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1.
BMC Evol Biol ; 19(1): 199, 2019 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-31684869

RESUMO

BACKGROUND: Secondary contact between closely related lineages can result in a variety of outcomes, including hybridization, depending upon the strength of reproductive barriers. By examining the extent to which different parts of the genome introgress, it is possible to infer the strength of selection and gain insight into the evolutionary trajectory of lineages. Following secondary contact approximately 8000 years ago in the Pacific Northwest, mule deer (Odocoileus hemionus hemionus) and black-tailed deer (O. h. columbianus) formed a hybrid swarm along the Cascade mountain range despite substantial differences in body size (up to two times) and habitat preference. In this study, we examined genetic population structure, extent of introgression, and selection pressures in freely interbreeding populations of mule deer and black-tailed deer using mitochondrial DNA sequences, 9 microsatellite loci, and 95 SNPs from protein-coding genes. RESULTS: We observed bi-directional hybridization and classified approximately one third of the 172 individuals as hybrids, almost all of which were beyond the F1 generation. High genetic differentiation between black-tailed deer and mule deer at protein-coding genes suggests that there is positive divergent selection, though selection on these loci is relatively weak. Contrary to predictions, there was not greater selection on protein-coding genes thought to be associated with immune function and mate choice. Geographic cline analyses were consistent across genetic markers, suggesting long-term stability (over hundreds of generations), and indicated that the center of the hybrid swarm is 20-30 km to the east of the Cascades ridgeline, where there is a steep ecological transition from wet, forested habitat to dry, scrub habitat. CONCLUSIONS: Our data are consistent with a genetic boundary between mule deer and black-tailed deer that is porous but maintained by many loci under weak selection having a substantial cumulative effect. The absence of clear reproductive barriers and the consistent centering of geographic clines at a sharp ecotone suggests that ecology is a driver of hybrid swarm dynamics. Adaptive introgression in this study (and others) promotes gene flow and provides valuable insight into selection strength on specific genes and the evolutionary trajectory of hybridizing taxa.


Assuntos
Cervos/classificação , Cervos/genética , Hibridização Genética , Animais , Evolução Biológica , DNA Mitocondrial/genética , Ecologia , Éxons , Feminino , Fluxo Gênico , Marcadores Genéticos , Genética Populacional , Masculino , Repetições de Microssatélites , Noroeste dos Estados Unidos , Polimorfismo de Nucleotídeo Único , Seleção Genética
2.
Cell Mol Biol Lett ; 24: 44, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31285745

RESUMO

Background: Deer antler is the only mammalian organ that can be completely regenerated every year. Its periodic regeneration is regulated by multiple factors, including transforming growth factor ß (TGF-ß). This widely distributed multi-functional growth factor can control the proliferation and differentiation of many types of cell, and it may play a crucial regulatory role in antler regeneration. This study explored the role of TGF-ß1 during the rapid growth of sika deer antler. Methods: Three CRISPR-Cas9 knockout vectors targeting the TGF-ß1 gene of sika deer were constructed and packaged with a lentiviral system. The expression level of TGF-ß1 protein in the knockout cell line was determined using western blot, the proliferation and migration of cartilage cells in vitro were respectively determined using EdU and the cell scratch test, and the expression levels of TGF-ß pathway-related genes were determined using a PCR array. Results: Of the three gRNAs designed, pBOBI-gRNA2 had the best knockout effect. Knockout of TGF-ß1 gene inhibits the proliferation of cartilage cells and enhances their migration in vitro. TGF-ß signaling pathway-related genes undergo significant changes, so we speculate that when the TGF-ß pathway is blocked, the BMP signaling pathway mediated by BMP4 may play a key role. Conclusions: TGF-ß1 is a newly identified regulatory factor of rapid growth in sika deer antler.


Assuntos
Cartilagem/metabolismo , Proliferação de Células , Cervos/metabolismo , Transdução de Sinais , Fator de Crescimento Transformador beta1/metabolismo , Animais , Animais Geneticamente Modificados , Chifres de Veado , Sistemas CRISPR-Cas , Cartilagem/fisiologia , Linhagem Celular , Cervos/genética , Cervos/fisiologia , Regulação da Expressão Gênica , Técnicas de Inativação de Genes , Masculino , Fator de Crescimento Transformador beta1/genética , Fator de Crescimento Transformador beta1/fisiologia
3.
PLoS One ; 14(7): e0219184, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31276519

