Mitochondrial DNA Reveal that Domestic Goat (Capra hircus) are Genetically Affected by Two Subspecies of Bezoar (Capra aegagurus)

This article describes the complete sequences of the mitochondrial DNA displacement loop (D-loop) region and cytochrome b gene from domestic goats in Laos (Laos native) and wild goat markhor (C. falconeri). The wild goat bezoar (Capra aegagrus) has been considered to be the strongest candidate for the ancestor of the domestic goats (C. hircus); however, there is not sufficient molecular data to verify the hypothesis at present. In phylogenetic analyses, two wild goats, the markhor and the ibex (C. ibex), appeared as an outgroup, while the bezoar was located in a cluster of domestic goats. Mitochondrial haplotypes of Laos natives revealed two distinct major clusters: one was the same as the bezoar, the second, unique to Laos natives. The topology and calibrated levels of sequence divergence suggests that these clusters might represent at least two different subspecies of ancestral bezoars.     

Evidence for Introgressive Hybridization of Captive Markhor (Capra falconeri) with Domestic Goat: Cautions for Reintroduction

Markhors (Capra falconeri) are among the most endangered mammal species, and several conservation measures, including ex situ breeding, are implemented to prevent their extinction. We studied sequence diversity and differentiation of the first hypervariable segment of the mitochondrial DNA control region among C. f. heptneri and C. f. megaceros kept in four zoos in relationship to lineages of other wild and domestic goats, to assess for the first time the level of molecular distinctness and variability among those subspecies, and to check for possible introgression by related Capra taxa, such as domestic goats. Levels of differentiation between some Capra falconeri lineages and modern domestic goats were similar to levels between other wild goat species (i.e., Capra aegagrus, Capra ibex) and domestic goats. Among pure markhor lineages, paraphyly was observed for C. f. heptneri, suggesting occurrence of shared ancestral polymorphism among markhor subspecies and/or ancient or recent gene exchange between subspecies. Interestingly, 35.7% of all studied markhors from three zoos are introgressed by the domestic goat. Furthermore, despite relatively small breeding group sizes, markhors have maintained a relatively high proportion of mtDNA variation within zoo groups. In any case, the existence of markhors introgressed with domestic goat DNA in zoos should be considered when selecting markhors for ex situ breeding programs with the aim of building up a stock for later reintroduction into the wild.     

Evolutionary history of the genus Capra (Mammalia, Artiodactyla): discordance between mitochondrial DNA and Y-chromosome phylogenies

The systematics of the genus Capra remain controversial in spite of studies conducted using morphology, mtDNA, and allozymes. Here, we assess the evolutionary history of Capra (i) using phylogenetic analysis of two nuclear genes located on the Y-chromosome and (ii) previously published and new cytochrome b sequences. For the Y-chromosome phylogeny, we sequenced segments from the amelogenin (AMELY) and zinc finger (ZFY) genes from all of the eight wild taxa and from domestic goats (Capra hircus). Phylogenetic analysis of the Y-chromosome data revealed two well-defined clades. The domestic goat (C. hircus), the bezoar (Capra aegagrus), and the markhor (C. falconeri) belong to one clade (ML bootstrap value [BP]: 98%), suggesting that domestic goats originated from one or both of these wild species. The second clade (ML BP: 92%) is comprised of all the other wild species. Horn morphology is generally concordant with the Y-chromosome phylogeny. The mtDNA data also revealed two well-defined clades. However, the species in each clade are different from those inferred from the Y-chromosome data. To explain the discordance between Y-chromosome and mtDNA phylogenies, several hypotheses are considered. We suggest that a plausible scenario involves mtDNA introgression between ancestral taxa before the relatively recent colonization of Western Europe, the Caucasus Mountains, and East Africa by Capra populations.     

The Origin and Genetic Status of Insular Caprines in the Eastern Mediterranean: A Case Study of Free-Ranging Goats (Capra aegagrus cretica) on Crete

The history and species status of free-ranging goats inhabiting the Eastern Mediterranean islands is discussed with reference to morphometric, archaeological and genetic findings. A case study on the free-ranging goats on Crete (Capra aegagrus cretica) is presented. The phenotype of the Cretan goat resembles that of the wild bezoar goat (C. aegagrus). However, the mitochondrial DNA of cytochrome b and d-loop sequences shows affinity with domestic goats. It has been suggested that the Cretan goat represents a feral animal that was introduced onto the island during the 6th millennium b.c. as a primitive domestic, and has retained the wild morphotype but has undergone significant genetic change. An alternative explanation, and the one that is proposed here, is that the goat was introduced onto the island in wild form and released as a food source. Subsequent introgressions with domestic animals, especially ewes, have influenced its genotype. These conclusions are applicable to other free-living goats and sheep which inhabit islands in the Eastern Mediterranean.     

