The cumulated effects of domestication and subsequent selection by humans have led to impressive diversification of the chicken at the phenotypic as well as the genome level. In theory, selection may ...reach a plateau when all favourable alleles have reached fixation. Yet, current data for poultry show that the selection response can still take place after 50 generations or more. The mechanisms maintaining selection response in closed populations may involve recombination, mutation and epistatic interactions. Furthermore, the continuous addition of new selection criteria can delay the possible limits associated to single trait selection. Selection response is mainly threatened by inbreeding, which occurs as a consequence of a narrow genetic base and/or a poor management of variability within the population. Biological limits are encountered when selection degrades fitness traits to a point that the survival of individuals is affected. Biological limits induced by extreme performance can be by-passed by adapting the breeding programme, introducing new selection criteria, changing the management or developing remedial technologies. Extreme situations affecting bird welfare raise ethical issues. Lameness in broilers or spontaneous bone breakage in layers is painful and one may question whether such pain is justified by the human need for protein consumption. Regulations or market requirements may be set up to limit the performance at a level, which is compatible with animal welfare, resulting in a voluntary limit to selection. Furthermore, highly performing animals need a well-controlled environment with high quality diets, which may divert food resources from humans and may not be sustainable. Breeding objectives have to integrate environmental impact and robustness towards the use of alternative feed sources, in addition to production level, product quality, health and welfare status.
The chocolate plumage color in chickens is due to a sex‐linked recessive mutation, choc, which dilutes eumelanin pigmentation. Because TYRP1 is sex‐linked in chickens, and TYRP1 mutations determine ...brown coat color in mammals, TYRP1 appeared as the obvious candidate gene for the choc mutation. By combining gene mapping with gene capture, a complete association was identified between the chocolate phenotype and a missense mutation leading to a His214Asn change in the ZnA zinc‐binding domain of the protein. A diagnostic test confirmed complete association by screening 428 non‐chocolate chickens of various origins. This is the first TYRP1 mutation described in the chicken. Electron microscopy analysis showed that melanosomes were more numerous in feather follicles of chocolate chickens but exhibited an abnormal structure characterized by a granular content and an irregular shape. A similar altered morphology was observed on melanosomes of another TYRP1 mutant in birds, the roux mutation of the quail.
Color patterns within individual feathers are common in birds but little is known about the genetic mechanisms causing such patterns. Here, we investigate the genetic basis for autosomal barring in ...chicken, a horizontal striping pattern on individual feathers. Using an informative backcross, we demonstrate that the MC1R locus is strongly associated with this phenotype. A deletion at SOX10, underlying the dark brown phenotype on its own, affects the manifestation of the barring pattern. The coding variant L133Q in MC1R is the most likely causal mutation for autosomal barring in this pedigree. Furthermore, a genetic screen across six different breeds showing different patterning phenotypes revealed that the most striking shared characteristics among these breeds were that they all carried the MC1R alleles Birchen or brown. Our data suggest that the presence of activating MC1R mutations enhancing pigment synthesis is an important mechanism underlying pigmentation patterns on individual feathers in chicken. We propose that MC1R and its antagonist ASIP play a critical role for determining within‐feather pigmentation patterns in birds by acting as activator and inhibitor possibly in a Turing reaction–diffusion model.
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.
ABSTRACT
For the past 50 yr, practices for ex situ preservation of endangered breeds have been extended. Semen and primordial germ cells, gonadic tissues have been frozen to create genetic stocks of ...chicken genetic diversity in cryobanks. Semen cryopreservation stays the preferred method since it is not invasive. Many protocols have been developed to cryopreserve chicken semen, but they give highly variable success rate. The aim of the present study was to standardize and prove the effectiveness of semen long-term storage for the restitution of lost families. We showed that semen straws stored for 18 yr in liquid nitrogen did not lose their fertilizing ability. We demonstrated the usefulness of cryopreserved semen stored in the French National Cryobank for the recovery of families of a subfertile experimental chicken line. In order to highlight the standardization of the cryopreserved method, different cryoprotectant protocols were also tested on a rare breed, freezing/thawing and insemination conditions were controlled. The best results were obtained using glycerol protocol, a sperm dilution of 1:4 (semen:extender). The insemination dose of 200 million sperm/female was as efficient as 400 million of sperm. Altogether, these results demonstrated the effectiveness of chicken semen long-term storage for the restoration of lost genetic resources and highlighted the importance of standardized chicken semen cryopreservation using procedures combining biophysical (cryoprotectants, freezing/thawing conditions) and zootechnical (artificial insemination) features.
