Managing genetic diversity in breeding programs of small populations: the case of French local chicken breeds.

BACKGROUND: On-going climate change will drastically modify agriculture in the future, with a need for more sustainable systems, in particular regarding animal production. In this context, genetic diversity is a key factor for adaptation to new conditions: local breeds likely harbor unique adaptive features and represent a key component of diversity to reach resilience. However, local breeds often suffer from small population sizes, which puts these valuable resources at risk of extinction. In chickens, population management programs were initiated a few decades ago in France, relying on a particular niche market that aims at promoting and protecting local breeds. We conducted a unique comprehensive study of 22 French local breeds, along with four commercial lines, to evaluate their genetic conservation status and the efficiency of the population management programs. RESULTS: Using a 57K single nucleotide polymorphism (SNP) chip, we demonstrated that both the between- and within-breed genetic diversity levels are high in the French local chicken populations. Diversity is mainly structured according to the breeds' selection and history. Nevertheless, we observed a prominent sub-structuring of breeds according to farmers' practices in terms of exchange, leading to more or less isolated flocks. By analysing demographic parameters and molecular information, we showed that consistent management programs are efficient in conserving genetic diversity, since breeds that integrated such programs earlier had older inbreeding. CONCLUSIONS: Management programs of French local chicken breeds have maintained their genetic diversity at a good level. We recommend that future programs sample as many individuals as possible, with emphasis on both males and females from the start, and focus on a quick and strong increase of population size while conserving as many families as possible. We also stress the usefulness of molecular tools to monitor small populations for which pedigrees are not always available. Finally, the breed appears to be an appropriate operational unit for the conservation of genetic diversity, even for local breeds, for which varieties, if present, could also be taken into account.

Prenatal maternal stress is associated with behavioural and epigenetic changes in Japanese quail.

Prenatal maternal stress (PMS) influences many facets of offspring's phenotype including morphology, behaviour and cognitive abilities. Recent research suggested that PMS also induced epigenetic modifications. In the present study, we analysed, in the Japanese quail, the effects of PMS on the emotional reactivity and cognitive abilities of the F1 offspring. We also investigated in the hippocampus, the paraventricular hypothalamic nucleus and subnuclei of the arcopallium/amygdala the level of two histone post-translational modifications, H3K4me2 and H3K27me3, known to be impacted by stress. We found that PMS does not affect F1 quail's learning abilities but increases their emotional reactivity. Moreover, we demonstrated that PMS induced an increased density of H3K27me3 positive cells, in the hippocampus, paraventricular hypothalamic nucleus and dorsal nucleus of the amygdala, but not variations of H3K4me2. As these brain regions are involved in the control of vertebrates' emotional responses, the effect of PMS on the epigenetic mark H3K27me3 could possibly be a mechanism involved in the behavioural effects we observed in F1 quail.

A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes.

The helmeted guinea fowl Numida meleagris belongs to the order Galliformes. Its natural range includes a large part of sub-Saharan Africa, from Senegal to Eritrea and from Chad to South Africa. Archaeozoological and artistic evidence suggest domestication of this species may have occurred about 2,000 years BP in Mali and Sudan primarily as a food resource, although villagers also benefit from its capacity to give loud alarm calls in case of danger, of its ability to consume parasites such as ticks and to hunt snakes, thus suggesting its domestication may have resulted from a commensal association process. Today, it is still farmed in Africa, mainly as a traditional village poultry, and is also bred more intensively in other countries, mainly France and Italy. The lack of available molecular genetic markers has limited the genetic studies conducted to date on guinea fowl. We present here a first-generation whole-genome sequence draft assembly used as a reference for a study by a Pool-seq approach of wild and domestic populations from Europe and Africa. We show that the domestic populations share a higher genetic similarity between each other than they do to wild populations living in the same geographical area. Several genomic regions showing selection signatures putatively related to domestication or importation to Europe were detected, containing candidate genes, most notably EDNRB2, possibly explaining losses in plumage coloration phenotypes in domesticated populations.

Objectives and applications of phenotyping network set-up for livestock.

Providing phenotypic information, which is accurate, reliable, repeatable and comparable across countries or laboratories, is critical to gain a better understanding of the relationship between genes and phenotypes. So far, it is indeed extremely difficult to combine different sources of phenotypic data from multiple origins, partly because of the variability in the methods of phenotyping. The phenotyping program of livestock involves the definition of complex phenotypes obtained from data integration at different levels (from molecules to herds), the implementation of the latest technologies to accurately characterize at high speed and low cost, the greatest number of animals in a better characterized environment, and the development and sharing of large databases for data analysis and modeling. Such a program also involves the construction of a coordinated network of research and professional facilities and a common language with shared definition of unambiguous animal traits and of methods to assess them. To this end, it will build on the 'Animal Trait Ontology of Livestock' (ATOL) project with the objective of defining precisely the phenotypes of interest for farm animals. Then, it will be necessary to combine an environmental information system related to animal husbandry and associated methods to capture the phenotypic differences between animals.