Influence of cohabitation between domestic goat (Capra aegagrus hircus) and Iberian ibex (Capra pyrenaica hispanica) on seroprevalence of infectious diseases

We have investigated the prevalence of infection with different pathogens in domestic goat (Capra hircus) and Iberian ibex (Capra pyrenaica hispanica) populations from two neighbouring geographical zones (with or without cohabitation between wild and domestic species) in Spain. No ibexes were found to be seropositive for Brucella melitensis, Mycoplasma mycoides supspecies mycoides (Mycoplasma mycoides), bovine leukaemia virus, and Chlamydophila abortus or bovine herpes virus type 1 (BHV-1). Domestic goats from both zones were detected with antibodies to Chlamydophila abortus and BHV-1. The percentage seroprevalence against Coxiella burnetii, Mycoplasma agalactiae, Mycobacterium avium subspecies paratuberculosis (MAP), caprine arthritis encephalitis virus (CAEV) and bluetongue virus (BTV) was clearly higher in domestic goats compared to wild ibexes in both zones, although CAEV showed negative results in a zone where species were isolated from each other. Moreover, Borrelia burgdorferi and Pestivirus infection showed moderate seroprevalence differences between domestic and wild goats in cohabitation zones, with the highest prevalence found in wild ibexes from a non-cohabitation zone. Our results showed that cohabitation between species was a risk factor (P?<?0.05) in Q fever infection.     

Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication

Background

Domestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics.

Results

We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which ASIP gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits.

Conclusion

Based on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1606-1) contains supplementary material, which is available to authorized users.     

A dig into the past mitochondrial diversity of Corsican goats reveals the influence of secular herding practices

The goat (Capra hircus) is one of the earliest domesticated species ca. 10,500 years ago in the Middle-East where its wild ancestor, the bezoar (Capra aegagrus), still occurs. During the Neolithic dispersal, the domestic goat was then introduced in Europe, including the main Mediterranean islands. Islands are interesting models as they maintain traces of ancient colonization, historical exchanges or of peculiar systems of husbandry. Here, we compare the mitochondrial genetic diversity of both medieval and extant goats in the Island of Corsica that presents an original and ancient model of breeding with free-ranging animals. We amplified a fragment of the Control Region for 21 medieval and 28 current goats. Most of them belonged to the A haplogroup, the most worldwide spread and frequent today, but the C haplogroup is also detected at low frequency in the current population. Present Corsican goats appeared more similar to medieval goats than to other European goat populations. Moreover, 16 out of the 26 haplotypes observed were endemic to Corsica and the inferred demographic history suggests that the population has remained constant since the Middle Ages. Implications of these results on management and conservation of endangered Corsican goats currently decimated by a disease are addressed.     

Investigation of the genetic diversity of domestic Capra hircus breeds reared within an early goat domestication area in Iran

Background

Iran is an area of particular interest for investigating goat diversity. Archaeological remains indicate early goat domestication (about 10 000 years ago) in the Iranian Zagros Mountains as well as in the high Euphrates valley and southeastern Anatolia. In addition, mitochondrial DNA data of domestic goats and wild ancestors (C. aegagrusor bezoar) suggest a pre-domestication management of wild populations in southern Zagros and central Iranian Plateau. In this study genetic diversity was assessed in seven Iranian native goat breeds, namely Markhoz, Najdi, Taleshi, Khalkhali, Naini, native Abadeh and Turki-Ghashghaei. A total of 317 animals were characterized using 14 microsatellite loci. Two Pakistani goat populations, Pahari and Teddy, were genotyped for comparison.

Results

Iranian goats possess a remarkable genetic diversity (average expected heterozygosity of 0.671 across loci, 10.7 alleles per locus) mainly accounted for by the within-breed component (G_ST = 5.9%). Positive and highly significant F_IS values in the Naini, Turki-Ghashghaei, Abadeh and Markhoz breeds indicate some level of inbreeding in these populations. Multivariate analyses cluster Iranian goats into northern, central and western groups, with the western breeds relatively distinct from the others. Pakistani breeds show some relationship with Iranian populations, even if their position is not consistent across analyses. Gene flow was higher within regions (west, north, central) compared to between regions but particularly low between the western and the other two regions, probably due to the isolating topography of the Zagros mountain range. The Turki-Ghashghaei, Najdi and Abadeh breeds are reared in geographic areas where mtDNA provided evidence of early domestication. These breeds are highly variable, located on basal short branches in the neighbor-joining tree, close to the origin of the principal component analysis plot and, although highly admixed, they are quite distinct from those reared on the western side of the Zagros mountain range.

