Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways ...underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total) using a high-density (58 K) SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The jungle fowl (Gallus gallus) is a tropical bird with important hereditary and phenotypical traits like disease resistance and resistance to harsh conditions and can often survive with scanty diet. ...However, as commercial chicken breeds replace them, their population is dwindling, which poses a significant threat to fowl genetic resources. There is minimal information on the variety of Indian poultry, mainly native chicken from Northeast India. As a result, the record of the fowl's genetic diversity is essential for its preservation and formulation of conservation strategies. The current study sought to identify indigenous chicken, Kaunayen (Gallus gallus domesticus), from Manipur using barcoding based on DNA sequences. A total of 5 CO1 DNA barcodes from several indigenous chickens were sequenced and compared to the previous data of diverse taxa of Phasianidae using the conventional methodology and were recognized as Gallus gallus. The Phasianid birds that were researched were accurately classified into their appropriate species. There is a minuscule genomic difference between G. gallus and G. varius (1.2%) and the highest between Arborophila rufipectus and Tympanuchus pallidicinctus (22.5%). The phylogenetic relationship established on the NJ tree revealed a coherent gathering of indigenous fowl with G. gallus and unique to all other species studied, showing their taxonomic classification. Nonetheless, the investigation offered a genetic identity tag for indigenous chicken for the first time. It will be a potential guide for identifying distinctive and genetically unique poultry sequences for later requirements.
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Dostopno za:
BFBNIB, DOBA, GIS, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Domestic chickens (Gallus gallus domesticus) fulfill various roles ranging from food and entertainment to religion and ornamentation. To survey its genetic diversity and trace the history of ...domestication, we investigated a total of 4938 mitochondrial DNA (mtDNA) fragments including 2843 previously published and 2095 de novo units from 2044 domestic chickens and 51 red junglefowl (Gallus gallus). To obtain the highest possible level of molecular resolution, 50 representative samples were further selected for total mtDNA genome sequencing. A fine-gained mtDNA phylogeny was investigated by defining haplogroups A-I and W-Z. Common haplogroups A-G were shared by domestic chickens and red junglefowl. Rare haplogroups H-I and W-Z were specific to domestic chickens and red junglefowl, respectively. We re-evaluated the global mtDNA profiles of chickens. The geographic distribution for each of major haplogroups was examined. Our results revealed new complexities of history in chicken domestication because in the phylogeny lineages from the red junglefowl were mingled with those of the domestic chickens. Several local domestication events in South Asia, Southwest China and Southeast Asia were identified. The assessment of chicken mtDNA data also facilitated our understanding about the Austronesian settlement in the Pacific.
Nearly three decades ago, zooarchaeologists postulated that chicken husbandry was practiced in Northern China by ∼8.0 ka calBP. Recently, ancient mitogenome analyses of galliform remains suggested ...that Red jungle fowl (Gallus gallus) was already present in the Yellow River basin several millennia earlier, shortly after the onset of the Holocene. If these conclusions are correct, the origins of chicken domestication and husbandry in the region may have been spurred by agricultural innovations in the lower Yellow River basin including millet cultivation, pig husbandry, and dog breeding. In addition, the dispersal of poultry farming from East Asia to Asia Minor and Europe could therefore date to the Neolithic along ancient trade routes across Central Asia rather than via South Asia and Mesopotamia. For this scenario to be plausible, the post-Pleistocene climatic conditions must have been favourable to allow for a northward extension of the native distribution of tropical Red jungle fowl currently not found north of ∼25°N. This study combines Holocene palaeoclimate and archaeofaunal archives with new zooarchaeological insights alongside a discussion of methodological issues and cultural aspects in order to revisit the hypothesis of an early Holocene Gallus domestication and Neolithic poultry husbandry in Northern China. Our results regarding the natural and cultural history of Red jungle fowl and domestic chickens in East Asia, and the timing of chicken dispersal across the Old World suggest that an early Holocene domestication of chickens is problematic at best. We conclude by postulating an alternative model for the early exploitation of a key domestic species in present-day East Asia.
•This study revisits the long-standing hypothesis of chicken domestication in Holocene Northern China.•Mammalian composition in Northern Chinese Neolithic sites is essentially Palaearctic.•Zooarchaeology points to the absence of Gallus in Northern China prior to ∼3.5 ka calBP.•The Shang Dynasty (∼1600-1046 BCE) likely marks the onset of poultry farming in Northern China.
Chickens represent by far the most important poultry species, yet the number, locations, and timings of their domestication have remained controversial for more than a century. Here we report ancient ...mitochondrial DNA sequences from the earliest archaeological chicken bones from China, dating back to ∼10,000 B.P. The results clearly show that all investigated bones, including the oldest from the Nanzhuangtou site, are derived from the genus Gallus , rather than any other related genus, such as Phasianus . Our analyses also suggest that northern China represents one region of the earliest chicken domestication, possibly dating as early as 10,000 y B.P. Similar to the evidence from pig domestication, our results suggest that these early domesticated chickens contributed to the gene pool of modern chicken populations. Moreover, our results support the idea that multiple members of the genus Gallus , specifically Gallus gallus and Gallus sonneratii contributed to the gene pool of the modern domestic chicken. Our results provide further support for the growing evidence of an early mixed agricultural complex in northern China.
Significance Ancient DNA analysis is a powerful tool to reveal the geographical origins of domesticated species. Here we obtained ancient mtDNA sequences from the earliest archaeological chicken bones from northern China as early as 10,000 y ago. Combined analyses of our ancient sequences with a large dataset of published modern and ancient chicken mtDNA sequences suggest that northern China was likely one of several regions of chicken domestication and provide further insights into the process of human-mediated spread of chickens across the globe. Our results not only suggest that the oldest archaeological chicken bones recovered so far are indeed from ancestors of domestic chickens, but also provide further evidence for one of the earliest, mixed agricultural complexes in the world.