RESUMO

Cervids are known to be reservoirs of zoonotic bacteria transmitted by ticks. This study aimed to identify the Anaplasma species carried by captive red deer and swamp deer in a wild fauna reserve in France. Blood from 59 red deer and 7 swamp deer was collected and analyzed over a period of two years. A semi-nested PCR targeting the 23S rRNA was performed to detect and characterize Anaplasma spp. and determine the presence of zoonotic species. Anaplasma phagocytophilum was identified in 14/59 red deer (23.7%) but it was not identified in any of the swamp deer (7 animals). Three sequences could not be assigned to any particular species based on the 23S rRNA sequences. Complementary nested PCR targeting 16S rRNA, gltA and groEL genes and sequencing analysis then identified these sequences as a recently reported zoonotic species, Anaplasma capra; this species was found in 2 red deer (Cervus elaphus) and 1 swamp deer (Rucervus duvaucelii). This is the first report of the tick-borne zoonotic bacterium A. capra in France, a species otherwise described only in China, Japan, Malaysia and South Korea in goats, sheep, deer, cattle and Japanese serows (Capricornis crispus). While this bacterium may have been introduced into the reserve by infected imported animals, its local epidemiological cycle via tick transmission seems possible as locally born deer were found infected. Diagnostic methods, especially molecular ones, should take into account the potential infection of animals and humans with this species.


Assuntos
Anaplasma/genética , Anaplasma/isolamento & purificação , Anaplasma/classificação , Anaplasma/patogenicidade , Anaplasma phagocytophilum/genética , Anaplasmose/microbiologia , Animais , Cervos/genética , Cervos/parasitologia , Reservatórios de Doenças/microbiologia , França , Filogenia , Ruminantes/genética , Zoonoses/genética
4.
Biomed Res Int ; 2019: 4370704, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31214615

RESUMO

The Chinese forest musk deer (Moschus berezovskii) is an economically important species distributed throughout southwest China and northern Vietnam. Occurrence and development of disease are aggravated by inbreeding and genetic diversity declines in captive musk deer populations. Deep transcriptomics investigation may provide a promising way to improve genetic health of captive and wild FMD population. MicroRNAs (miRNAs), which regulate gene expression by targeting and suppressing of mRNAs, play an important role in physiology and organism development control. In this study, RNA-seq technology was adopted to characterize the miRNA transcriptome signature among six tissues (heart, liver, spleen, lung, kidney, and muscle) in Chinese forest musk deer at two years of age. Deep sequencing generated a total of 103,261,451 (~87.87%) good quality small RNA reads; of them 6,622,520 were unique across all six tissues. A total of 2890 miRNAs were identified, among them 1129 were found to be expressed in all tissues. Moreover, coexpression of 20 miRNAs (>2000RPM) in all six tissues and top five highly expressed miRNAs in each tissue implied the crucial and particular function of them in FMD physiological processes. Our findings of forest musk deer miRNAs supplement the database of transcriptome information for this species and conduce to our understanding of forest musk deer biology.


Assuntos
Cervos , Regulação da Expressão Gênica/fisiologia , MicroRNAs , Animais , China , Cervos/genética , Cervos/metabolismo , Perfilação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , MicroRNAs/biossíntese , MicroRNAs/genética , Especificidade de Órgãos/fisiologia
5.
J Genet ; 98(2)2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31204725

RESUMO

Burgeoning pressures of habitat loss is a major cause of herbivore decline across India, forcing them to coexist with humans in non-protected areas. Their conservation in such landscapes is challenging due to paucity of ecological and demographic information. The northern subspecies of swamp deer, Rucervus duvaucelii duvaucelii, is one such herbivore that lives across human dominated landscapes in Terai region and upper Gangetic plains of north India. Here, we describe species-specific molecular markers and a cervid-specific molecular sexing assay for swamp deer and four other coexisting cervids sambar, chital, barking deer and hog deer. Our markers show species-specific band patterns and a high success rate of 88.21% in large number of field collected referencesamples for all species. Faecal pellets from pilot swamp deer survey samples from upper Ganges basin show 93.81% success rate, and only 5.5% misidentification based on morphological characteristics. Our cervid-specific molecular sexing multiplex assay accurately ascertained 81.15% samples to respective sexes. These molecular approaches provide an easy, quick and cheap option to generate critical information on herbivore population parameters and aid their conservation in this mosaic of protected and non-protected grassland habitats.