Conclusions

These observations call for further investigation of the nuclear DNA diversity of these breeds within a much wider geographic context to confirm or re-discuss the current hypothesis (based on maternal lineage data) of an almost exclusive contribution of the eastern Anatolian bezoar to the domestic goat gene pool.     

中国部分家养山羊mtDNA D环区遗传多样性与进化

对我国10个家养山羊品种140只个体的mtDNA D-loop区进行测序分析, 测得结果: 整个D-loop区为 1 211~1 213 bp, 共检测到84种单倍型, 171个多态位点。其中核苷酸多样性(Nucleotide diversity, Pi)为: 0.02063 ± 0.00225, 单倍型多样性(Haplotype gene diversity, Hd)为: 0.988 ± 0.003, 平均核苷酸差异数(Average number of nucleotide differences) k为: 24.896。表明我国家养山羊品种遗传多样性丰富。通过构建NJ网络进化树, 得出中国家养山羊主要分为两大支系, 并且其中一支与角骨羊(Capra aegagrus)聚在一起, 而旋角野山羊(Capra fal-coneri)单独聚为一支, 说明角骨羊对中国家养山羊贡献较大。     

Density-Dependent Spacing Behaviour and Activity Budget in Pregnant,Domestic Goats (Capra hircus)

Very little is known about the spacing behaviour in social groups of domestic goats (Capra hircus) in the farm environment. In this experiment, we studied interindividual distances, movement patterns and activity budgets in pregnant goats housed at three different densities. Norwegian dairy goats were kept in stable social groups of six animals throughout pregnancy at 1, 2 or 3 m² per individual and their spacing behaviours (i.e. distance travelled, nearest and furthest neighbour distance) and activity budgets (e.g. resting, feeding, social activities) were monitored. Observations were made in the first, second and last thirds of pregnancy in the mornings, at noon and in the afternoons of each of these phases (4.5 hours per observation period). The findings show that goats held at animal densities of 2 and 3 m² moved longer distances when they had more space per animal and kept larger nearest and furthest neighbour distances when compared to the 1 m² per animal density. Less feeding activity was observed at the high animal density compared to the medium and low density treatments. The phase of gestation also had an impact on almost all behavioural variables. Closer to parturition, animals moved further distances and the increase in nearest and furthest neighbour distance was more pronounced at the lower animal densities. During the last period of gestation, goats spent less time feeding and more on resting, social behaviours and engaging in other various activities. Our data suggest that more space per goat is needed for goats closer to parturition than in the early gestation phase. We concluded that in goats spacing behaviour is density-dependent and changes with stages of pregnancy and activities. Finally, the lower density allowed animals to express individual preferences regarding spacing behaviour which is important in ensuring good welfare in a farming situation.     

The Genetic Diversity of mtDNA D-loop and the Origin of Chinese Goats

The complete sequences of mitochondrial DNA D-loop of 128 individuals in nine Chinese goat (Capra hircu) breeds were analyzed by DNA sequencing technology. The results show that the length of mtDNA D-loop in Chinese goats is 1 212-1 213 bp. There are 102 polymorphic sites, accounting for 8.42% of 1 212 bp sequence. Ninety-two mtDNA haplotypes were determined. The haplotype diversity and nucleotide diversity are 0.9333-1 .0000 and 0.7062%-1.8265%, respectively. The results indicate that the genetic diversity of Chinese goats is very abundant. The NJ tree indicates that Chinese goats have two types of maternal origins from lineage A and lineage B. The possibility of lineage B originating from China is also discussed.     

Cloning,characterization, and expression analysis of goat (Capra hircus) phospholipid hydroperoxide glutathione peroxidase (PHGPx)

Phospholipid hydroperoxide glutathione peroxidase (PHGPx), as a ubiquitous antioxidant enzyme in the glutathione peroxidases (GPx) family, plays multiple roles in organisms. However, there is very little information on PHGPx in goats (Capra hircus). In this study, a full-length cDNA was cloned and characterized from Taihang black goat testes. The 844 bp cDNA contains an open reading frame (ORF) of 597 bp. The goat PHGPx nucleotide sequence contains a selenocysteine (sec) codon TGA^244-246, two potential start codons ATG^20-22 and ATG^108-110, a polyadenylation signal AATAAA^813-818 and selenocysteine insertion sequence (SECIS) motif AUGA^688-691, UGA^729-731 and AAA^703-705. As a selenoprotein, the active-site motifs and GPx family signature motifs LAFPCNQF^101-108 and WNFEK^165-170 were also found. The order of PHGPx mRNA expression levels was: testes >> heart > brain > epididymis > kidney > liver > lung > spleen > muscle. Real-time PCR and immunohistochemistry results revealed similar expression differences in different age testes, with high expression levels during adolescence. Immunofluorescence results suggested that PHGPx mainly expressed in Leydig cells and spermatids in mature goat testes.     