Effect of one week of stress on emotional reactivity and learning and memory performances in Japanese quail.

Chronic stress is known to induce long term alterations of emotional behaviours as well as cognitive performances leading thereby to welfare or husbandry problems. These stress-induced consequences are observed following long periods of stress lasting from several weeks to several years. The current study examined whether a shorter period of stress (one week) produced similar impairing effects. Two-week old Japanese quail were either submitted to a series of aversive events over consecutive 8 days, at unpredictable times each day (treated animals) or left undisturbed (controls). Following the treatment period, animals were weighed and basal as well as aversive events-induced levels of plasma corticosterone were quantified. Quail were also tested for emotional reactivity in three tests (the tonic immobility test, the hole-in-the-wall and novel object tests) and for spatial reference memory. Although there was no difference in corticosterone levels between the two groups, the treated animals had lower body weight than controls. Behavioural investigations after the treatment period did not reveal any difference between the groups in the three emotional reactivity tests. In the spatial task, treated quail displayed enhanced behavioural flexibility as revealed by their higher performances during the reversal phase of the task. The alteration of growth suggests that a short period of repetitive exposures to unpredictable aversive events can be perceived by quail as stressful. Such a stress period can improve spatial learning performances in quail supporting the critical role played by the duration of the stress period on cognitive performance.

Social instability in laying quail: consequences on yolk steroids and offspring's phenotype.

Individual phenotypic characteristics of many species are influenced by non-genetic maternal effects. Female birds can influence the development of their offspring before birth via the yolk steroid content of their eggs. We investigated this prenatal maternal effect by analysing the influence of laying females' social environment on their eggs' hormonal content and on their offspring's development. Social instability was applied to groups of laying Japanese quail females. We evaluated the impact of this procedure on laying females, on yolk steroid levels and on the general development of chicks. Agonistic interactions were more frequent between females kept in an unstable social environment (unstable females) than between females kept in a stable social environment (stable females). Testosterone concentrations were higher in unstable females' eggs than in those of stable females. Unstable females' chicks hatched later and developed more slowly during their first weeks of life than those of stable females. The emotional reactivity of unstable females' chicks was higher than that of stable females' chicks. In conclusion, our study showed that social instability applied to laying females affected, in a non-genetic way, their offspring's development, thus stressing the fact that females' living conditions during laying can have transgenerational effects.

Gene array analysis of adrenal glands in broiler chickens following ACTH treatment.

BACKGROUND: Difference in adaptability responses to stress has been observed amongst bird species, strains, and individuals. Components of the HPA axis, one of the internal systems involved in homeostasis re-establishment following stress, could play a role in this variability of responses. The aim of the present study was 1) to identify genes involved in the regulation of adrenal activity following ACTH stimulation and 2) to examine adrenal genes differentially expressed in individuals with high and low plasma corticosterone response following ACTH treatment. RESULTS: Analysis with 21 K poultry oligo microarrays indicated that ACTH treatment affected the expression of 134 genes. Several transcripts assigned to genes involved in the adrenal ACTH signaling pathway and steroidogenic enzymes were identified as differentially expressed by ACTH treatment. Real-time PCR on 18 selected genes confirmed changes in transcript levels of 11 genes, including MC2R, CREM, Cry, Bmal1, Sqle, Prax1, and StAR. Only 4 genes revealed to be differentially expressed between higher and lower adrenal responders to ACTH treatment. CONCLUSION: The results from the present study reveal putative candidate genes; their role in regulation of adrenal functions and adaptability to stress should be further investigated.

Adrenal reactivity in lines of domestic fowl selected on feather pecking behavior.

Domestic chicken lines of the White Leghorn layer type differing in their level of feather pecking have been developed by divergent selection specifically on feather pecking behavior. This paper describes an investigation of basal level, reactivity to manual restraint and maximal adrenal response to 1-24 ACTH in breeder birds of the sixth generation of selection (S6) and their control line. Birds from the three lines had comparable basal levels of corticosterone (1.6 ng/ml, anova F(2,101)=0.62, ns), whereas males had higher basal levels than females, lsmean 1.9 vs. 1.5 ng/ml (anova F(1,103)=6.03, P<0.05). Reactivity to handling and restraint for 10 min differed with HFP birds showing higher reactivity than LFP birds, lsmean 11.0 vs. 7.9 ng/ml (t=-2.00, P<0.05), while control birds showed intermediate levels (10.2 ng/ml). Males had higher reactivity than females, lsmean 11.2 vs. 8.2 ng/ml (anova F(1,103)=3.96, P<0.05). Maximal response did not differ between lines (average 35.7 ng/ml, anova F(2,101)=1.38, P>0.05). Males had higher maximal response than females, lsmean 41.3 vs. 33.6 ng/ml (anova F(1,103)=5.77, P<0.05). The present study shows that selection against feather pecking behavior have resulted in lower levels of feather pecking as well as lower sensitivity to human handling and restraint in White Leghorn laying hen lines. From an animal welfare point of view this is a positive relationship.