Assuntos
Cervos/classificação , Cervos/genética , Ecossistema , Genética Populacional , Animais , Feminino , Geografia , Humanos , Índia , Masculino , Tipagem Molecular , Reação em Cadeia da Polimerase , Dinâmica Populacional , Especificidade da Espécie
6.
DNA Cell Biol ; 38(7): 670-677, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31188027

RESUMO

Cutis laxa represents a heterogeneous group of rare, inherited, or acquired connective tissue disorders with the common feature of loose and redundant skin with decreased elasticity. The skin of affected deer showed abnormal collagen fiber morphology. To identify the differentially expressed genes of the unusual localized skin laxity in sika deer, we performed transcriptome analysis in the affected and control sika deer. The transcriptome analysis showed 700 genes with significant differential expression in the affected skin as compared with normal skin. Pathway analysis revealed an enrichment of genes involved in tumor necrosis factor signaling, the extracellular matrix-receptor interaction, platelet activation, and Huntington's disease. A gene network was constructed, and the hub nodes such as PTGS2, THBS1, COL1A1, FOS, and NOS3 were found through PPI network analysis, which may contributed to the unusual localized skin laxity in sika deer. Abnormal expression patterns of genes during the development of the affected sika deer were successfully uncovered in the present study, which provides a reference for revealing the related mechanism underlying cutis laxa in sika deer and human beings.


Assuntos
Cútis Laxa/veterinária , Cervos/genética , Transcriptoma , Animais , Colágeno/genética , Colágeno/metabolismo , Cútis Laxa/genética , Ciclo-Oxigenase 2/genética , Ciclo-Oxigenase 2/metabolismo , Redes Reguladoras de Genes , Óxido Nítrico Sintase Tipo III/genética , Óxido Nítrico Sintase Tipo III/metabolismo , Proteínas Proto-Oncogênicas c-fos/genética , Proteínas Proto-Oncogênicas c-fos/metabolismo , Trombospondina 1/genética , Trombospondina 1/metabolismo
7.
BMC Genet ; 20(1): 49, 2019 06 06.
Artigo em Inglês | MEDLINE | ID: mdl-31170908

RESUMO

BACKGROUND: Microsatellite loci have been used extensively over the past two decades to study the genetic characteristics of non-model species. The ease of microsatellite development and ability to adapt markers from related species has led to the proliferation of available markers for many commonly studied species. Because it is often infeasible to genotype individuals across all available loci, researchers generally rely on subsets of markers. Marker choice can bias inferences made using disparate suites of loci. This has been a primary motivation for efforts to identify uniform marker panels. Here, we use the geographic distribution of previous studies to identify microsatellite loci for white-tailed deer (Odocoileus virginianus) with the potential for widespread use, and we evaluate the effectiveness of this panel in a portion of the range where few previous studies have been conducted. The purpose was to consolidate the numerous genetic resources for this species into a manageable panel and to provide a uniform methodology that improves comparisons between past and future studies. RESULTS: We reviewed microsatellite panels from 58 previous or ongoing projects and identified 106 candidate loci. We developed a multiplex protocol and evaluated the efficacy of 17 of the most commonly used loci using 720 DNA samples collected from the Mid-Atlantic region of the United States of America. Amplification errors were detected in six of these loci. The 11 remaining loci were highly polymorphic, exhibited low frequencies of null alleles, and were easy to interpret with the aid of allele binning software. CONCLUSIONS: The development of broadly-applicable, core microsatellite panels has the potential to improve repeatability and comparative ability for commonly studied species. The properties of the consolidated 11 microsatellite panel suggest that they are applicable for many common research objectives for white-tailed deer. The geographic distribution of previous studies using these markers provides a greater degree of confidence regarding the robustness to common sources of error related to amplification anomalies, such as null alleles, relative to loci with more limited use. While this does not replace further evaluation of genotyping errors, it does provide a common platform that benefits future research studies.


Assuntos
Cervos/genética , Evolução Molecular , Repetições de Microssatélites , Alelos , Animais , Variação Genética , Genótipo , Locos de Características Quantitativas , Estados Unidos
8.
Food Chem ; 295: 395-402, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31174774

RESUMO

A simple and rapid method for animal species identification to prevent food adulteration based on mitochondrial DNA using two independent multiplex polymerase chain reactions (PCRs) and microchip electrophoresis was developed. This method was designed to identify fourteen domestic animals (Group I: cattle, donkey, dog, fox, raccoon-dog, deer and horse; Group II: pig, sheep, goat, chicken, duck, cat and mouse) simultaneously using ten pairs of primers and three of which were degenerate primers. Sequences for species-specific primers were generated based on mitochondrial genes, including 12S rRNA, 16S rRNA, ND2 and CO I. This method was validated in terms of the specificity, sensitivity and practicability, and the developed multiplex PCR method was able to correctly identify animal species of raw meats and processed meat products. The detection limits of two multiplex PCRs were 0.02 ng DNA for animal species in Group I and 0.2 ng DNA for Group II, respectively.