Sequencing primers and SNPs for rapidly evolving reproductive loci in endangered ibex and their kin (Bovidae,Capra spp.)

Rapidly evolving genes (e.g. candidate selected loci) are of increasing interest to molecular ecologists and conservation geneticists. Here, we report primers for five regions from three independent nuclear reproductive genes that reliably generate polymorphic sequences across the widespread wild goats of the Capra ibex species group and likely many other species of bovids. From three to nine single‐nucleotide polymorphisms (SNPs) were identified in each gene region among C. ibex subspecies. Average numbers of SNPs per 1000 bp across all five gene regions was 15.0, with a high of 25.3 in the ZP3 exons 3 and 4 sequence and a low of 6.1 in the TNP1 sequence.     

Changes in liver and fat depots of West African dwarf goats (Capra aegagus hircus) after an infection with T. vivax

Nine West African dwarf goats (Capra aegagus hircus) were each infected experimentally with 3 × 10⁷ Trypanosoma vivax parasites. The changes in the plasma concentration of nonesterified fatty acids (NEFA) were monitored during the infection and the level of hepatic triacylglycerols and glycogen was measured postmortem. During the infection they had higher plasma NEFA concentrations than nine uninfected control goats and at postmortem their total liver triacylglycerol and glycogen contents were found to be increased. These observations suggest that the mobilization of the goats' defense mechanisms against the T. vivax infection induced a more intensive fat mobilization resulting in changes in fat metabolism of the liver.     

Energy and water use by invasive goats (Capra hircus) in an Australian rangeland, and a caution against using broad-scale allometry to predict species-specific requirements

Feral goats (Capra hircus) are ubiquitous across much of Australia's arid and semi-arid rangelands, where they compete with domestic stock, contribute to grazing pressure on fragile ecosystems, and have been implicated in the decline of several native marsupial herbivores. Understanding the success of feral goats in Australia may provide insights into management strategies for this and other invasive herbivores. It has been suggested that frugal use of energy and water contributes to the success of feral goats in Australia, but data on the energy and water use of free-ranging animals are lacking. We measured the field metabolic rate and water turnover rate of pregnant and non-pregnant feral goats in an Australian rangeland during late summer (dry season). Field metabolic rate of pregnant goats (601 ± 37 kJ kg^− 0.73 d^− 1) was 1.3 times that of non-pregnant goats (456 ± 24 kJ kg^− 0.73 d^− 1). The water turnover rate of pregnant goats (228 ± 18 mL kg^− 0.79 d^− 1) was also 1.3 times that of non-pregnant goats (173 ± 18 kg^− 0.79 d^− 1), but the difference was not significant (P = 0.07). There was no significant difference in estimated dry matter digestibility between pregnant and non-pregnant goats (mean ca. 58%), blood or urine osmolality, or urine electrolyte concentrations, indicating they were probably eating similar diets and were able to maintain osmohomeostasis. Overall, the metabolic and hygric physiology of non-pregnant goats conformed statistically to the predictions for non-marine, non-reproductive placental mammals according to both conventional and phylogenetically independent analyses. That was despite the field metabolic rate and estimated dry matter intake of non-pregnant goats being only 60% of the predicted level. We suggest that general allometric analyses predict the range of adaptive possibilities for mammals, but that specific adaptations, as present in goats, result in ecologically significant departures from the average allometric curve. In the case of goats in the arid Australian rangelands, predictions from the allometric regression would overestimate their grazing pressure by about 40% with implications for the predicted impact on their local ecology.     

