Microsatellite analysis of genetic diversity in wild and farmed Emus (Dromaius novaehollandiae)

The emu (Dromaius novaehollandiae) occupies most regions of the Australian continent and in recent times has been farmed for meat, oil, and leather. Very little is known about the genetic structure of natural or farmed populations of these birds. We report a preliminary study of genetic variation in emus undertaken by typing birds from five farms and two natural populations at five polymorphic microsatellite loci. Genetic diversity was high for all populations and there was little evidence of inbreeding, with most populations conforming to Hardy-Weinberg equilibrium for most loci. Significant heterozygote deficiencies at one locus in a number of populations were detected and may indicate the presence of null alleles. Comparisons of allele frequencies showed little evidence of genetic differentiation either among farmed populations or between farmed and natural populations.     

The emu oil emulsified in egg lecithin and butylated hydroxytoluene enhanced the proliferation,stemness gene expression,and in vitro wound healing of adipose-derived stem cells

In recent decades, mesenchymal stem cells originated from adipose tissue (adipose-derived stem cells, ASCs) have gained increased attention for production of cell-based therapeutics. Emu oil as a natural compound showed antioxidant effects in previous studies. The goal of this study was to investigate the effect of crude emu oil on the proliferation, cell cycle progression, stemness genes expression, and in vitro wound healing potential of ASCs. An emulsion of emu oil was prepared using egg lecithin and butylated hydroxytoluene to improve bioavailability and solubility of emu oil in the expansion medium. The ASCs were treated using a series of emu oil concentrations in emulsion form, diluted in expansion medium (0.03–3 mg/ml). The emu oil-free emulsion was used as control treatment. The results revealed that emu oil (1.25 mg/ml) in emulsion form significantly (p?<?0.001) increased ASCs proliferation and colony formation. Additionally, emu oil caused upregulation of stemness marker genes (Sox2, Oct4, Nanog, and Nestin) (p?<?0.05). The cell cycle analysis after emu oil treatments showed an increase in the population of ASCs in S-phase of the cell cycle. Besides, an accelerated in vitro scratch wound healing was observed in emu oil-treated ASCs. Emu oil enhanced proliferation, colony formation, stemness genes expression, and in vitro wound healing of ASCs. These findings suggest that emu oil treatment could maintain the stemness of ex vivo cultivated ASCs and enhance their regenerative potential.     

Microsatellite DNA variation in wild populations and farmed strains of turbot from Ireland and Norway: a preliminary study

Turbot Scophthalmus maximus is the focus of a rapidly expanding aquaculture industry, while at the same time wild catches appear to be in decline. As a preliminary investigation into the effects of hatchery rearing, genetic variation at three polymorphic microsatellite loci was assessed in two wild populations and two farmed strains of turbot, from Ireland and Norway. Although a considerable loss of rare alleles was observed in the Irish farmed strain, no statistically significant reductions were found in mean heterozygosity or allelic diversity in farmed strains compared to wild populations. Significant genetic heterogeneity was found between wild and farmed samples from each country but not between the two wild populations. Genetic differentiation between the farmed strains was presumed to be caused by drift in the hatcheries. The utility of these particular microsatellite loci in comparing these samples and the importance of molecular genetic testing of farmed strains is stressed.     

Microsatellite variability of wild and farmed populations of Sparus aurata

The genetic diversity of Greek wild and farmed populations of Sparus aurata was investigated using seven microsatellite markers. Selective breeding programmes and founder effects have altered the composition of farmed populations leading to significant population differentiation between wild and cultured populations and lower allelic richness in farmed populations.     

