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Xing Guo Jiangxian Wang Chendong Ma Zhicheng Wang Hong Chen Hu Su Yi Wan Runshen Jiang 《Animal Science Journal》2020,91(1)
To determine the causative variations associated with two chicken comb phenotypes, pendulous comb (PC) or upright comb (UC), two pooled genomic DNA samples from PC and UC chickens were re‐sequenced by Next‐Generation Sequencer, and genome‐wide Single nucleotide polymorphisms (SNPs) were detected. Using three selective sweep approaches, FST, θπ, and Tajima's D, with top 5% window values serving as the threshold, a total of 84 positively selective genes (PSGs) were identified. There were no SNPs in exons of the PSGs with significant differences in allele frequencies between the two comb phenotype groups. Then, 515 differentially expressed genes (DEGs) between the PC and UC were identified by RNA‐seq. Three genes including CD36 (CD36 molecule), ADAMTSL3 (ADAMTS‐like 3), and AOX1 (aldehyde oxidases 1) are overlapped between PSGs and DEGs. After genotyping seven candidate SNPs in the regulatory regions of the three overlapping genes in 120 chickens from two other breeds, two variants (rs14607046 and rs731818051) in the regulatory regions of AOX1 and ADAMTSL3 were found to have significant differences in allele frequency between the PC and UC, suggesting that the two variants may be causative mutations for PC. Overall, our study shed light on the genetic basis underlying the PC phenotype in chickens. 相似文献
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Salvatore Mastrangelo Slim Ben Jemaa Gianluca Sottile Sara Casu Baldassare Portolano Elena Ciani Fabio Pilla 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2019,136(6):526-534
Selective breeding has led to modifications in the genome of many livestock breeds. In this study, we identified the genomic regions that may explain some of the phenotypic differences between two closely related breeds from Sardinia. A total of 44 animals, 20 Sardinian Ancestral Black (SAB) and 24 Sardinian White (SW), were genotyped using the Illumina Ovine 50K array. A total of 68, 38 and 15 significant markers were identified using the case–control genome‐wide association study (GWAS), the Bayesian population differentiation analysis (FST) and the Rsb metric, respectively. Comparisons among the approaches revealed a total of 22 overlapping markers between GWAS and FST and one marker between GWAS and Rsb. Three markers detected by Rsb were also located near (<2 Mb) to highly significant regions identified by GWAS and FST analyses. Moreover, one candidate marker identified by GWAS and FST approaches was located in a run of homozygosity island that was shared by both breeds. We identified several genes involved in many phenotypic differences (such as stature and growth, reproduction, ear size, coat colour, behaviour) between the two analysed breeds. This study shows that combining several genome‐wide approaches could improve discovery of regions involved in the variability of breeding traits and responsible for the phenotypic diversity even between closely related breeds. Overall, the combination of such genome‐wide methods can be extended to other livestock breeds that share between them a similar genetic background, to understand the process that shapes the patterns of genetic variability between closely related populations. 相似文献
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Bárbara Machado Campos Adriana Santana do Carmo Andrea Alves do Egito Arthur Silva da Mariante Maria Socorro Muaés do Albuquerque João José Simoni de Gouveia Carlos Henrique Mendes Malhado Lucas Lima Verardo Marcos Vinícius Gualberto Barbosa da Silva Paulo Luiz Souza Carneiro 《Tropical animal health and production》2017,49(8):1677-1684
