Subfamily Caprinae Research Articles

The complete mitochondrial genome sequence of the dwarf blue sheep, Pseudois schaeferi haltenorth in China

The dwarf blue sheep (Pseudois schaeferi haltenorth) belongs the subfamily Caprinae, which is distributed in Sichuan, Tibet, Yunnan, and Qinghai in China. In this study, the complete mitochondrial genome of Pseudois schaeferi haltenorth was sequenced. The mitogenome was 16 741 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding control region (D-loop region). As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the Pseudois schaeferi haltenorth is 33.54% A, 26.37% T, 26.91% C, and 13.18% G, A + T (59.91%) was higher than G + C (40.09%). The phylogenetic relationships was analyzed using the complete mitogenome sequence, results show that P. schaeferi haltenorth should be a different species differ from the Genus pseudois hodgson. These information provide useful data for further study on the protection of genetic resources and the taxonomy of Caprinae.

Complete mitochondrial genome of red goral (Naemorhedus baileyi) and a complete estimate of the phylogenetic relationships in Caprinae

Naemorhedus baileyi belongs to the genera Naemorhedus within the subfamily Caprinae. Because of small population, narrow distribution and difficult sampling, the taxonomic status of red goral in Caprinae is still not clear. We extracted the sample DNA and amplified whole mtDNA genome with different primers. We downloaded other gene sequences of Caprinae from GenBank. All sequences included 24 species of 11 genera. Phylogenetic analyses confirmed that the subfamily Caprinae is not monophyletic, bootstrap support for this cluster is high (100%).

Looking for adaptive footprints in the HSP90AA1 ovine gene

BackgroundClimatic factors play an important role in determining species distributions and phenotypic variation of populations over geographic space. Since domestic sheep is managed under low intensive systems animals could have retained some genome adaptive footprints. The gene encoding the Hsp90α has been extensively studied in sheep and some polymorphisms located at its promoter have been associates with differences in the transcription rate of the gene depending on climatic conditions. In this work the relationships among the distribution and frequencies of 11 polymorphisms of the ovine HSP90AA1 gene promoter in 31 sheep breeds and the climatic and geographic variables prevailing in their regions of origin have been studied. Also the promoter sequence has been characterized in 9 species of the Caprinae subfamily.ResultsCorrelations among several climatic variables and allele frequencies of the polymorphisms of the HSP90AA1 gene promoter linked with differences in the transcription activity of the gene under heat stress conditions have been assessed. A group of breeds reared in semi dry climates have high frequencies of the insertion allele of the g.667-668insC associated with the heat stress response. Other group of breeds native to semi arid conditions showed very low frequencies of this same allele. However, in some cases, this previous correlation has not been achieved, revealing the high levels of gene flow among populations occurred following domestication. The Bayesian Test of Beaumont and Balding identified two outlier loci, the g.522A > G and g.703_704del(2)A candidates to balancing and directional selection, respectively. Polymorphisms detected in O. aries are also present in several species of the Caprinae subfamily being C. hircus, O. musimon and O. moschatus those sharing the highest number of them with O. aries.ConclusionsDespite domestication, sheep breeds showed some genetic footprints related to climatic variables. Adaptation of breeds to heat climates can suppose a selective advantage to cope with global warming caused by climatic change. Polymorphisms of the HSP90AA1 gene detected in the Ovis aries species are also present in wild species from the Caprinae subfamily, indicating a great antiquity of these mutations and its importance in the adaptation of species to past climatic conditions existing in its native environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0280-x) contains supplementary material, which is available to authorized users.

Characterization of buffalo interleukin 8 (IL-8) and its expression in endometritis.

River buffalo (Bubalus bubalis bubalis) with a population over 135 million heads is an important livestock. Interleukin 8 (IL-8) is a member of the chemokine family and is an important chemoattractant for neutrophils associated with a wide variety of inflammatory diseases such as endometritis. Tissue samples from the mammary gland, uterus and ovary were obtained from river buffalo (Mediterranean type) with and without endometritis. Bacteriological examination showed the presence of both gram positive and negative in all buffalo with endometritis. RNA extraction and complementary DNA (cDNA) synthesis were conducted from all tissues. Specific primer for IL8 full coding regions was designed using known cDNA sequences of Bubalus bubalis, Genbank accession number AY952930.1. IL-8 gene expression was investigated in buffalo tissues. Expression of IL-8 in buffalo with endometritis was found to increase significantly over buffalo without endometritis only in the uterus (P = 0.0159). PCR products from uterus tissues (target organs) of buffalo with and without endometritis, were purified and sequenced. No polymorphic sites were detected in the investigated samples. IL-8 cDNA nucleotide sequences of buffalo with and without endometritis were 100% identical (accession number JX413057). Buffalo IL8 cDNAs were compared with corresponding sequences of member of subfamily Bovinae (buffalo and cattle) and subfamily Caprinae (sheep and goat). IL-8 species specific differences were identified.

