The lavender plumage colour in Japanese quail is associated with a complex mutation in the region of MLPH that is related to differences in growth, feed consumption and body temperature

Background The lavender phenotype in quail is a dilution of both eumelanin and phaeomelanin in feathers that produces a blue-grey colour on a wild-type feather pattern background. It has been previously demonstrated by intergeneric hybridization that the lavender mutation in quail is homologous to the same phenotype in chicken, which is caused by a single base-pair change in exon 1 of MLPH. Results In this study, we have shown that a mutation of MLPH is also associated with feather colour dilution in quail, but that the mutational event is extremely different. In this species, the lavender phenotype is associated with a non-lethal complex mutation involving three consecutive overlapping chromosomal changes (two inversions and one deletion) that have consequences on the genomic organization of four genes (MLPH and the neighbouring PRLH, RAB17 and LRRFIP1). The deletion of PRLH has no effect on the level of circulating prolactin. Lavender birds have lighter body weight, lower body temperature and increased feed consumption and residual feed intake than wild-type plumage quail, indicating that this complex mutation is affecting the metabolism and the regulation of homeothermy. Conclusions An extensive overlapping chromosome rearrangement was associated with a non-pathological Mendelian trait and minor, non deleterious effects in the lavender Japanese quail which is a natural knockout for PRLH

Microsatellite mapping of QTL affecting growth, feed consumption, egg production, tonic immobility and body temperature of Japanese quail

BACKGROUND: The Japanese quail (Coturnix japonica) is both an animal model in biology and a commercial bird for egg and meat production. Modern research developments with this bird, however, have been slowed down by the limited information that is available on the genetics of the Japanese quail. Recently, quail genetic maps with microsatellites and AFLP have been produced which open the way to comparative works with the chicken (Gallus gallus), and to QTL detection for a variety of traits. The purpose of this work was to detect for the first time QTL for commercial traits and for more basic characters in an F2 experiment with 434 female quail, and to compare the nature and the position of the detected QTL with those from the first chicken genome scans carried out during the last few years. RESULTS: Genome-wide significant or suggestive QTL were found for clutch length, body weight and feed intake on CJA01, age at first egg and egg number on CJA06, and eggshell weight and residual feed intake on CJA20, with possible pleiotropy for the QTL affecting body weight and feed intake, and egg number and age at first egg. A suggestive QTL was found for tonic immobility on CJA01, and chromosome-wide significant QTL for body temperature were detected on CJA01 and CJA03. Other chromosome-wide significant QTL were found on CJA02, CJA05, CJA09 and CJA14. Parent-of-origin effects were found for QTL for body weight and feed intake on CJA01. CONCLUSION: Despite its limited length, the first quail microsatellite map was useful to detect new QTL for rarely reported traits, like residual feed intake, and to help establish some correspondence between the QTL for feed intake, body weight and tonic immobility detected in the present work and those reported on GGA01 in the chicken. Further comparative work is now possible in order to better estimate and understand the genetic similarities and differences of these two Phasianidae species

Cryptic patterning of avian skin confers a developmental facility for loss of neck feathering

Vertebrate skin is characterized by its patterned array of appendages, whether feathers, hairs, or scales. In avian skin the distribution of feathers occurs on two distinct spatial levels. Grouping of feathers within discrete tracts, with bare skin lying between the tracts, is termed the macropattern, while the smaller scale periodic spacing between individual feathers is referred to as the micropattern. The degree of integration between the patterning mechanisms that operate on these two scales during development and the mechanisms underlying the remarkable evolvability of skin macropatterns are unknown. A striking example of macropattern variation is the convergent loss of neck feathering in multiple species, a trait associated with heat tolerance in both wild and domestic birds. In chicken, a mutation called Naked neck is characterized by a reduction of body feathering and completely bare neck. Here we perform genetic fine mapping of the causative region and identify a large insertion associated with the Naked neck trait. A strong candidate gene in the critical interval, BMP12/GDF7, displays markedly elevated expression in Naked neck embryonic skin due to a cis-regulatory effect of the causative mutation. BMP family members inhibit embryonic feather formation by acting in a reaction-diffusion mechanism, and we find that selective production of retinoic acid by neck skin potentiates BMP signaling, making neck skin more sensitive than body skin to suppression of feather development. This selective production of retinoic acid by neck skin constitutes a cryptic pattern as its effects on feathering are not revealed until gross BMP levels are altered. This developmental modularity of neck and body skin allows simple quantitative changes in BMP levels to produce a sparsely feathered or bare neck while maintaining robust feather patterning on the body. © 2011 Mou et al