Genetic diversity is one of the most important issues in studies on conservation of cattle breeds and endangered species. The objective of this study was to estimate the levels of genetic differentiation between locally adapted taurine (Bos taurus taurus) and zebu (Bos taurus indicus) breeds in Brazil, which were genotyped for more than 777,000 SNPs. The fixation index (F ST), principal component analysis (PCA), and Bayesian clustering were estimated. The F ST highlighted genetic differentiation between taurine and zebu breeds. The taurine lines, Caracu and Caracu Caldeano, had significant genetic differentiation (F ST close to 5%) despite their recent selection for different uses (meat and milk). This genetic variability can be used for conservation of locally adapted animals, as well as for breeding programs on zebu breeds. Introgression of zebu in locally adapted breeds was identified, especially in Curraleiro Pé-Duro breed. The Gyr breed, however, had low breed purity at genomic level due to its very heterogeneous mixing pattern. 相似文献
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Between-breed genetic diversity is classically considered as a major criterion to be taken into account when setting priorities for conservation of domestic animal breeds. However, it has been argued that methods based on the between-breed component of genetic diversity may not be optimal because they ignore the within-breed component of variation. The paper considers the most common methods used to evaluate those two components when genetic diversity is evaluated on the basis of genetic markers, and proposes to define an aggregate diversity combining linearly the two components. This implies defining for each breed (or population) its contributions to the between-breed and to the within-breed diversity. When defining an aggregate diversity, one can weight these contributions by FST and 1−FST, respectively, since the fixation index FST of Wright represents the proportion of the total genetic variation which is due to differences in allelic frequencies between populations. Such an approach is valid when the objective is genetic improvement by selection within a so-called “meta-population”. However, in a more general context of animal breeding, when heterosis and complementarities between breeds have to be considered, as well as adaptation to specific environments, more weight should be given to the between-breed variation. The proper weight to apply may require solutions adapted to each particular situation. In a long-term conservation perspective, priorities should also take into account the degree of endangerment of each breed. By combining diversity contributions and probability of extinction, a cryopreservation potential (or priority) may be estimated for each breed. The problem is illustrated on a sample of 11 European pig breeds typed for 18 microsatellite loci. 相似文献
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试验旨在通过对藏鸡和白羽肉鸡垂体转录组测序和生物信息学分析,筛选出与鸡生长发育相关的差异表达基因(differentially expression genes,DEGs)及信号通路。本研究选用42日龄健康藏鸡和白羽肉鸡各3只,分别采集垂体组织利用Illumina HiSeq 2000平台进行转录组mRNA测序,对筛选到的DEGs筛选DEGs,GO和KEGG数据库功能注释和富集分析,实时荧光定量PCR验证随机挑选的DEGs表达水平。结果显示,藏鸡和白羽肉鸡分别获得126 094 302和125 666 442条clean reads。与白羽肉鸡相比,藏鸡垂体组织中共有DEGs 392个,其中196个为上调基因,196个为下调基因(P<0.05),其中包括生长激素(GH)基因、生长激素释放激素受体(GHRHR)基因和胰岛素样生长因子2 mRNA结合蛋白1(IGF2BP1)基因。GO和KEGG富集分析发现,DEGs显著富集于细胞黏附分子信号通路和神经活性配体-受体相互作用信号通路等细胞通讯相关的信号通路,GH、GHRHR和IGF2BP1基因也显著富集于神经活性配体-受体相互作用信号通路。实时荧光定量PCR结果显示,转录组测序结果准确可靠。综上研究,本研究初步揭示了影响藏鸡和白羽肉鸡生长发育速度差异的关键候选基因和信号通路,为了解鸡垂体组织调节生长发育的分子机制提供了理论依据。 相似文献
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Microsatellite-based diversity analysis and genetic relationships of three Indian sheep breeds 总被引:2,自引:0,他引:2
M. Mukesh M. Sodhi & S. Bhatia 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2006,123(4):258-264
The genetic structure of three Indian sheep breeds from two different geographical locations (Nali, Chokla from north‐western arid and semi‐arid region; Garole from eastern saline marshy region) of India was investigated by means of 11 ovine‐specific microsatellite markers as proposed in FAOs MoDAD programme. Microsatellite analysis revealed high allelic and gene diversity in all the three breeds. Nali sheep showed higher mean number of alleles and gene diversity (6.27 and 0.65) than Chokla (5.63 and 0.64) and Garole (5.63 and 0.59). High within population inbreeding estimates observed in the three breeds (FIS, Chokla = 0.286, Nali = 0.284, Garole = 0.227) reflected deficit of heterozygotes. The overall estimates for F‐statistics were significantly (p < 0.05) different from zero. High values of FST (0.183) across all the loci revealed substantial degree of breed