Assuntos
Análise de Alimentos/métodos , Contaminação de Alimentos/análise , Carne/análise , Reação em Cadeia da Polimerase Multiplex/métodos , Animais , Bovinos/genética , Galinhas/genética , Primers do DNA , DNA Mitocondrial/genética , Cervos/genética , Patos/genética , Equidae/genética , Análise de Alimentos/instrumentação , Genes Mitocondriais , Cabras/genética , Cavalos/genética , Camundongos/genética , Reação em Cadeia da Polimerase Multiplex/instrumentação , RNA Ribossômico , RNA Ribossômico 16S , Ovinos/genética , Especificidade da Espécie , Suínos/genética
9.
BMC Genomics ; 20(1): 384, 2019 May 17.
Artigo em Inglês | MEDLINE | ID: mdl-31101010

RESUMO

BACKGROUND: Previous investigations of phylogeny in Cervus recovered many clades without whole genomic support. METHODS: In this study, the genetic diversity and phylogeny of 5 species (21 subspecies/populations from C. unicolor, C. albirostris, C. nippon, C. elaphus and C. eldii) in the genus Cervus were analyzed using reduced-representation genome sequencing. RESULTS: A total of 197,543 SNPs were identified with an average sequencing depth of 16 x. A total of 21 SNP matrices for each subspecies/population and 1 matrix for individual analysis were constructed, respectively. Nucleotide diversity and heterozygosity analysis showed that all 21 subspecies/populations had different degrees of genetic diversity. C. eldii, C. unicolor and C. albirostris showed relatively high expected and observed heterozygosity, while observed heterozygosity in C. nippon was the lowest, indicating there was a certain degree of inbreeding rate in these subspecies/populations. Phylogenetic ML tree of all Cervus based on the 21 SNP matrices showed 5 robustly supported clades that clearly separate C. eldii, C. unicolor, C. albirostris, C. elaphus and C. nippon. Within C. elaphus clade, 4 subclades were well differentiated and statistically highly supported: C. elaphus (New Zealand), C. e. yarkandensis, C. c. canadensis and the other grouping the rest of C. canadensis from China. In the C. nippon clade, 2 well-distinct subclades corresponding to C. n. aplodontus and other C. nippon populations were separated. Phylogenetic reconstruction indicated that the first evolutionary event of the genus Cervus occurred approximately 7.4 millions of years ago. The split between C. elaphus and C. nippon could be estimated at around 3.6 millions of years ago. Phylogenetic ML tree of all samples based on individual SNP matrices, together with geographic distribution, have shown that there were 3 major subclades of C. elaphus and C. canadensis in China, namely C. e. yarkandensis (distributed in Tarim Basin), C. c. macneilli/C. c. kansuensis/C. c. alashanicus (distributed in middle west of China), and C. c. songaricus/C. c. sibiricus (distributed in northwest of China). Among them, C. e. yarkandensis was molecularly the most primitive subclade, with a differentiation dating back to 0.8-2.2 Myr ago. D statistical analysis showed that there was high probability of interspecific gene exchange between C. albirostris and C. eldii, C. albirostris and C. unicolor, C. nippon and C. unicolor, and there might be 2 migration events among 5 species in the genus Cervus. CONCLUSIONS: Our results provided new insight to the genetic diversity and phylogeny of Cervus deer. In view of the current status of these populations, their conservation category will need to be reassessed.


Assuntos
Cervos/classificação , Cervos/genética , Variação Genética , Estudo de Associação Genômica Ampla , Genoma , Genômica/métodos , Filogenia , Animais , Evolução Biológica , Sequenciamento de Nucleotídeos em Larga Escala
10.
Anim Genet ; 50(4): 358-366, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31106883