Complete mitochondrial genome sequence of the blue sheep, Pseudois nayaur szechuanensis (Cetartiodactyla: Caprinae)

The blue sheep (Pseudois nayaur szechuanensis) belongs to the subfamily Caprinae, which distributes in Sichuan, Gansu, Qinghai, southeastern Xinjiang, northern Yunnan and Ningxia-Inner Mongolia border, China. In this study, the complete mitochondrial genome of P. n. szechuanensis was sequenced. The mitogenome was 16,738 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the P. n. szechuanensis is 33.5% A, 26.4% T, 27.0% C, and 13.2% G. The alignment of the Pseudois species control regions exhibited high genetic variability and rich A + T content. The complete mitogenome of P. n. szechuanensis can provide an important data for the studies on phylogenetic relationship and population genetics to further explore the taxonomic status of this species.

The complete mitochondrial genome sequence of the blue sheep, Pseudois nayaur nayaur (Cetartiodactyla: Caprinae)

The blue sheep (Pseudois nayaur nayaur) belongs to the subfamily Caprinae, and is distributed in the Qinghai-Tibet Plateau and peripheral mountains of China. In this study, the complete mitochondrial genome of P. n. nayaur was sequenced. It was determined to be of 16,700 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of P. n. nayaur and other 29 caprine species were used for phylogenetic analysis. Phylogenetic trees were reconstructed by Bayesian and maximum likelihood methods, and it suggested that P. n. nayaur was the sister group of P. schaeferi and P. nayaur, and also indicated a close relationship of genus Pseudois with genus Capra.

107 GENETIC INACTIVATION OF THE Sry GENE IN ARGALI WILD AND ROMNEY DOMESTIC SHEEP WITH CRISPR/Cas SYSTEMS FOR PRODUCING SEX-REVERSED FEMALE ANIMALS

The Tibetan Argali (Ovis ammon hodgsoni), a wild sheep of the subfamily Caprinae (Bovidae), primarily found in the Tibetan Plateau, is categorized as near threatened on the International Union for Conservation of Nature (IUCN) Red List. For the conservation of this species, we have achieved the cloning of a full-term live Argali lamb (died shortly after birth) from a male Argali cell line that has been cryopreserved for more than 20 years. While working towards the goal of cloning a live Argali, we also recognised the need to establish a reproductive herd of animals by producing both fertile males and females. However, as in the case of Argali, it is difficult, and in some cases impossible, to obtain male and female cell lines from an endangered mammalian species. Therefore, for demonstrating a proof of concept of using an assisted reproduction technology (ART) for the conservation of endangered species or reviving extinct species, we used the Argali as an experimental model to produce both fertile males and females through ART. The Sry gene plays a central role in mammalian sex determination: mutations in the Sry gene result in the development of XY females; in mice, Sry knockout (KO) results in fertile XY females. Therefore, we created sex-reversed Argali cell lines through the KO of the Sry gene. In parallel, for potentially comparing the fertility of sex-reversed XY females between the Argali and domestic sheep [Romney (Ovis aries)], we also knocked out the Sry gene in the domestic sheep. Specifically, we used the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system to introduce mutations to the high-mobility group (HMG) box of the Sry gene. Skin fibroblasts from either adult Argali or Romney sheep were cultured in DMEM (HyClone) supplemented with 10% fetal bovine serum (FBS). Cells were harvested at 100% confluence with 0.25% trypsin-EDTA and transfected with the CRISPR/Cas DNA constructs by using the Amaxa Nucleofector system. For each experiment, 106 cells were transfected with 5 μg of CRISPR/Cas DNA constructs. After 72 hours post-transfection, cells were harvested, with half being used for genomic DNA isolation (for examining KO efficiency) and the other half for limited dilution for obtaining single-cell-derived colonies. With the Surveyor assay and a restriction enzyme digestion assay (successfully knocked-out cells lose the Dde I site in the HMG box of the Sry gene, rendering resistance to Dde I digestion), we demonstrated that the Sry KO efficiency was about 10% both in Argali and Romney sheep. By screening single-cell-derived colonies from the transfected Romney sheep cells, an Sry-KO cell line harboring a 2-nucleotide deletion in the HMG box was successfully established. Multiple vials of cells from this Sry-KO cell line have been cryopreserved and will be used for animal cloning via somatic cell nuclear transfer (SCNT) in the sheep-breeding season this fall.