Comparative analysis of microbial diversity and bacterial seedling disease‐suppressive activity in organic‐farmed and standardized commercial conventional soils for rice nursery cultivation

The outbreak of rice plant diseases can be effectively suppressed in organic farming systems. However, the mechanisms of disease suppression by organic farming systems are not well understood. When Burkholderia‐infected rice seeds were sown and cultivated on nine organic‐farmed soils which were supplied by nine independent organic rice farmers or standardized commercial conventional soils, the emergence of bacterial seedling diseases was suppressed to equivalent degrees in nine organic‐farmed soils, whereas the diseases occurred in two commercial conventional soils. In any organic or commercial conventional soil sown with healthy rice seeds as a control, the diseases did not appear. Upon physicochemical analysis of the nine organic‐farmed soils, component common to these organic‐farmed soils seemed to not be directly associated with disease‐suppressive activity. However, microbiome analyses indicated that the bacterial population in these nine organic‐farmed soils was more diverse than those in commercial conventional soils. Intriguingly, the diverse bacterial population structures of organic‐farmed soils were preserved after irrigating and sowing rice seeds, but that of commercial conventional soils was clearly changed by them. Thus, organic‐farmed soils seem to maintain robust bacterial populations despite the irrigation and seedling growth. Indeed, pathogenic Burkholderia in infected rice seeds also did not proliferate in the seedling grown on organic‐farmed soils. Taken together, the common feature of organic‐farmed soils might be the correlation between bacterial seedling disease‐suppressive activity and higher robustness of the diversified microbiome.     

Genetic divergence and interactions in the wild among native, farmed and hybrid Atlantic salmon

There is concern that the progeny resulting from the spawnings of escaped farmed Atlantic salmon may compete with and disrupt native salmon populations. This study compared, both in the hatchery and in the wild, fitness-related traits and examined interactions among farmed, native and hybrid 0+ parr derived from controlled crosses and reared under common conditions. The farmed salmon were seventh-generation fish from the principal commercial strain in Norway and native salmon were from the rivers Imsa and Lone, Norway. In the hatchery, farmed salmon were more aggressive than both native populations and tended to dominate them in pairwise contests. Farmed salmon were also more prone to risk, leaving cover sooner after a simulated predator attack, and had higher growth rates than native fish. Interbreeding between farmed and native fish generally resulted in intermediate expression of the above traits. There was, however, evidence of hybrid vigour in Lone/farmed crosses which were able to dominate both pure Lone and farmed parr in pairwise contests. In the wild, observations of habitat use and diet suggested that the populations compete for territory and food, and both farmed fish and hybrids expressed higher growth rates than native fish. Our results suggest that these innate differences in behaviour and growth, that probably are linked closely to fitness, will threaten native populations through competition and disruption of local adaptations.     

SSU rRNA gene sequence reveals two genotypes of Spironucleus barkhanus (Diplomonadida) from farmed and wild Arctic charr Salvelinus alpinus

Spironucleus barkhanus isolated from the blood of Arctic charr Salvelinus alpinus from a marine fish farm were genetically compared with S. barkhanus isolated from the gall bladder of wild Arctic charr. The wild Arctic charr were caught in the lake used as the water source for the hatchery from which the farmed fish originated. Sequencing of the small subunit ribosomal RNA gene (SSU rDNA) from these 2 populations showed that the isolates obtained from farmed and wild Arctic charr were only 92.7 % similar. Based on the sequence differences between these isolates, it is concluded that the parasites isolated from the farmed fish have not been transmitted from wild Arctic charr in the hatchery's fresh water source. It is therefore most likely that the farmed fish were infected by S. barkhanus after they were transferred to seawater. S. barkhanus isolated from diseased farmed Arctic charr were 99.7% similar to the isolates obtained from diseased farmed Chinook (Canada) and Atlantic salmon (Norway). The high degree of sequence similarity between S. barkhanus from farmed Arctic charr, Chinook and Atlantic salmon indicates that systemic spironucleosis may be caused by specific strains/variants of this parasite. The genetic differences between the isolates of farmed and wild fish are of such magnitude that their conspecificity should be questioned.     