RESUMO

Olfactory receptors (ORs) are encoded by OR genes. The OR genes in forest musk deer (Moschus berezovskii), which rely on olfaction for reproductive and social communication, are poorly understood. In this study, we analyzed the genome sequence of the forest musk deer to obtain its olfactory subgenome and compared it to other species. A total of 1378 OR-related sequences were detected in the forest musk deer genome including 864 functional genes, 366 pseudogenes and 148 partial genes. These OR genes were classified into Class I and Class II and were further classified into 18 families and 244 subfamilies through sequence identity. Comparative analyses of the OR genes' protein sequences in species from different orders (forest musk deer, human, mouse and dog) showed that 12 clusters were specific to forest musk deer. However, when compared to other Artiodactyl species (i.e. cattle, yak and pig) only two clusters were specific to forest musk deer. The odor identification potential of the OR genes in the forest musk deer was focused mainly on floral, woody, lemon, sweet and fatty odors. We also found that OR genes specific to forest musk deer were involved in the identification of spearmint and caraway. Our work is the first genome-wide analysis of OR genes in forest musk deer. These findings will assist with better understanding the relationship between behavior and olfaction in the forest musk deer and the characteristics of the olfactory subgenome in Artiodactyl mammals.


Assuntos
Cervos/genética , Receptores Odorantes/genética , Animais , Humanos , Masculino , Odorantes , Filogenia
11.
Zoolog Sci ; 36(2): 128-135, 2019 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-31120647

RESUMO

Rapid expansion of sika deer, in both number and distribution, in the Japanese Archipelago has resulted in serious ecological disturbance. In the present study, the population structure and migration patterns of sika deer (Cervus nippon) among Toyama and adjacent Prefectures were investigated using 11 polymorphic microsatellite loci. Deviation from Hardy-Weinberg equilibrium was detected in both total and individual regional sika deer samples from Toyama Prefecture. Results of pairwise FST results, factorial correspondence analysis, and STRUCTURE analysis indicated that sika deer in Toyama are not genetically distinct from those in adjacent Prefectures. Bayesian STRUCTURE results suggested the existence of two distinct clusters. However, multiple lines of genetic structure and high admixture were detected across the populations located in the central region of Toyama Prefecture. Both contemporary and historical migration analyses showed that dispersal into Toyama Prefecture from neighboring prefectures was high, especially migration from the prefecture on the east into Toyama Prefecture, and bidirectional dispersion between Toyama Prefecture and the prefecture to the south. Knowledge of such genetic structures and population dynamics is required for appropriate management and conservation of sika deer populations in the Japanese Archipelago.


Assuntos
Migração Animal , Cervos/genética , Dinâmica Populacional , Animais , Teorema de Bayes , Cervos/fisiologia , Feminino , Variação Genética , Japão , Masculino , Repetições de Microssatélites
12.
Mol Ecol Resour ; 19(5): 1205-1217, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31058463

RESUMO

Estimating the evolutionary potential of quantitative traits and reliably predicting responses to selection in wild populations are important challenges in evolutionary biology. The genomic revolution has opened up opportunities for measuring relatedness among individuals with precision, enabling pedigree-free estimation of trait heritabilities in wild populations. However, until now, most quantitative genetic studies based on a genomic relatedness matrix (GRM) have focused on long-term monitored populations for which traditional pedigrees were also available, and have often had access to knowledge of genome sequence and variability. Here, we investigated the potential of RAD-sequencing for estimating heritability in a free-ranging roe deer (Capreolous capreolus) population for which no prior genomic resources were available. We propose a step-by-step analytical framework to optimize the quality and quantity of the genomic data and explore the impact of the single nucleotide polymorphism (SNP) calling and filtering processes on the GRM structure and GRM-based heritability estimates. As expected, our results show that sequence coverage strongly affects the number of recovered loci, the genotyping error rate and the amount of missing data. Ultimately, this had little effect on heritability estimates and their standard errors, provided that the GRM was built from a minimum number of loci (above 7,000). Genomic relatedness matrix-based heritability estimates thus appear robust to a moderate level of genotyping errors in the SNP data set. We also showed that quality filters, such as the removal of low-frequency variants, affect the relatedness structure of the GRM, generating lower h2 estimates. Our work illustrates the huge potential of RAD-sequencing for estimating GRM-based heritability in virtually any natural population.