Investigations of pestivirus infection in wild Caprinae in Europe

PESTIVIRUSES (family Flaviviridae) are single-stranded, positive-sense RNA viruses that are traditionally classified in four species: bovine viral diarrhoea virus type 1 (BVDV-1) and type 2 (BVDV-2), which affect cattle, Border...

Organization and variation of the mitochondrial DNA control region in five Caprinae species

The complete mitochondrial DNA (mtDNA) control region was analyzed from five species of the subfamily Caprinae; Naemorhedus caudatus, N. goral, Capra hircus, Capricornis swinhoei, and Capricornis crispus. Among these species, the control region ranged from 1,096 to 1,212 bp in length. Our results were compatible with the scheme of three domains (ETAS, Central, and CSB) within the control region. A + T < G + C was observed in all the domains. In the Korean gorals, of the 31 variable sites in the whole control region resulting in 15 haplotypes, 27 variable sites were in the ETAS domain. We found two to three tandem repeat in all five species examined in this study, three in N. caudatus and N. goral, two in Capra hircus and C. crispus, and one in C. swinhoei, respectively. All of these repeat units include two short sections of mirror symmetry (TACAT and ATGTA). Short mirror symmetries were well-resolved among five different species, although left domain has high substitution rates. By Kimura’s two parameter method, the genetic distances between the genera Naemorhedus and Capricornis were calculated and divergence time between Naemorhedus and Capricornis may be nearly 2Myr.

Sexual size dimorphism in domestic goats, sheep, and their wild relatives

Sexual size dimorphism (SSD) is a widespread phenomenon in different animal taxa, including the subfamily of goats and sheep (Caprinae), which belongs to the most dimorphic mammalian groups. Rensch's rule describes the pattern of SSD, claiming that larger species generally exhibits higher male to female body size ratio. Agreement with Rensch's rule is manifested by slope of the allometric relationship between male and female body size exceeding one. To test this rule, we analysed the data available in the literature on adult body mass of males and females in domestic goat and sheep breeds (169 and 303, respectively) and 37 wild species/subspecies of the subfamily Caprinae. According to the current phylogenetical hypotheses, there are six distinct monophyletic groups with different levels of SSD (expressed as M/F): (1) wild goats (1.83); (2) wild sheep (1.67); (3) non-European chamoises, including Ovibos moschatus (1.18); (4) European chamoises (1.27); (5) Budorcas taxicolor (1.01); and (6) Pantholops hodgsonii (1.65). Domestication has led to a remarkable decline in SSD of both domestic goats (1.36) and sheep (1.41). The highest regression slope of the relationship between male and female body size is that estimated for wild goats (1.32), followed by wild sheep (1.24), non-European chamoises (1.14), domestic sheep (1.13), and domestic goats (1.10). Nevertheless, only the last two values are statistically different from one and thus corroborate Rensch's rule. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 872–883.

Linajes fantasma y correlación con variables ecológicas: el caso de la Subfamilia Caprinae

Integration between systematic phylogenetics and palaeontological data has been probed to be an effective methodology to value palaeodiversities because it identifies periods in the evolutionary history of the clade without fossil representation. These are called ghost lineages. In this work we explore the possible relationship of ghost lineages duration with biometric, biogeografic or ecological variables in the Subfamily Caprinae (Bovidae, Mammalia). Variables were codified as binary characters and their relationship was examined using the concentrated-changes test. Our results indicate that species appearing in rainforest, warm temperate forest, taiga and desert biomes are related with high proportion of ghost lineages, while those from steppe biome present lower proportions. Zones inhabited by species of Caprinae in rainforest, warm temperate forest, taiga and desert are usually associated with high altitudes and a steep topography. Thus, we interpret that proportions in ghost lineages would be determined by probabilities of sedimentation and fossil site development .

Haematological and serum biochemical values of southern chamois (Rupicapra pyrenaica)

Blood samples were taken from 75 free-ranging southern chamois (Rupicapra pyrenaica) captured in drive-nets in Catalonia, north-eastern Spain, and 20 haematological and 24 serum biochemical variables were analysed. The values...