Molecular characterization of goose- and chicken-type lysozymes in emu (Dromaius novaehollandiae): evidence for extremely low lysozyme levels in emu egg white

Lysozyme (LZ), a bacteriolytic enzyme, is found in the egg white of many avian eggs and plays an important role in host defense; however, LZ activity in emu (Dromaius novaehollandiae) egg white is exceptionally undetectable. We cloned and characterized emu goose-type LZ (LZG) and chicken-type LZ (LZC) genes. RT-PCR analysis revealed very low LZG gene expression levels and absence of LZC gene expression in the emu oviduct. Sequencing of full-length LZG and LZC cDNAs indicated that their amino acid sequences show high similarities to ostrich LZG and LZC, respectively, with conserved catalytic residues for enzymatic activities. Whereas recombinant emu LZG prepared using Pichia pastoris exhibited similar enzyme activity as ostrich LZG, recombinant emu LZC exhibited significantly higher lytic activity than chicken LZC. We concluded that emus have functional genes for both LZG and LZC like many other avians, and the LZG gene is expressed in oviduct probably as in other ratite, however, its expression levels in egg white were low to be detected.     

Migratory behaviour of wild and farmed Atlantic salmon (Salmo salar) during spawning

Migratory behaviour at spawning of wild and newly-escaped farmed Atlantic salmon was analysed by radio telemetry in the River Alta, North Norway. Spawning areas were located by aerial surveys. Farmed females moved significantly more than wild females ( P <0.01). There was no such difference between the two groups of males. About 83% of the wild fish stayed within identified spawning areas for 1 day or longer. The corresponding figure for farmed salmon was only 43% ( P <0.05). Wild salmon stayed 8.1 days inside spawning areas and farmed salmon 5.2 days. The present results suggest that escaped farmed salmon had reduced spawning success compared with wild fish.     

Hatching Time and Alevin Growth Prior to the Onset of Exogenous Feeding in Farmed,Wild and Hybrid Norwegian Atlantic Salmon

The onset of exogenous feeding, when juveniles emerge from the gravel, is a critical event for salmonids where early emergence and large size provide a competitive advantage in the wild. Studying 131 farmed, hybrid and wild Norwegian Atlantic salmon families, originating from four wild populations and two commercial strains, we investigated whether approximately 10 generations of selection for faster growth has also resulted in increased somatic growth prior to the onset of exogenous feeding. In addition, we tested whether relaxed selection in farms has allowed for alterations in hatching time between farmed and wild salmon. Across three cohorts, wild salmon families hatched earlier than farmed salmon families, while hybrid families displayed intermediate hatching times. While the observed differences were small, i.e., 1–15 degree-days (0–3 days, as water temperatures were c. 5–6°C), these data suggest additive genetic variation for hatching time. Alevin length prior to exogenous feeding was positively related to egg size. After removal of egg size effects, no systematic differences in alevin length were observed between the wild and farmed salmon families. While these results indicate additive genetic variation for egg development timing, and wild salmon families consistently hatched earlier than farmed salmon families, these differences were so small they are unlikely to significantly influence early life history competition of farmed and wild salmon in the natural environment. This is especially the case given that the timing of spawning among females can vary by several weeks in some rivers. The general lack of difference in size between farmed and wild alevins, strongly suggest that the documented differences in somatic growth rate between wild and farmed Norwegian Atlantic salmon under hatchery conditions are first detectable after the onset of exogenous feeding.     

Experimental infection of rainbow trout Oncorhynchus mykiss with viral haemorrhagic septicaemia virus isolates from European marine and farmed fishes

The susceptibility of rainbow trout Oncorhynchus mykiss to infection with various isolates of viral haemorrhagic septicaemia virus (VHSV) was examined. A total of 8 experiments with rainbow trout ranging from 0.6 to 6.2 g was conducted for 139 isolates originating from wild marine fishes in European waters (115 isolates), farmed turbot from Scotland and Ireland (2 isolates), and farmed rainbow trout (22 isolates). The isolates were tested by immersion and/or intraperitoneal injection either as pooled or single isolates. The isolates from wild marine fishes did not cause mortality by immersion while some of the isolates caused mortality when injected. All VHSV isolates from farmed rainbow trout caused significant mortality by immersion. Currently, pathogenicity trials are the only way to differentiate VHSV isolates from wild marine fishes and farmed rainbow trout. The 2 farmed turbot isolates did not cause mortality by immersion, supporting the view that they originated from the marine environment.     

