Vietnamese chickens: a gate towards Asian genetic diversity

BACKGROUND: Chickens represent an important animal genetic resource and the conservation of local breeds is an issue for the preservation of this resource. The genetic diversity of a breed is mainly evaluated through its nuclear diversity. However, nuclear genetic diversity does not provide the same information as mitochondrial genetic diversity. For the species Gallus gallus, at least 8 maternal lineages have been identified. While breeds distributed westward from the Indian subcontinent usually share haplotypes from 1 to 2 haplogroups, Southeast Asian breeds exhibit all the haplogroups. The Vietnamese Ha Giang (HG) chicken has been shown to exhibit a very high nuclear diversity but also important rates of admixture with wild relatives. Its geographical position, within one of the chicken domestication centres ranging from Thailand to the Chinese Yunnan province, increases the probability of observing a very high genetic diversity for maternal lineages, and in a way, improving our understanding of the chicken domestication process. RESULTS: A total of 106 sequences from Vietnamese HG chickens were first compared to the sequences of published Chinese breeds. The 25 haplotypes observed in the Vietnamese HG population belonged to six previously published haplogroups which are: A, B, C, D, F and G. On average, breeds from the Chinese Yunnan province carried haplotypes from 4.3 haplogroups. For the HG population, haplogroup diversity is found at both the province and the village level (0.69).The AMOVA results show that genetic diversity occurred within the breeds rather than between breeds or provinces. Regarding the global structure of the mtDNA diversity per population, a characteristic of the HG population was the occurrence of similar pattern distribution as compared to G. gallus spadiceus. However, there was no geographical evidence of gene flow between wild and domestic populations as observed when microsatellites were used. CONCLUSIONS: In contrast to other chicken populations, the HG chicken population showed very high genetic diversity at both the nuclear and mitochondrial levels. Due to its past and recent history, this population accumulates a specific and rich gene pool highlighting its interest and the need for conservation

Morphometric and allozyme variation in the African catfishes <i>Clarias gariepinus</i> and <i>C. anguillaris</i>

This study investigated morphological characters and electrophoretic polymorphism at 25 protein loci in nine wild populations of the African clariid catfish Clarias gariepinus and seven wild populations of C. anguillaris. Two other clariid species, Clarias albopunctatus and Heterobranchus longifilis, were used as outgroups in the allozyme study. Morphometric and allozyme data are congruent for the Nilo-Sudanian populations of C. gariepinus and C. anguillaris. Both approaches also distinguished two groups amongst the C. gariepinus populations, one containing Nilo-Sudanian populations and the other including Lake Victoria and southern African populations. However, allozyme data suggest that C. gariepinus is not a monophyletic group and show that C. albopunctatus is more divergent from C. gariepinus and C. anguillaris than it is from H. longifilis, stressing the need for a revision of clariid systematics. The variation observed in C. gariepinus is discussed in terms of palaeogeographical events and its use in aquaculture

Phenotypic characterisation and molecular polymorphism of indigenous poultry populations of the species Gallus gallus of Savannah and Forest ecotypes of Benin

The study of the phenotypic characterisation and molecular polymorphism of local chicken populations was carried out in Benin on 326 chickens of the Forest ecological area and 316 of the Savannah ecological area, all were 7 months old at least. The collection of blood for the molecular typing wasachieved on 121 indigenous chickens of which 60 from the Savannah ecological area and 61 from the Forest ecological area. The genotyping was carried out for 22 microsatellite loci. Weight and body measures of the Savannah chickens were significantly higher (P &lt; 0.001) than those of the Forest chickens. In the Savannah ecological area, the most frequent plumage colours were the black (22.15%), the white (19.62%), the coppery black (7.59%) and the golden partridge (7.59%). In the Forest area, thefawn (15.34%), the black (10.43%), the white (6.8%), the silver white (6.8%) and the golden partridge (6.75%) were the dominant feather colours. Thus, phenotypic characterisation showed significant differences between Savannah and Forest local chickens. The FST calculated between the Savannah and Forest populations revealed a low genetic differentiation and the dendogram showed that Savannah and Forest chickens were quite intermingled. In conclusion, local populations from Savannah andForest area may be considered as ecotypes, but not as two distinct breeds

Inference of breed structure in farm animals: Empirical comparison between snp and microsatellite performance

Knowledge of population structure is essential to improve the management and conservation of farm animal genetic resources. Microsatellites, which have long been popular for this type of analysis, are more and more neglected in favor of whole-genome single nucleotide polymorphism (SNP) chips that are now available for the main farmed animal species. In this study, we compared genetic patterns derived from microsatellites to that inferred by SNPs, considering three pairs of datasets of sheep and cattle. Population genetic differentiation analyses (Fixation index, FST ), as well as STRUCTURE analyses showed a very strong consistency between the two types of markers. Microsatellites gave pictures that were largely concordant with SNPs, although less accurate. The best concordance was found in the most complex dataset, which included 17 French sheep breeds (with a Pearson correlation coefficient of 0.95 considering the 136 values of pairwise FST, obtained with both types of markers). The use of microsatellites reduces the cost and the related analyses do not require specific computer equipment (i.e., information technology (IT) infrastructure able to provide adequate computing and storage capacity). Therefore, this tool may still be a very appropriate solution to evaluate, in a first stage, the general state of livestock at national scales. At a time when local breeds are disappearing at an alarming rate, it is urgent to improve our knowledge of them, in particular by promoting tools accessible to the greatest number