Molecular dating of caprines using ancient DNA sequences of Myotragus balearicus, an extinct endemic Balearic mammal

BackgroundMyotragus balearicus was an endemic bovid from the Balearic Islands (Western Mediterranean) that became extinct around 6,000-4,000 years ago. The Myotragus evolutionary lineage became isolated in the islands most probably at the end of the Messinian crisis, when the desiccation of the Mediterranean ended, in a geological date established at 5.35 Mya. Thus, the sequences of Myotragus could be very valuable for calibrating the mammalian mitochondrial DNA clock and, in particular, the tree of the Caprinae subfamily, to which Myotragus belongs.ResultsWe have retrieved the complete mitochondrial cytochrome b gene (1,143 base pairs), plus fragments of the mitochondrial 12S gene and the nuclear 28S rDNA multi-copy gene from a well preserved Myotragus subfossil bone. The best resolved phylogenetic trees, obtained with the cytochrome b gene, placed Myotragus in a position basal to the Ovis group. Using the calibration provided by the isolation of Balearic Islands, we calculated that the initial radiation of caprines can be dated at 6.2 ± 0.4 Mya. In addition, alpine and southern chamois, considered until recently the same species, split around 1.6 ± 0.3 Mya, indicating that the two chamois species have been separated much longer than previously thought.ConclusionSince there are almost no extant endemic mammals in Mediterranean islands, the sequence of the extinct Balearic endemic Myotragus has been crucial for allowing us to use the Messinian crisis calibration point for dating the caprines phylogenetic tree.

Phylogenomic study of the subfamily Caprinae by cross-species chromosome painting with Chinese muntjac paints

Chromosomal homologies have been established between the Chinese muntjac (Muntiacus reevesi, MRE, 2n = 46) and five ovine species: wild goat (Capra aegagrus, CAE, 2n = 60), argali (Ovis ammon, OAM, 2n = 56), snow sheep (Ovis nivicola, ONI, 2n = 52), red goral (Naemorhedus cranbrooki, NCR, 2n = 56) and Sumatra serow (Capricornis sumatraensis, CSU, 2n = 48) by chromosome painting with a set of chromosome-specific probes of the Chinese muntjac. In total, twenty-two Chinese muntjac autosomal painting probes detected thirty-five homologous segments in the genome of each species. The chromosome X probe hybridized to the whole X chromosomes of all ovine species while the chromosome Y probe gave no signal. Our results demonstrate that almost all homologous segments defined by comparative painting show a high degree of conservation in G-banding patterns and that each speciation event is accompanied by specific chromosomal rearrangements. The combined analysis of our results and previous cytogenetic and molecular systematic results enables us to map the chromosomal rearrangements onto a phylogenetic tree, thus providing new insights into the karyotypic evolution of these species.

Development of two multiplex PCRs for microsatellite analysis in Alpine chamois (Rupicapra r. rupicapra)

RiassuntoAllestimento di due PCR multiple per l’analisi di popolazioni di Camoscio delle Alpi (Rupicapra r. rupicapra) mediante marcatori microsatelliti. Allo scopo di elaborare un protocollo per l’analisi della struttura genetica di popolazioni di camosci italiani dell’arco alpino, sono stati individuati 16 microsatelliti già utilizzati per gli ungulati selvatici e mappati su cromosomi diversi in capra, pecora e bovino. Sulla base di analisi preliminari condotte su un ristretto numero di campioni dodici marcatori sono risultati sufficientemente polimorfi nel camoscio e coamplificabili. Per automatizzare le analisi e ridurre i tempi sono state messe a punto due PCR multiple con cui sono stati analizzati 42 campioni provenienti da differenti colonie. L’elevato contenuto informativo dei marcatori coamplificati dimostra che le due PCR multiple sono strumenti utili nelle indagini di genetica di popolazione nel camoscio.

Twenty polymorphic microsatellites in two of North Africa's most threatened ungulates: Gazella dorcas and Ammotragus lervia (Bovidae; Artiodactyla)

AbstractDuring the last century, North African ungulate species have suffered from habitat loss and over‐hunting. Gazella dorcas (Antilopidae subfamily) and Ammotragus lervia (Caprinae subfamily) are among the ungulates that have suffered most. To help to protect these species, conservation programs and population genetics studies are being implemented. Here, we tested 30 published microsatellite primer‐pairs from Bovids (cattle, sheep and goat) on eight individuals from each species. From the 30 loci tested, 20 amplified well and showed moderate allelic richness (3.75 and 4.65 mean number of alleles per species, respectively, for G. dorcas and A. lervia), and moderatly high heterozygosity (0.53 and 0.63 per species, respectively). These 20 polymorphic markers will facilitate conservation and genetic studies in these two species, and promise to be widely useful across divergent ungulate taxa.