Escape of farmed tilapiines into the wild and entry of wild forms in fishponds,and the possible interactions between wild and farmed tilapiines from a sample of smallholder farms in Central Uganda

Seven smallholder fishponds in central Uganda were studied between 2000 and 2001 to investigate the interaction of farmed tilapiines with their wild conspecifics. Emphasis was on the features that facilitate escape of fish and/or entry of fish into the farms and interactions between the farmed and the wild. These included number of species, source of seed, connection between pond and natural watercourses, purpose of the farm, destination of cultured fish and interaction between farmed and wild fish. Fishponds had no screens against entry of wild fish into the farm or escape of farmed fish into the wild and occurred within wetlands close to natural watercourses. Ponds stocked with one fish species were found to have multispecies with some individuals that were apparently intermediate morphs between the species. Fry produced within the growout fishponds was shared with other farmers within and outside the watersheds. This study showed that smallholder farms with little or no control of escape or entry of fish out and into the fishponds, and little or no management present circumstances that facilitate continued movement of tilapiines within and across watersheds in Ugandan waters. The study also indicated possible genetic interaction between farmed and their wild conspecifics through interactions within fishponds.     

Generic genetic differences between farmed and wild Atlantic salmon identified from a 7K SNP-chip

Genetic interactions between farmed and wild conspecifics are of special concern in fisheries where large numbers of domesticated individuals are released into the wild. In the Atlantic salmon (Salmo salar), selective breeding since the 1970's has resulted in rapid genetic changes in commercially important traits, such as a doubling of the growth rate. Each year, farmed salmon escape from net pens, enter rivers, and interbreed with wild salmon. Field experiments demonstrate that genetic introgression may weaken the viability of recipient populations. However, due to the lack of diagnostic genetic markers, little is known about actual rates of gene flow from farmed to wild populations. Here we present a panel of 60 single nucleotide polymorphisms (SNPs) that collectively are diagnostic in identifying individual salmon as being farmed or wild, regardless of their populations of origin. These were sourced from a pool of 7000 SNPs comparing historical wild and farmed salmon populations, and were distributed on all but two of the 29 chromosomes. We suggest that the generic differences between farmed and wild salmon at these SNPs have arisen due to domestication. The identified panel of SNPs will permit quantification of gene flow from farmed to wild salmon populations, elucidating one of the most controversial potential impacts of aquaculture. With increasing global interest in aquaculture and increasing pressure on wild populations, results from our study have implications for a wide range of species.     

Comparative morphology,morphometry and distribution pattern of the trigeminal nerve branches supplying the bill tip in the ostrich (Struthio camelus) and emu (Dromaius novaehollandiae)

The subdivisions of the trigeminal nerve (N. ophthalmicus R. medialis and N. intramandibularis) innervating the upper and lower bill tip, respectively, were well developed in both the ostrich and emu and displayed extensive branching. Transmission electron microscopy revealed that both nerves displayed features typical of a mixed, peripheral nerve. Nerve fibre size in the ostrich and emu was larger than that reported in domestic poultry. There were a significantly higher number of myelinated nerve fibres in the N. ophthalmicus R. medialis in the emu by comparison with the same nerve in the ostrich, or by comparison with the N. intramandibularis of either species. As myelinated nerve fibres supply Herbst corpuscles, and these structures have been demonstrated in this region in these two species, this may indicate that the upper bill of the emu is more sensitive to vibrational stimuli than the upper bill of the ostrich or the lower bill of both species. The large size of the nerve fibres, the high nerve fibre count and the particular distribution of the nerves in the bill tip support the existence of a well‐developed sensory area in this region of the ostrich and emu.     

Eggs of extinct dwarf island emus retained large size

Islands off southern Australia once harboured three subspecies of the mainland emu (Dromaius novaehollandiae), the smaller Tasmanian emu (D. n. diemenensis) and two dwarf emus, King Island emu (D. n. minor) and Kangaroo Island emu (D. n. baudinianus), which all became extinct rapidly after discovery by European settlers. Little was recorded about their life histories and only a few historical museum specimens exist, including a number of complete eggs from Tasmania and a unique egg from Kangaroo Island. Here, we present a detailed analysis of eggs of dwarf emus, including the first record of an almost complete specimen from King Island. Our results show that despite the reduction in size of all island emus, especially the King Island emu that averaged 44% smaller than mainland birds, the egg remained similar sized in linear measurements, but less in volume and mass, and seemingly had a slightly thinner eggshell. We provide possible reasons why these phenomena occurred.     

