸡中;而且B等位基因频率在3个鸡品系中均明显高于A等位基因频率。对于引物2扩增片段,3个鸡品系均检测到HH和Hh基因型,hh基因型只出现在E1矮小鸡中;H等位基因频率在3个品系中均明显高于h等位基因频率。引物1和引物2的多态性片段测序分析表明,EX-FABP基因第641位点和645位点分别发生了单碱基的转换(G-A和T-C),第3264位点发生了转换(T-C)。 相似文献
16.
Rendo F Iriondo M Manzano C Estonba A 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2012,129(3):234-243
Here, we present the results of a genetic analysis of 463 Pottoka ponies corresponding to four generations, using 17 microsatellite markers. Ten years after the beginning of the Pottoka conservation programme, the values for the genetic diversity of the breed are still high and stable, indicating the success of the programme. We found null alleles in Pottoka for the ASB23, HMS3 and HTG10 microsatellites. Together with information obtained from other pony breeds from the Iberian Peninsula, this finding indicates that these microsatellites should not be used for phylogenetic analyses or parentage tests, at least for these breeds. The high heterozygosity exhibited by this breed in comparison to other ponies, together with its genetic proximity to the centroid of the allele frequencies, suggest that Pottoka allele frequencies are close to those initially exhibited by the ancestors of current European ponies. The results obtained in the current work, together with results from previous studies of ponies and horses from the Iberian Peninsula, corroborate the idea of a unique origin of all ponies from the European Atlantic Area. In contrast, our results do not corroborate the idea that these are derived from a domestication event in the Iberian Peninsula, nor that they have incorporated ancient Iberian horse genes into their genetic pool to a larger extent than other horse breeds. 相似文献
17.
Stephen A. Barwick David J. Johnston Bradley J. Walmsley M. Gilbert Jeyaruban Vincent Boerner 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2020,137(5):510-519
A method is described for deriving the genetic matrix G needed for breeders to select across breeds for any breeding objective. The matrix comprises partitions among selection criteria ( G11 ), between selection criteria and the breeding objective traits ( G12 ), and among the breeding objective traits ( G22 ). A weighting procedure is used to combine the G matrix of individual breeds with known breed differences. Between-breed variances are added to the diagonals of the matrix. Selection across many breeds can be quite different from that across a subset of the breeds. The particular breeds, and the numbers of each breed, that the breeder is prepared to consider in selection changes the genetic matrix and the selection index that should be used. 相似文献
18.
Sharat Chandra Mehta 《Tropical animal health and production》2014,46(8):1397-1406
The genetic and demographic bottleneck analysis of Indian camel breeds was carried out utilizing 40 microsatellite markers. Allelic polymorphism was observed at 20 loci in the Indian dromedary breeds. A total of 66 alleles were scored. The average number of alleles, expected heterozygosity and polymorphic information content were, respectively, 3.25?±?0.27, 0.56?±?0.04 and 0.49?±?0.04 in Bikaneri; 3.25?±?0.25, 0.53?±?0.03 and 0.46?±?0.03 in Jaisalmeri; 3.0?±?0.21, 0.53?±?0.04 and 0.45?±?0.03 in Kachchhi and 3.1?±?0.19, 0.51?±?0.03 and 0.44?±?0.03 in Mewari breed. Higher genetic variation was observed in most numerous Bikaneri breed. Genetic distances were least between the breed pair Bikaneri and Jaisalmeri which was closely placed with the Kachchhi breed. The Mewari camels had relatively higher genetic distance from the other three Indian dromedary breeds. The bottleneck analysis revealed the presence of genetic bottleneck in all four breeds of Indian dromedary. However, the qualitative graphical method resulted in normal L-shaped distribution of allele frequencies in Jaisalmeri breeds and shifted mode in Bikaneri, Kachchhi and Mewari breeds. The demographic bottleneck analysis revealed minimum reduction (?9.65 %) in the population of camels in Jaisalmeri breeding tract as compared to that of Bikaneri (?14.18 %), Kachchhi (?27.78 %) and Mewari (?32 %) breeding tracts. Conclusively, the genetic bottleneck analysis could explain the demographic bottleneck in the Indian dromedary populations. Therefore, appropriate conservation and improvement efforts are needed in all four dromedary breeds with immediate attention on Mewari and Kachchhi breeds. The present study is the first report in demonstrating the genetic basis of demographic bottleneck in the Indian dromedary populations. 相似文献
19.
A total of 438 calves was produced by 123 sires of Hereford, Simmental, Friesian and Brahman breeds when mated to Hereford cows. Faecal egg counts and larval differentiation of nematode species were undertaken on one or two occasions prior to weaning at 7 to 8 months. Significant breed of sire and sire within breed effects were observed, but heritabilities, repeatabilities and phenotypic correlations were generally low to moderate. 相似文献
20.
B. Moioli F. Napolitano L. Orrù & G. Catillo 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2005,122(6):418-420
Three novel SNPs were identified in the locus OAR292286, encoding the DNA sequence of promoter III of the ovine acetyl‐CoA carboxylase‐α gene, in Italian sheep of four breeds: Gentile di Puglia (25 individuals) and Sopravissana (31) which are triple‐purpose local endangered breeds, Comisana (25) which is a local non‐selected, non‐endangered dairy breed and Sarda (15) which is a popular selected high yielding dairy breed. Variant alleles are: G/T at 1330 bp, C/G at 1338 bp and C/T at 1430 bp. Frequencies of the variant alleles were calculated and chi‐squared analysis of the differences in allele frequency between breed pairs was performed. Allele frequencies of the Sarda breed differ significantly from the other considered breeds. 相似文献