Assuntos
Cervos/classificação , Cervos/genética , Genética Populacional/métodos , Técnicas de Genotipagem/métodos , Linhagem , Análise de Sequência de DNA/métodos , Animais , Genótipo , Polimorfismo de Nucleotídeo Único , Característica Quantitativa Herdável
13.
Anim Genet ; 50(3): 307-310, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30957265

RESUMO

Gender assignment errors are common in some animal species and lead to inaccuracies in downstream analyses. Procedures for detecting gender misassignment are available for array-based SNP data but are still being developed for genotyping-by-sequencing (GBS) data. In this study, we describe a method for using GBS data to predict gender using X and Y chromosomal SNPs. From a set of 1286 X chromosomal and 23 Y chromosomal deer (Cervus sp.) SNPs discovered from GBS sequence reads, a prediction model was built using a training dataset of 422 Red deer and validated using a test dataset of 868 Red deer and Wapiti deer. Prediction was based on the proportion of heterozygous genotypes on the X chromosome and the proportion of non-missing genotypes on the Y chromosome observed in each individual. The concordance between recorded gender and predicted gender was 98.6% in the training dataset and 99.3% in the test dataset. The model identified five individuals across both datasets with incorrect recorded gender and was unable to predict gender for another five individuals. Overall, our method predicted gender with a high degree of accuracy and could be used for quality control in gender assignment datasets or for assigning gender when unrecorded, provided a suitable reference genome is available.


Assuntos
Cervos/genética , Análise para Determinação do Sexo , Animais , Cervos/fisiologia , Feminino , Masculino , Polimorfismo de Nucleotídeo Único , Cromossomo X , Cromossomo Y
14.
BMC Genomics ; 20(1): 173, 2019 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-30836939

RESUMO

BACKGROUND: With the unprecedented rapid growth rate (up to 2.75 cm/day), velvet antler is an invaluable model for the identification of potent growth factors and signaling networks for extremely fast growing tissues, mainly cartilage. Antler growth center (AGC) locates in its tip and consists of five tissue layers: reserve mesenchyme (RM), precartilage (PC), transition zone (TZ), cartilage (CA) and mineralized cartilage (MC). The aim of this study was to investigate the transcription dynamics in the AGC using RNA-seq technology. RESULTS: Five tissue layers in the AGC were collected from three 3-year-old male sika deer using our previously reported sampling method (morphologically distinguishable). After sequencing (15 samples; triplicates/tissue layer), we assembled a reference transcriptome de novo and used RNA-seq to measure gene expression profiles across these five layers. Nine differentially expressed genes (DEGs) were selected from our data and subsequently verified using qRT-PCR. The results showed a high consistency with the RNA-seq results (R2 = 0.80). Nine modules were constructed based on co-expression network analysis, and these modules contained 370 hub genes. These genes were found to be mainly involved in mesenchymal progenitor cell proliferation, chondrogenesis, osteogenesis and angiogenesis. Combination of our own results with the previously published reports, we found that Wnt signaling likely plays a key role not only in stimulating the antler stem cells or their immediate progeny, but also in promoting chondrogenesis and osteogenesis during antler development. CONCLUSION: We have successfully assembled a reference transcriptome, generated gene expression profiling across the five tissue layers in the AGC, and identified nine co-expressed modules that contain 370 hub genes and genes predorminantly expressed in and highly relevant to each tissue layer. We believe our findings have laid the foundation for the identification of novel genes for rapid proliferation and chondrogenic differentiation of antler cells.


Assuntos
Diferenciação Celular/genética , Cervos/genética , Perfilação da Expressão Gênica , Transcriptoma/genética , Animais , Chifres de Veado/crescimento & desenvolvimento , Cartilagem/crescimento & desenvolvimento , Condrogênese/genética , Cervos/crescimento & desenvolvimento , Regulação da Expressão Gênica no Desenvolvimento/genética , Masculino , Especificidade de Órgãos/genética , Osteogênese/genética
15.
J Biosci ; 44(1)2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30837362

RESUMO

Antler growth is a unique event compared to other growth and development processes in mammals. Antlers grow extremely fast during the rapid growth stage when growth rate peaks at 2 cm per day. Antler growth is driven by a specific endochondral ossification process in the growth center that is in the distal region of the antler tip. In this study, we used state-of-art RNA-seq technology to analyze the expression profiles of mRNAs and miRNAs during antler growth. Our results indicated that the expression levels of multiple genes involved in chondrogenesis and endochondral ossification, including Fn1, Sox9, Col2a1, Acan, Col9a1, Col11a1, Hapln1, Wwp2, Fgfr3, Comp, Sp7 and Ihh, were significantly increased at the rapid growth stage. Our results also indicated that there were multiple differentially expressed miRNAs interacting with differentially expressed genes with opposite expression patterns. Furthermore, some of the miRNAs, including miR-3072-5p, miR-1600, miR-34-5p, miR-6889-5p and miR-6729-5p, simultaneously interacted with and controlled multiple genes involved in the process of chondrogenesis and endochondral ossification. Therefore, we established a miRNA-mRNA regulatory network by identifying miRNAs and their target genes that were differentially expressed in the antler growth centers by comparing the rapid growth stage and the initial growth stage.