In vivo bone strain and ontogenetic growth patterns in relation to life-history strategies and performance in two vertebrate taxa: goats and emu

This study examined ontogenetic patterns of limb loading, bone strains, and relative changes in bone geometry to explore the relationship between in vivo mechanics and size-related changes in the limb skeleton of two vertebrate taxa. Despite maintaining similar relative limb loads during ontogeny, bone strain magnitudes in the goat radius and emu tibiotarsus generally increased. However, while the strain increases in the emu tibiotarsus were mostly insignificant, strains within the radii of adult goats were two to four times greater than in young goats. The disparity between ontogenetic strain increases in these taxa resulted from differences in ontogenetic scaling patterns of the cross-sectional bone geometry. While the cross-sectional and second moments of area scaled with negative allometry in the goat radius, these measures were not significantly different from isometry in the emu tibiotarsus. Although the juveniles of both taxa exhibited lower strains and higher safety factors than the adults, the radii of the young goats were more robust relative to the adult goats than were the tibiotarsi of the young compared with adult emu. Differences in ontogenetic growth and strain patterns in the limb bones examined likely result from different threat avoidance strategies and selection pressures in the juveniles of these two taxa.     

Persistence of Meckel's cartilage in sub-adult Struthio camelus and Dromaius novaehollandiae

This study describes the persistence of an embryonal structure through to sub-adulthood in the ostrich and emu. Mandibles from sub-adult ostrich and emu were subjected to special staining, light microscopy and dissected to reveal and describe Meckel's cartilage. Meckel's cartilage, composed of hyaline cartilage, was present within the neurovascular canal of both species. The persistence through to sub-adulthood of Meckel's cartilage in the ostrich and emu is a feature not previously reported in any other avian species. The proximal end of Meckel's cartilage was ossified in the region of the articular bone and the distal end was ossified in some specimens. Although this structure may ossify at a much later stage in life, the function in young and sub-adult birds may be to dampen shockwaves along the intramandibular nerve that result from the action of pecking. In the ostrich, the M. pseudotemporalis superficialis tendon inserted onto the supra-angular bone and Meckel's cartilage. In the emu, a small portion of the tendon was attached to the supra-angular bone and the main part to Meckel's cartilage. The persistence of Meckel's cartilage in adult lepidosaurs, crocodilians and ratites represents an unusual shared trait between the extant members of the above groups.     

Positivity and intensity of Gnathostoma spinigerum infective larvae in farmed and wild-caught swamp eels in Thailand

From July 2008 to June 2009, livers of the swamp eels (Monopterus alba) were investigated for advanced third-stage larvae (AL3) of Gnathostoma spinigerum. Results revealed that 10.2% (106/1,037) and 20.4% (78/383) of farmed eels from Aranyaprathet District, Sa Kaeo Province and those of wild-caught eels obtained from a market in Min Buri District of Bangkok, Thailand were infected, respectively. The prevalence was high during the rainy and winter seasons. The infection rate abruptly decreased in the beginning of summer. The highest infection rate (13.7%) was observed in September and absence of infection (0%) in March-April in the farmed eels. Whereas, in the wild-caught eels, the highest rate (30.7%) was observed in November, and the rate decreased to the lowest at 6.3% in March. The average no. (mean±SE) of AL3 per investigated liver in farmed eels (1.1±0.2) was significantly lower (P=0.040) than those in the caught eels (0.2±0.03). In addition, the intensity of AL3 recovered from each infected liver varied from 1 to 18 (2.3±0.3) in the farmed eels and from 1 to 47 (6.3±1.2) in the caught eels, respectively. The AL3 intensity showed significant difference (P=0.011) between these 2 different sources of eels. This is the first observation that farmed eels showed positive findings of G. spinigerum infective larvae. This may affect the standard farming of the culture farm and also present a risk of consuming undercooked eels from the wild-caught and farmed eels.