Genetic differences in coping strategies in response to prolonged and repeated restraint in Japanese quail divergently selected for long or short tonic immobility.

Exposure to fearful situations elicits behavioral and Hypothalamic-Pituitary-Adrenal (HPA) axis responses characteristic of the coping response of individual animals to counteract environmental challenges. The aim of this study was to investigate behavioral and corticotropic responses concomitantly following prolonged or repeated restraint stress by placing two genotypes of Japanese quail divergently selected for long (LTI) or short (STI) duration of tonic immobility (TI) in a crush cage. In our study, STI quail exhibited higher corticosterone (CORT) levels than LTI quail in response to prolonged restraint. STI quail struggled sooner and much more than LTI quail, and struggling behavior in STI quail progressively decreased during the course of restraint whereas LTI quail displayed very little struggling behavior in the crush cage. LTI quail are thus more likely to adopt a passive behavior coping strategy upon exposure to threat whereas STI quail behave more as active copers. The corticosterone responses shown by LTI and STI quail under restraint stress suggest that adrenocortical correlates of coping behavior in these genotypes of quail may be different from the coping styles previously described in other species. Repeated restraint slightly decreased CORT responses to stress in all experimental groups, but more markedly in male STI quail, whereas adrenal sensitivity and maximum adrenal corticosterone response capacity did not change in any group. On the other hand, neither behavioral habituation nor sensitization processes occurred in the context of repeated restraint in female and male LTI quail and female STI quail, whereas the decreases observed in some behavioral responses were interpreted to be the result of a habituation process in male STI quail.

Exploration of the hypothalamic-pituitary-adrenal function as a tool to evaluate animal welfare.

Measuring HPA axis activity is the standard approach to the study of stress and welfare in farm animals. Although the reference technique is the use of blood plasma to measure glucocorticoid hormones (cortisol or corticosterone), several alternative methods such as the measurement of corticosteroids in saliva, urine or faeces have been developed to overcome the stress induced by blood sampling itself. In chronic stress situations, as is frequently the case in studies about farm animal welfare, hormonal secretions are usually unchanged but dynamic testing allows the demonstration of functional changes at several levels of the system, including the sensitization of the adrenal cortex to ACTH and the resistance of the axis to feedback inhibition by corticosteroids (dexamethasone suppression test). Beyond these procedural aspects, the main pitfall in the use of HPA axis activity is in the interpretation of experimental data. The large variability of the system has to be taken into consideration, since corticosteroid hormone secretion is usually pulsatile, follows diurnal and seasonal rhythms, is influenced by feed intake and environmental factors such as temperature and humidity, age and physiological state, just to cite the main sources of variation. The corresponding changes reflect the important role of glucocorticoid hormones in a number of basic physiological processes such as energy metabolism and central nervous system functioning. Furthermore, large differences have been found across species, breeds and individuals, which reflect the contribution of genetic factors and environmental influences, especially during development, in HPA axis functioning. Usually, these results will be integrated with data from behavioral observation, production and pathology records in a comprehensive approach of farm animal welfare.

Cloning of duck PRL cDNA and genomic DNA.

Complementary DNA (cDNA) and genomic DNA, including flanking regions of the prolactin (PRL) gene of domesticated duck, were cloned and sequenced. Duck PRL was found to have 92.0, 91.7, and 91.4% sequence identity at the cDNA level to PRL of chicken, turkey, and quail, respectively. The predicted amino acid sequence had an overall similarity with a comparable region of chicken (93.4%), turkey (91.3%), and quail (91.3%) PRL. Mature duck PRL contains the consensus sequence for N-linked glycoslylation at position 6 which is not present in either chickens or turkeys. Thus, duck PRL is likely to be post-translationally modified differently from other avian species. Based on the cDNA sequence, the genomic structure of the gene was characterized. The duck PRL gene consists of 5 exons and 4 introns. Moreover, sequence analysis of the proximal region of duck PRL promoter revealed a high degree of similarity to that of chicken and turkey PRL promoter. These results suggest that the mechanisms, which regulate expression of the PRL gene, may be widely conserved in avian species.