G- and C-banded karyotype of the markhorCapra falconeri heptneri, and comparison of its banding patterns with the Alpine ibexCapra ibex and cattleBos taurus

Here we present the first data on chromosome banding forCapra falconeri heptneri (Zalkin, 1945) (Bovidae: Caprinae), a critically endangered subspecies of the markhor, and compare its G- and C-banding patterns with those of the congeneric Alpine ibexC. ibex Linnaeus, 1758 and the evolutionarily more distant cattleBos taurus Linnaeus, 1758. The two goat species have identical karyotypes whereasB. taurus, which has the same diploid number (2n = 60) and autosomal fundamental number (aFN) differs in the morphology of two pairs of autosomes (9 and 14) and of the X chromosome, as well as in the amount of C heterochromatin. Although the study supports the earlier idea of karyotype homogeneity within the genusCapra, new comparative cytogenetic data for unstudied yet congeneric and other related species are necessary for our understanding of the pattern of chromosome evolution within the subfamily Caprinae and, more broadly, the family Bovidae.

Molecular Support for the Placement of Saiga and Procapra in Antilopinae (Artiodactyla, Bovidae)

The evolutionary history of the bovid subfamily Antilopinae is unclear. Traditionally, this subfamily is subdivided into two tribes: Neotragini (dwarf antelopes) and Antilopini (gazelles and their relatives). Here, we report new sequences for the 12S and 16S rRNA genes in the enigmatic antilopine taxa Procapra gutturosa and Saiga tatarica and analyze the phylogenetic relationships of these taxa relative to other antilopines. Our study demonstrates the close affinity of the saiga antelope to Gazella despite the conventional systematic allocation of Saiga to the Caprinae subfamily. The second member of the Saigini tribe, Pantholops hodgsoni (Tibetan gazelle), falls within Caprinae. In all of our analyses, Procapra gutturosa occupied a basal position in the Antilopinae clade or was a sister-group to the dwarf antelope Madoqua. This suggests early separation of Procapra from other antelopes.

A basic residue at position 36p of the propeptide is not essential for the correct folding and subsequent autocatalytic activation of prochymosin.

Position 36p in the propeptides of gastric aspartic proteinases is generally occupied by lysine or arginine. This has led to the conclusion that a basic residue at this position, which interacts with the active-site aspartates, is essential for folding and activation of the zymogen. Lamb prochymosin has been shown by cDNA cloning to possess glutamic acid at 36p. To investigate the effect of this natural mutation which appears to contradict the proposed role of this residue, calf and lamb prochymosins and their two reciprocal mutants, K36pE and E36pK, respectively, were expressed in Escherichia coli, refolded in vitro, and autoactivated at pH 2 and 4.7. All four zymogens could be activated to active chymosin and, at both pH values, the two proteins with Glu36p showed higher activation rates than the two Lys36p forms. Glu36p was also demonstrated in natural prochymosin isolated from the fourth stomach of lamb, as well as being encoded in the genomes of sheep, goat and mouflon, which belong to the subfamily Caprinae. A conserved basic residue at position 36p of prochymosin is thus not obligatory for its folding or autocatalytic activation. The apparently contradictory results for porcine pepsinogen A [Richter, C., Tanaka, T., Koseki, T. & Yada, R.Y. (1999) Eur. J. Biochem. 261, 746-752] can be reconciled with those for prochymosin. Lys/Arg36p is involved in stabilizing the propeptide-enzyme interaction, along with residues nearer the N-terminus of the propeptide, the sequence of which varies between species. The relative contribution of residue 36p to stability differs between pepsinogen and prochymosin, being larger in the former.

Mitochondrial DNA from Myotragus balearicus, an extinct bovid from the Balearic Islands.

DNA was extracted from teeth and bones of Myotragus balearicus, a bovid that evolved in isolation on the Balearic Islands (Western Mediterranean) from the end of the Miocene, becoming extinct 4,000 years BP, after the arrival of humans in the islands. The numerous morphological apomorphies of Myotragus, most strikingly its dwarfism, frontal eyes, and ever-growing incisors, obscure its phylogenetic relationships with extant bovids. Therefore, the recovery of genetic information from Myotragus is of significant interest to help clarify the taxonomic position of this species. In this study we amplified and sequenced a 95 bp (base pair) fragment of the mtDNA cytochrome b gene from 6,000-year-old specimens of Myotragus. Several experimental controls, such as amino acid analysis, independent reproduction in two different laboratories, and cloning of the PCR product, support the authenticity of the ancient DNA sequence recovered. Phylogenetic comparison with orthologous sequences from supposedly related extant genera (serow, goral, mountain goat, chamois, takin, sheep, goat, Himalayan tahr, arctic musk ox, barbary sheep, blue sheep, and saiga) from the Caprinae subfamily suggests that Myotragus is related to some of these species. However, the real phylogenetic position of Myotragus is difficult to assess, due to the lack of resolution of the present molecular study, which can be partially attributed to the short length of the genetic fragment recovered.