differentiation. Based on pair wise FST and Nm between different breeds, Nali and Chokla (FST = 6.62% and Nm = 4.80) were observed to be the closest followed by Garole and Nali (FST = 20.9% and Nm = 1.80), and Garole and Chokla (FST = 21.4% and Nm = 1.71). In addition, genetic distance estimates, phylogeny analysis and individual assignment test used to evaluate interbreed genetic proximity and population structure also revealed substantial genetic differentiation between Garole and the other two Rajasthani (Nali and Chokla) sheep. This divergent status of Garole sheep indicated genetic uniqueness of this breed suggesting higher priority for its conservation. 相似文献
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Effects of prostaglandin f(2alpha) on corpora lutea formation and function in mated bitches 下载免费PDF全文
Paradis M Post K Mapletoft RJ 《The Canadian veterinary journal. La revue veterinaire canadienne》1983,24(8):239-242
Fifteen mated bitches were used to study the effects of prostaglandin F2α on ovarian endocrine function during the early and midluteal phase. Five dogs were kept as controls, five were given 250 μg/kg prostaglandin F2α twice daily between the first and fifth day of metestrus, and five were similarly treated with prostaglandin F2α between 31 and 35 days of metestrus. Function of corpora lutea was monitored by measuring serum progesterone concentrations during the first 45 days of gestation.
Dogs treated with prostaglandin F2α during the early luteal phase had progesterone concentrations similar to controls and pregnancies were undisturbed in both groups. A dramatic decrease in serum progesterone concentration and abortion resulted after prostaglandin F2α administration at midpregnancy.
These results indicate that prostaglandin F2α was not luteolytic during the early luteal phase and was therefore ineffective for preventing pregnancy at that time. However, at the dosage and frequency used in this study, prostaglandin F2α was luteolytic and abortifacient at midgestation.
相似文献10.
通过对比不同尾椎数的蒙古绵羊群体在基因组上的遗传分化水平,对全基因组选择信号、蒙古羊尾长性状的相关基因及可能的突变位点进行检测,试图解析尾椎形成的分子机制。基于全基因组重测序数据,使用两组群间的遗传分化系数(Fst)和遗传多样性比率(pi ratio)检测尾椎选择信号,将Fst值和pi ratio较大的染色体区段作为受选择候选区域。结果表明,共找到76个选择区域,这些区域分别落在了尾脂肪沉积和骨骼发育的QTL上,进一步对这些候选区域所包含的63个基因进行基因功能及通路的注释分析,富集到骨骼再生相关的Wnt和FGF信号通路,同时发现LRP6等功能候选基因。该研究确定了与尾椎数相关的受选择区域,推测不同尾椎数蒙古绵羊群体的形成可能由非基因编码区域的一个或者多个突变造成。 相似文献
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Camila Tangari Meira MD Rogério Abdallah Curi Josineudson Augusto II Vasconcelos Silva Marcio José Monteiro CorrêaMarcilio Dias Silveira da Mota PhD 《Journal of Equine Veterinary Science》2013
To investigate morphological and genomic differences between cutting and racing lines of Quarter Horses, 120 racing and 68 cutting animals of both sexes, registered at the Brazilian Association of Quarter Horse Breeders, were used. Blood samples were collected, and the following physical traits were measured: weight; height at withers; body length; length of the shank, pastern, rump, head, and neck; and chest, shank, and hoof circumference. For analysis of genomic differences, 54,602 single-nucleotide polymorphisms (SNPs) were genotyped using the Equine SNP50 BeadChip, and the quality of individual and SNP genotype data were evaluated. The fixation index, FST, was used to identify genome regions that were altered in the lines by selection. The results showed significant differences between the lines in all physical traits. Quality control led to the exclusion of four cutting animals with a call rate of <0.95. After filtering, 12,544, 13,815, and 13,370 SNPs were excluded for the whole population (n = 184), the 120 racing animals, and the 64 cutting animals, respectively. The number of informative polymorphisms detected in each line and in the whole population indicated that the Equine SNP50 BeadChip can be used in genetic studies of Quarter Horses. The fixation index, FST, identified 2,558 genome regions that may have been modified by divergent selection. 相似文献
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Aurino de Araújo Rego Neto José Lindenberg Rocha Sarmento Natanael Pereira da Silva Santos José Elivalto Guimarães Campelo Luciano Silva Sena Daniel Biagiotti Gleyson Vieira dos Santos 《Tropical animal health and production》2018,50(3):503-508