Genetic selection for enhanced growth rate in meat-type chickens (Gallus domesticus) is usually accompanied by excessive adiposity, which has negative impacts on both feed efficiency and carcass ...quality. Enhanced visceral fatness and several unique features of avian metabolism (i.e., fasting hyperglycemia and insulin insensitivity) mimic overt symptoms of obesity and related metabolic disorders in humans. Elucidation of the genetic and endocrine factors that contribute to excessive visceral fatness in chickens could also advance our understanding of human metabolic diseases. Here, RNA sequencing was used to examine differential gene expression in abdominal fat of genetically fat and lean chickens, which exhibit a 2.8-fold divergence in visceral fatness at 7 wk. Ingenuity Pathway Analysis revealed that many of 1687 differentially expressed genes are associated with hemostasis, endocrine function and metabolic syndrome in mammals. Among the highest expressed genes in abdominal fat, across both genotypes, were 25 differentially expressed genes associated with de novo synthesis and metabolism of lipids. Over-expression of numerous adipogenic and lipogenic genes in the FL chickens suggests that in situ lipogenesis in chickens could make a more substantial contribution to expansion of visceral fat mass than previously recognized. Distinguishing features of the abdominal fat transcriptome in lean chickens were high abundance of multiple hemostatic and vasoactive factors, transporters, and ectopic expression of several hormones/receptors, which could control local vasomotor tone and proteolytic processing of adipokines, hemostatic factors and novel endocrine factors. Over-expression of several thrombogenic genes in abdominal fat of lean chickens is quite opposite to the pro-thrombotic state found in obese humans. Clearly, divergent genetic selection for an extreme (2.5-2.8-fold) difference in visceral fatness provokes a number of novel regulatory responses that govern growth and metabolism of visceral fat in this unique avian model of juvenile-onset obesity and glucose-insulin imbalance.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Underlying the study of animal welfare is the assumption that animals experience emotional states. Although there has been a bias towards studying negative emotions, research into positive emotions ...is necessary for an overall welfare assessment. The aim of the current study was to find behavioural expressions specific for anticipation of different events in domestic fowl,
Gallus gallus domesticus. To this aim, we used a Pavlovian conditioning paradigm by which we induced anticipation of a positive, neutral and negative event. We investigated whether birds were able to discriminate between sound cues signalling these events with different valences and, if so, whether anticipation of different events is reflected in different behavioural responses. The birds showed a response of increased attention to all sound cues. In anticipation of the negative event, the birds showed more head movements and locomotion than in anticipation of both the neutral and positive event, possibly reflecting the aversive nature of the negative event. In anticipation of the positive event, the birds showed more comfort behaviours, such as preening and wing flapping, which have been associated with a state of relaxation. Our study shows that laying hens are able to anticipate differentially a positive, neutral and negative event announced by different sound cues. It is also the first study to identify comfort behaviours as specifically associated with anticipation of a positive event in domestic fowl. Comfort behaviours may therefore be associated with a positive emotional state in domestic fowl.
With the aim of elucidating in greater detail the genealogical origin of the present domestic fowls of the world, we have determined mtDNA sequences of the D-loop regions for a total of 21 birds, of ...which 12 samples belong to red junglefowl (Gallus gallus) comprising three subspecies (six Gallus gallus gallus, three Gallus gallus spadiceus, and three Gallus gallus bankiva) and nine represent diverse domestic breeds (Gallus gallus domesticus). We also sequenced four green junglefowl (Gallus varius), two Lafayette's junglefowl (Gallus lafayettei), and one grey junglefowl (Gallus sonneratii). We then constructed a phylogenetic tree for these birds by the use of nucleotide sequences, choosing the Japanese quail (Coturnix coturnix japonica) as an outgroup. We found that a continental population of G. g. gallus was the real matriarchic origin of all the domestic poultries examined in this study. It is also of particular interest that there were no discernible differences among G. gallus subspecies; G. g. bankiva was a notable exception. This was because G. g. spadiceus and a continental population of G. g. gallus formed a single cluster in the phylogenetic tree. G. g. bankiva, on the other hand, was a distinct entity, thus deserving its subspecies status. It implies that a continental population of G. g. gallus sufficed as the monophyletic ancestor of all domestic breeds. We also discussed a possible significance of the initial dispersal pattern of the present domestic fowls, using the phylogenetic tree.
The effect of endocannabinoids on synaptic plasticity has been demonstrated in a variety of species and brain regions. Relatively little is known about the localization and significance of ...cannabinoid (CB) receptors in the avian brain. The objective of the present study was to investigate the effect of a specific CB@d1 receptor antagonist upon the acquisition and consolidation of memory in young domestic chicks. One-day-old domestic chicks (Gallus domesticus) were trained and tested by the passive avoidance paradigm. Systemic (i.p.) administration of the CB@d1 receptor antagonist rimonabant in a dose of 1mg/kg 30min before the training failed to affect learning, but a similar treatment 30min before the recall (5.5h after training) attenuated the retention in 60% of animals. In another set of animals, a dose of 0.01mg/kg produced no significant impairment, whereas doses 0.1mg/kg and 1.0mg/kg resulted in significant attenuation in passive avoidance performance when tested 30min prior to recall. The results are discussed in terms of a putative mediating role of CB receptors in the consolidation of memory.
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