Current knowledge on chicken domestication is reviewed on the basis of archaeological, historical and molecular data. Several domestication centres have been identified in South and South-East Asia. ...Gallus gallus is the major ancestor species, but Gallus sonneratii has also contributed to the genetic make-up of the domestic chicken. Genetic diversity is now distributed among traditional populations, standardized breeds and highly selected lines. Knowing the genome sequence has accelerated the identification of causal mutations determining major morphological differences between wild Gallus and domestic breeds. Comparative genome resequencing between Gallus and domestic chickens has identified 21 selective sweeps, one involving a non-synonymous mutation in the TSHR gene, which functional consequences remain to be explored. The resequencing approach could also identify candidate genes responsible of quantitative traits loci (QTL) effects in selected lines. Genomics is opening new ways to understand major switches that took place during domestication and subsequent selection.
Domestic animals are excellent models for genetic studies of phenotypic evolution. They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven ...selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor. We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research.
Genetic diversity is a necessary condition for populations to evolve under natural adaptation, artificial selection, or both. However, genetic diversity is often threatened, in particular in domestic ...animal populations where artificial selection, genetic drift and inbreeding are strong. In this context, cryopreserved genetic resources are a promising option to reintroduce lost variants and to limit inbreeding. However, while the use of ancient genetic resources is more common in plant breeding, it is less documented in animals due to a longer generation interval, making it difficult to fill the gap in performance due to continuous selection. This study investigates one of the only concrete cases available in animals, for which cryopreserved semen from a bull born in 1977 in a lost lineage was introduced into the breeding scheme of a French local dairy cattle breed, the Abondance breed, more than 20 years later.
We found that this re-introduced bull was genetically distinct with respect to the current population and thus allowed part of the genetic diversity lost over time to be restored. The expected negative gap in milk production due to continuous selection was absorbed in a few years by preferential mating with elite cows. Moreover, the re-use of this bull more than two decades later did not increase the level of inbreeding, and even tended to reduce it by avoiding mating with relatives. Finally, the reintroduction of a bull from a lost lineage in the breeding scheme allowed for improved performance for reproductive abilities, a trait that was less subject to selection in the past.
The use of cryopreserved material is an efficient way to manage the genetic diversity of an animal population, by mitigating the effects of both inbreeding and strong selection. However, attention should be paid to mating of animals to limit the disadvantages associated with incorporating original genetic material, notably a discrepancy in the breeding values for selected traits or an increase in inbreeding. Therefore, careful characterization of the genetic resources available in cryobanks could help to ensure the sustainable management of populations, in particular local or small populations. These results could also be transferred to the conservation of wild threatened populations.
Pea-comb is a dominant mutation in chickens that drastically reduces the size of the comb and wattles. It is an adaptive trait in cold climates as it reduces heat loss and makes the chicken less ...susceptible to frost lesions. Here we report that Pea-comb is caused by a massive amplification of a duplicated sequence located near evolutionary conserved non-coding sequences in intron 1 of the gene encoding the SOX5 transcription factor. This must be the causative mutation since all other polymorphisms associated with the Pea-comb allele were excluded by genetic analysis. SOX5 controls cell fate and differentiation and is essential for skeletal development, chondrocyte differentiation, and extracellular matrix production. Immunostaining in early embryos demonstrated that Pea-comb is associated with ectopic expression of SOX5 in mesenchymal cells located just beneath the surface ectoderm where the comb and wattles will subsequently develop. The results imply that the duplication expansion interferes with the regulation of SOX5 expression during the differentiation of cells crucial for the development of comb and wattles. The study provides novel insight into the nature of mutations that contribute to phenotypic evolution and is the first description of a spontaneous and fully viable mutation in this developmentally important gene.
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. 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. 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.
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