This study aimed to describe the population genetic structure and evaluate the state of conservation of the genetic variability of Santa Inês sheep in Brazil. We used pedigree data of the Santa Inês breed available in electronic processing of the Brazilian Association of Sheep Breeders. A file with 20,206 records, which enabled the calculation of the genetic conservation index (GCI), individual inbreeding coefficient (F), change in inbreeding (ΔF), effective population size (Ne), effective number of founders (?e), effective number of ancestors (?ɑ), generation interval (L), average relatedness coefficient of each individual (AR), and Wright’s F-statistics (F IT, F IS, and F ST). For pedigree analysis and calculation of population parameters, the program ENDOG was used. The average inbreeding coefficient (\( \overline{F} \)) was 0.97% and the mean average relatedness (\( \overline{\mathrm{AR}} \)) 0.49%. The effective numbers of founders and ancestors were, respectively, 199 and 161. The average values of F and AR increased significantly over the years. The effective population size fluctuated over the years concurrently to oscillations in inbreeding rates, wherein N e reached just 68 in the year 2012. The mean average generation interval was 5.3 years. The Santa Inês breed in Brazil is under genetic drift process, with loss of genetic variation. It requires the implementation of a genetic management plan in the herd, for conservation and improvement of the breed. 相似文献
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Fuki Kawaguchi Hiroto Kigoshi Moriyuki Fukushima Eiji Iwamoto Eiji Kobayashi Kenji Oyama Hideyuki Mannen Shinji Sasazaki 《Animal Science Journal》2019,90(4):467-472
In our previous study, we detected a QTL for the oleic acid percentage (C18:1) on BTA9 in Japanese Black cattle through a genome‐wide association study (GWAS). In this study, we performed whole‐genome resequencing on eight animals with higher and lower C18:1 to identify candidate polymorphisms for the QTL. A total of 39,658 polymorphisms were detected in the candidate region, which were narrowed to 1993 polymorphisms within 23 genes based on allele differences between the high and low C18:1 groups. We subsequently selected three candidate genes, that is, CYB5R4, MED23, and VNN1, among the 23 genes based on their function in fatty acid metabolism. In each candidate gene, three SNPs, that is, CYB5R4 c.*349G > T, MED23 c.3700G > A, and VNN1 c.197C > T, were selected as candidate SNPs to verify their effect on C18:1 in a Japanese Black cattle population (n = 889). The statistical analysis showed that these SNPs were significantly associated with C18:1 (p < 0.05), suggesting that they were candidates for the QTL. In conclusion, we successfully narrowed the candidates for the QTL by detecting possible polymorphisms located within the candidate region. It is expected that the responsible polymorphism can be identified by demonstrating their effect on the gene's function. 相似文献
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Seung-Won YI Tae-Ho CHUNG Seong-Joon JOH Chul PARK Byoung-Yong PARK Gee-Wook SHIN 《The Journal of veterinary medical science / the Japanese Society of Veterinary Science》2014,76(12):1589-1593
The prevalence of resistant
genes against β-lactams in 119 Aeromonas strains was determined. A large
number (99.2%) of the present fish strains were resistant to one or more β- lactams
including ceftiofur, amoxicillin-clavulanic acid, ampicillin, piperacillin and
cefpodoxime. Among antibiotic resistance phenotypes, the simultaneous resistance to all
β-lactams occurred in 25.2% (n=30) of all strains, which consisted of 18 strains of
A. dhakensis, 8 strains of A. caviae, 2 strains of
A. hydrophila and only one strain of A. veronii. For
exploring genetic background of the antibiotic resistances, multiple PCR assays were
subjected to detect β-lactamase-encoding genes, blaTEM,
blaOXA-B and blaCTX-M. In the
results, the blaTEM-1 gene was harbored in all strains,
whereas only 3 strains harbored blaOXA gene. In the case of
blaCTX-M gene, the gene was detected in 21.0% (25 out of
119) of all strains, which countered with 80% (20 out of 25) of A.