Comparison of growth performance, carcass characteristics and meat quality of Benin indigenous chickens and Label Rouge (T55×SA51)

A study on growth performance, carcass traits and meat quality was carried out on Savannah and Forest  ecotype chicken of Benin, using Label Rouge (T55 X SA51) as a control genotype. All the animals were fed ad  libitum with three diets (starter, grower and layer feed). They were individually weighed at hatching and during the growing stage, and the daily feed intake was recorded. A sample of 12 males of each genetic type was  slaughtered for carcass characteristics. Sensory analysis was done on each genetic type after boiling or  roasting. The Label Rouge chickens were heavier than the local chickens at hatch (P&lt;0.001). At the end of 40  weeks, the weight of the Label Rouge was double that of the Savannah ecotype and 2.8 times that of the Forest ecotype. The feed efficiency of the Label Rouge was higher than that of the local chickens (P&lt;0.001). The  genetic type influenced tenderness and juiciness, with the local Savannah chicken being the most tender and  juiciest (P&lt;0.001). However, the cooking method and the carcass cut influenced tenderness only. The overall assessment of the meat of the Label Rouge chickens was similar to that of the local chickens, whereas the  assessment of the meat was significantly lower for local chickens of Forest ecotype compared to the Savannah ecotype (P&lt;0.001). The local chickens would therefore be suitable for improving traditional poultry production, whereas controlled crossbreeding programmes using Label Rouge could be recommended to improve local chicken weight.Key words: Growth, carcass, sensory characters, indigenous chicken, Label Rouge

Haptic Guidance with a Soft Exoskeleton Reduces Error in Drone Teleoperation

Haptic guidance has been shown to improve performance in many fields as it can give additional information without overloading other sensory channels such as vision or audition. Our group is investigating new intuitive ways to interact with robots, and we developed a suit to control drones with upper body movement, called the FlyJacket. In this paper, we present the integration of a cable-driven haptic guidance in the FlyJacket. The aim of the device is to apply a force relative to the distance between the drone and a predetermined trajectory to correct user torso orientation and improve the flight precision. Participants (n=10) flying a simulated fixed-wing drone controlled with torso movements tested four different guidance profiles (three linear profiles with different stiffness and one quadratic). Our results show that a quadratically shaped guidance, which gives a weak force when the error is small and a strong force when the error becomes significant, was the most effective guidance to improve the performance. All participants also reported through questionnaires that the haptic guidance was useful for flight control

Genetic analysis of local Vietnamese chickens provides evidence of gene flow from wild to domestic populations

<p>Abstract</p> <p>Background</p> <p>Previous studies suggested that multiple domestication events in South and South-East Asia (Yunnan and surrounding areas) and India have led to the genesis of modern domestic chickens. Ha Giang province is a northern Vietnamese region, where local chickens, such as the H'mong breed, and wild junglefowl coexist. The assumption was made that hybridisation between wild junglefowl and Ha Giang chickens may have occurred and led to the high genetic diversity previously observed. The objectives of this study were i) to clarify the genetic structure of the chicken population within the Ha Giang province and ii) to give evidence of admixture with <it>G. gallus</it>. A large survey of the molecular polymorphism for 18 microsatellite markers was conducted on 1082 chickens from 30 communes of the Ha Giang province (HG chickens). This dataset was combined with a previous dataset of Asian breeds, commercial lines and samples of Red junglefowl from Thailand and Vietnam (Ha Noï). Measurements of genetic diversity were estimated both within-population and between populations, and a step-by-step Bayesian approach was performed on the global data set.</p> <p>Results</p> <p>The highest value for expected heterozygosity (> 0.60) was found in HG chickens and in the wild junglefowl populations from Thailand. HG chickens exhibited the highest allelic richness (mean A = 2.9). No significant genetic subdivisions of the chicken population within the Ha Giang province were found. As compared to other breeds, HG chickens clustered with wild populations. Furthermore, the neighbornet tree and the Bayesian clustering analysis showed that chickens from 4 communes were closely related to the wild ones and showed an admixture pattern.</p> <p>Conclusion</p> <p>In the absence of any population structuring within the province, the H'mong chicken, identified from its black phenotype, shared a common gene pool with other chickens from the Ha Giang population. The large number of alleles shared exclusively between Ha Giang chickens and junglefowl, as well as the results of a Bayesian clustering analysis, suggest that gene flow has been taking place from junglefowl to Ha Giang chickens.</p

Genetic variability in the Skyros pony and its relationship with other Greek and foreign horse breeds

In Greece, seven native horse breeds have been identified so far. Among these, the Skyros pony is outstanding through having a distinct phenotype. In the present study, the aim was to assess genetic diversity in this breed, by using different types of genetic loci and available genealogical information. Its relationships with the other Greek, as well as foreign, domestic breeds were also investigated. Through microsatellite and pedigree analysis it appeared that the Skyros presented a similar level of genetic diversity to the other European breeds. Nevertheless, comparisons between DNA-based and pedigree-based results revealed that a loss of genetic diversity had probably already occurred before the beginning of breed registration. Tests indicated the possible existence of a recent bottleneck in two of the three main herds of Skyros pony. Nonetheless, relatively high levels of heterozygosity and Polymorphism Information Content indicated sufficient residual genetic variability, probably useful in planning future strategies for breed conservation. Three other Greek breeds were also analyzed. A comparison of these with domestic breeds elsewhere, revealed the closest relationships to be with the Middle Eastern types, whereas the Skyros itself remained isolated, without any close relationship, whatsoever