Assuntos
Chifres de Veado/crescimento & desenvolvimento , Cervos/genética , MicroRNAs/genética , RNA Mensageiro/genética , Animais , Chifres de Veado/metabolismo , Condrogênese/genética , Cervos/crescimento & desenvolvimento , Regulação da Expressão Gênica no Desenvolvimento , Sequenciamento de Nucleotídeos em Larga Escala , Osteogênese/genética
16.
G3 (Bethesda) ; 9(4): 1037-1044, 2019 04 09.
Artigo em Inglês | MEDLINE | ID: mdl-30737238

RESUMO

Musk deer (Moschidae), whose secretion is an expensive and irreplaceable component of traditional medicine, have become endangered in the wild due to habitat fragmentation and over-exploitation. In recent years, China has had success in the artificial breeding of forest musk deer, thus relieving the pressure on wild populations. However, many farmed populations are experiencing degradation, and little genetic information is available for conservation management. In this study, we selected 274 individuals from three typical captive populations (originated from the Ta-pa Mountains (Tp), the midrange of the Qinling Mountains (Ql) and the Western Sichuan Plateau (WS), respectively) to evaluate the genetic variations. A total of more than 3.15 billion high-quality clean reads and 4.37 million high-quality SNPs were generated by RAD sequencing. Based on the analysis, we found that captive forest musk deer populations exhibit a relatively low level of genetic diversity. Ql displayed a higher level of genetic diversity than the Tp and WS populations. Tp and WS had experienced population bottlenecks in the past as inferred from the values of Tajima's D. There were high levels of heterozygote deficiency caused by inbreeding within the three populations. Population structure analysis suggested that the three populations have evolved independently, and a moderate amount of genetic differentiation has developed, although there was a low level of gene flow between the Ql and Tp populations. Furthermore, the average quantities of musk secreted by musk deer in the Tp and WS populations were significantly higher than that in the Ql population. The present genetic information should be considered in management plans for the conservation and utilization of musk deer from captive breeding.


Assuntos
Cruzamento/métodos , Cervos/genética , Variação Genética , Animais , China , Conservação dos Recursos Naturais , Filogenia , Polimorfismo de Nucleotídeo Único
17.
Prion ; 13(1): 65-76, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30777498

RESUMO

Genetic variability in the prion protein (Prnp) gene influences host susceptibility to many pathogenic prion diseases. Understanding the distribution of susceptible Prnp variants and determining factors influencing spatial genetic patterns are important components of many chronic wasting disease mitigation strategies. Here, we describe Prnp variability in white-tailed deer (Odocoileus virginianus) from the Mid-Atlantic region of the United States of America, an area with a recent history of infection and low disease incidence. This population is characterized by lower rates of polymorphism and significantly higher frequencies of the more susceptible 96GG genotype compared to previously surveyed populations. The prevalence of the most susceptible genotypes at disease-associated loci did vary among subregions, indicating that populations have innate differences in genotype-dictated susceptibility.


Assuntos
Cervos/genética , Polimorfismo Genético , Proteínas Priônicas/genética , Doença de Emaciação Crônica/genética , Animais , Predisposição Genética para Doença , Genótipo , Príons/genética
18.
Arq. bras. med. vet. zootec. (Online) ; 71(1): 77-85, jan.-fev. 2019. tab, graf
Artigo em Inglês | LILACS, VETINDEX | ID: biblio-989378

RESUMO

Epizootic hemorrhagic disease viruses (EHDV) are dsRNA arboviruses transmitted by biting midges of the genus Culicoides that cause disease in domestic and wild ruminants. Epizootic hemorrhagic disease (EHD) is considered the most important infectious disease of white tailed deer (WTD) in North America, some studies in Northeast Mexico reported EHDV-seropositive WTD and EHDV-infected Culicoides vectors. The increasing population of WTD that share habitat with livestock in Northeast México highlights the importance of EHD for the livestock industry in the transboundary region with the U.S. One hundred and twenty two samples from WTD in Tamaulipas state, Mexico were tested by ELISA and RT-PCR for EHDV antibodies and nucleic acid, respectively. Twelve animals were seropositive to ELISA and eleven animals were positive by RT-PCR. This is the first report of EHDV nucleic acid detection in WTD from Mexico. It is hypothesized that applying the transboundary disease approach to interdisciplinary research will help fill knowledge gaps, which could help develop countermeasures to mitigate the threat of EHDV infection in wildlife and livestock along the U.S.-Mexico border.(AU)