dhakensis, 8% (2 out of 25) of A. caviae and 12% (3 out of 25)
of A. hydrophila. In addition, most of the
blaCTX-M positive strains showed simultaneous resistance to
all β-lactams (18 out of 30 strains). In sequence analysis for
blaCTX-M genes detected, they were CTX-M group 1-encoding
genes including blaCTX-M-33 from 3 eel strains of A.
dhakensis. Therefore, A. dhakensis obtained from cultured fish
could represent a reservoir for spreading genes encoding CTX-M group 1 enzymes and hence
should be carefully monitored, especially for its potential risk to public health. 相似文献
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L. Varona L. Gómez-Raya W.M. Rauw C. Ovilo A. Clop & J.L. Noguera 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2005,122(1):37-48
A Bayesian procedure is presented for detecting quantitative trait loci (QTL) affecting longitudinal traits. The statistical model assumes a QTL affecting the prior distribution of the parameters of a given production function, under a hierarchical Bayesian scheme. Marginal posterior distributions for the effects associated with the QTL are calculated using Markov chain Monte Carlo methods. Furthermore, the Bayesian analysis allows the use of some available relevant information that can improve the detection of the QTL substantially. To illustrate the procedure, an example of QTL detection using the Von Bertalanffy growth function is presented with a F2 pig population bred from Iberian boars and Landrace sows. Animals of the F2 population were genotyped for seven markers in chromosome 2 (SSC2). Two prior distributions for the mean effect of the parameters related with birth and adult weight were compared. On the one hand, vague prior distributions were used, and, on the other, there were assumed univariate Gaussian distributions that ensure biologically meaningful adult and birth weights on the posterior growth curves. Results from the second prior distribution supported the presence of QTL, by showing that individuals with both alleles of Iberian origin had lower rates of maturation. On the contrary, when vague priors were used, the procedure was not able to detect QTL. 相似文献
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Min Zhang Dan Zheng Zhimei Peng Yuting Zhu Rongrong Li Qiong Wu Yan Li Hongyi Li Weihua Xu Mao Zhang Qichun Hung Yanfa Sun 《The Journal of Poultry Science》2021,58(2):131
In this study, signaling pathways and key differentially expressed genes (DEGs) involved in lipid metabolism in muscle and fat tissues were investigated. Muscle and abdominal fat tissues were obtained from 35-day-old female broilers for RNA sequencing. DEGs between muscle and fat tissues were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of DEGs were performed. A total of 6130 DEGs were identified to be significantly enriched in 365 GO terms, most of which were involved in biological processes, cellular components, and molecular functions in muscle and fat tissues. Three important lipid signaling pathways (pyruvate metabolism, the insulin signaling pathway, and the adipocytokine signaling pathway) were identified among the fat and muscle tissues of broilers. The key common DEGs in these pathways included phosphoenolpyruvate carboxykinase 2 (PCK2), acetyl-CoA carboxylase 1 alpha and beta (ACACA and ACACB), and the mitogen-activated protein kinase (AMPK) gene family. Hence, our findings revealed the pathways and key genes and gene families involved in the regulation of fat deposition in the muscle and fat tissues of broilers. 相似文献