Power of 22 microsatellite markers in fluorescent multiplexes for parentage testing in goats (Capra hircus)

Two multiplex systems, each containing 11 microsatellite loci, were developed for semiautomated parentage testing in goats. Eight of the loci originate from goats, nine from cattle and five from sheep. Eighteen of the loci have been mapped to 16 different autosomes (in goats and cattle). Parentage exclusion probabilities were computed from allele frequencies in approximately 30 unrelated individuals from each of four economically important breeds: Mongolian Native Cashmere, Turkish Angora, Swiss Saanen, and Spanish Murciana-Grenadina. In cases where genotypes are known for one parent and an offspring, the 22 markers will exclude an (erroneously) alleged parent with a probability of > 0.999999 in the cashmere breed, > 0.99999 in Angora and Murciana-Grenadina, and > 0.9999 in Saanen. The multiplexes provide very high power for individual identification as the probability of finding two identical genotypes for the 22 loci is < 1 in 1.10(15) in each of the four breeds. The multiplexes will also be useful for studies of population structure, history, and diversity in goats and also in wild Capra species that represent important resources for genetic improvement of domestic breeds.     

Phylogenetic analysis of Sicilian goats reveals a new mtDNA lineage

The mitochondrial hypervariable region 1 (HVR1) sequence of 67 goats belonging to the Girgentana, Maltese and Derivata di Siria breeds was partially sequenced in order to present the first phylogenetic characterization of Sicilian goat breeds. These sequences were compared with published sequences of Indian and Pakistani domestic goats and wild goats. Mitochondrial lineage A was observed in most of the Sicilian goats. However, three Girgentana haplotypes were highly divergent from the Capra hircus clade, indicating that a new mtDNA lineage in domestic goats was found.     

Past and present distribution of the genus Capra in Greece

The Alpine ibex Capra ibex and the wild goat Capra aegagrus are the only caprids known to have existed in the Balkan Peninsula. The agrimi is a feral primitive form of the domestic goat Capra hircus but may constitute an island subspecies of C. aegagrus endemic to Crete, Greece. Here, the distribution of C. ibex and C. aegagrus in this southernmost Balkan country was reviewed for the period from Middle Pleistocene until today through a scientific and historical document search. Such knowledge should provide directions to future conservation plans for these species and aid in tracing the origins of agrimi. Fossil locations indicate that both species lived in this country at elevations of similar altitude (≥10–?≤?2,497 m a.s.l.). C. ibex colonised Greece naturally, perhaps, not earlier than 126,000 years ago. It was spread over most of the mainland (36–41° N and 20–24° E) where from it disappeared after 5600 BC due to hunting. C. aegagrus constituted an exotic in Europe. Man introduced it to insular and mainland Greece (between 35–40° N and 19–26° E) from around 8600 and 7000 BC, respectively. It went extinct on the mainland probably before 6000 BC. Only C. ibex should, therefore, be restored to its former Balkan ranges. This review provides further support for the wild origin hypothesis for agrimi.     

Mitochondrial DNA diversity of Pakistani goats

Pakistan contains numerous domestic goat breeds, but until now there has been no comprehensive study on genetic diversity or a phylogenetic analysis of Pakistani goats. In this study, we analysed the complete mitochondrial DNA D-loop and the cytochrome b gene of 13 Pakistani domestic goat breeds (Capra hircus) and one wild goat, the Sindh Ibex (Capra aegagrus blythi). The phylogenetic analyses and sequence divergence (SD) established four distinct mt-lineages termed as A, B and C (previously reported) and a new lineage D. The Sindh Ibex appeared as an outgroup of domestic goats. The estimated divergence times between the most recently evolved mt-lineages A and D were from 260,483 to 371,052 YA. This suggested that at least four different strains of wild Capra might have been the source of the modern domestic goats. The new mt-lineage D revealed high SD from mt-lineage A and may be the oldest branch under domestication, while mt-lineages B and C showed lower SD and might have been domesticated during an advanced stage of the domestication process.     

Distribution of rhodanese in tissues of goat (Capra hircus)

Rhodanese (thiosulfate: cyanide sulfurtransferase, EC. 2.8.1.1) is a ubiquitous enzyme present in all living organisms, from bacteria to humans and plays a central role in cyanide detoxification. The purpose of this investigation is to determine and compare rhodanese activity in different tissues of adult male and female goats (Capra hircus). The results showed that the specific activity of rhodanese in different tissues was significantly different (P<0.05). The highest activity of rhodanese was in epithelium of rumen, followed by epithelia of reticulum and omasum and liver. No significant difference was observed when tissues of male and female goats were compared. The lowest specific activity of rhodanese was observed in spleen, urinary bladder, lymph node, ovary, skeletal muscle and pyloric muscle of abomasum. The results of this study may indicate the involvement of rhodanese in cyanide detoxification in goat tissues that have greater potential to be exposed to higher levels of cyanide.