Virus da doença hemorrágica epizoótica (EHDV) são arbovírus dsRNA transmitidos por mordidas do genus Culicoides que causam doenças em ruminantes domésticos e selvagens. Doença hemorrágica epizoótica (EHD) é considerada uma das doenças infecciosas mais importantes dos veados de cauda branca (WTD) na América do Norte. Alguns estudos no Nordeste do México relatam soropositividade para EHDV em WTD e vetores Culicoides infectados com EHDV. A crescente população de WTD que compartilham hábitats com pecuária no Nordeste do México realçam a importância de EHD para a indústria pecuária na região de fronteira com os Estados Unidos. Cento e vinte duas amostras de WTD no estado de Tamaulipas, Mexico, foram testados por ELISA e RT-PCR para anticorpos e ácido nucleico de EHDV, respectivamente. Esse é o primeiro relato de detecção de ácido nucleico de EHDV em WTD do México. A hipótese é de que a aplicação de uma resposta transfronteira e pesquisa interdisciplinar ajudará a preencher lacunas de conhecimento levando a medidas reativas para mitigar a ameaça de infecção por EHDV na pecuária e animais selvagens na fronteira entre os Estados Unidos e o Mexico.(AU)


Assuntos
Animais , Cervos/genética , Testes Sorológicos/veterinária , Vírus da Doença Hemorrágica Epizoótica
19.
G3 (Bethesda) ; 9(3): 911-919, 2019 03 07.
Artigo em Inglês | MEDLINE | ID: mdl-30670611

RESUMO

Mule deer (Odocoileus hemionus) are endemic to a wide variety of habitats in western North America, many of which are shared in sympatry with their closely related sister-species white-tailed deer (Odocoileus virginianus), whom they hybridize with in wild populations. Although mule deer meet many ideal conditions for a molecular ecological research species, such as high abundance, ecological importance, and broad dispersal and gene flow, conservation genetic studies have been limited by a relative lack of existing genomic resources and inherent difficulties caused by introgression with white-tailed deer. Many molecular tools currently available for the study of cervids were designed using reference assemblies of divergent model species, specifically cattle (Bos taurus). Bovidae and Cervidae diverged approximately 28 million years ago, therefore, we sought to ameliorate the available resources by contributing the first mule deer whole genome sequence draft assembly with an average genome-wide read depth of 25X, using the white-tailed genome assembly (Ovir.te_1.0) as a reference. Comparing the two assemblies, we identified ∼33 million single nucleotide polymorphisms (SNPs) and insertion/deletion variants. We then verified fixed SNP differences between the two species and developed a 40-loci SNP assay capable of identifying pure mule deer, white-tailed deer, and interspecific hybrids. Assignment capacity of the panel, which was tested on simulated datasets, is reliable up to and including the third backcross hybrid generation. Identification of post-F1 hybrids will be necessary for hybrid zone population studies going forward, and the new mule deer assembly will be a valuable resource for genetic and comparative genomics studies.


Assuntos
Cervos/genética , Genoma , Polimorfismo de Nucleotídeo Único , Sequenciamento Completo do Genoma , Animais , Bovinos/genética , Núcleo Celular/genética , Genômica
20.
Sci Data ; 6: 180305, 2019 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-30620341

RESUMO

Hog deer (Axis porcinus) is a small deer species in family Cervidae and has been undergoing a serious and global decline during the past decades. Chengdu Zoo currently holds a captive population of hog deer with sufficient genetic diversity in China. We sequenced and de novo assembled its genome sequence in the present study. A total of six different insert-size libraries were sequenced and generated 395 Gb of clean data in total. With aid of the linked reads of 10X Genomics, genome sequence was assembled to 2.72 Gb in length (contig N50, 66.04 Kb; scaffold N50, 20.55 Mb), in which 94.5% of expected genes were detected. We comprehensively annotated 22,473 protein-coding genes, 37,019 tRNAs, and 1,058 Mb repeated sequences. The newly generated reference genome is expected to significantly contribute to comparative analysis of genome biology and evolution within family Cervidae.


Assuntos
Cervos/genética , Genoma , Animais , China , Anotação de Sequência Molecular , Análise de Sequência de DNA
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