Performance comparison of dwarf laying hens segregating for the naked neck gene in temperate and subtropical environments

This study compares laying performances between two environments of dwarf laying hen lines segregating for the naked neck mutation (NA locus), a selected dwarf line of brown-egg layers and its control line. Layers with one of the three genotypes at the NA locus were produced from 11 sires from the control line and 12 sires from the selected line. Two hatches produced 216 adult hens in Taiwan and 297 hens in France. Genetic parameters for laying traits were estimated in each environment and the ranking of sire breeding values was compared between environments. Laying performance was lower, and mortality was higher in Taiwan than in France. The line by environment interaction was highly significant for body weight at 16 weeks, clutch length and egg number, with or without Box-Cox transformation. The selected line was more sensitive to environmental change but in Taiwan it could maintain a higher egg number than the control line. Estimated heritability values in the selected line were higher in France than in Taiwan, but not for all the traits in the control line. The rank correlations between sire breeding values were low within the selected line and slightly higher in the control line. A few sire families showed a good ranking in both environments, suggesting that some families may adapt better to environmental change

Search for QTL affecting the shape of the egg laying curve of the Japanese quail

BACKGROUND: Egg production is of critical importance in birds not only for their reproduction but also for human consumption as the egg is a highly nutritive and balanced food. Consequently, laying in poultry has been improved through selection to increase the total number of eggs laid per hen. This number is the cumulative result of the oviposition, a cyclic and repeated process which leads to a pattern over time (the egg laying curve) which can be modelled and described individually. Unlike the total egg number which compounds all variations, the shape of the curve gives information on the different phases of egg laying, and its genetic analysis using molecular markers might contribute to understand better the underlying mechanisms. The purpose of this study was to perform the first QTL search for traits involved in shaping the egg laying curve, in an F(2 )experiment with 359 female Japanese quail. RESULTS: Eight QTL were found on five autosomes, and six of them could be directly associated with egg production traits, although none was significant at the genome-wide level. One of them (on CJA13) had an effect on the first part of the laying curve, before the production peak. Another one (on CJA06) was related to the central part of the curve when laying is maintained at a high level, and the four others (on CJA05, CJA10 and CJA14) acted on the last part of the curve where persistency is determinant. The QTL for the central part of the curve was mapped at the same position on CJA06 than a genome-wide significant QTL for total egg number detected previously in the same F(2). CONCLUSION: Despite its limited scope (number of microsatellites, size of the phenotypic data set), this work has shown that it was possible to use the individual egg laying data collected daily to find new QTL which affect the shape of the egg laying curve. Beyond the present results, this new approach could also be applied to longitudinal traits in other species, like growth and lactation in ruminants, for which good marker coverage of the genome and theoretical models with a biological significance are available

Cryptic Patterning of Avian Skin Confers a Developmental Facility for Loss of Neck Feathering

Vertebrate skin is characterized by its patterned array of appendages, whether feathers, hairs, or scales. In avian skin the distribution of feathers occurs on two distinct spatial levels. Grouping of feathers within discrete tracts, with bare skin lying between the tracts, is termed the macropattern, while the smaller scale periodic spacing between individual feathers is referred to as the micropattern. The degree of integration between the patterning mechanisms that operate on these two scales during development and the mechanisms underlying the remarkable evolvability of skin macropatterns are unknown. A striking example of macropattern variation is the convergent loss of neck feathering in multiple species, a trait associated with heat tolerance in both wild and domestic birds. In chicken, a mutation called Naked neck is characterized by a reduction of body feathering and completely bare neck. Here we perform genetic fine mapping of the causative region and identify a large insertion associated with the Naked neck trait. A strong candidate gene in the critical interval, BMP12/GDF7, displays markedly elevated expression in Naked neck embryonic skin due to a cis-regulatory effect of the causative mutation. BMP family members inhibit embryonic feather formation by acting in a reaction-diffusion mechanism, and we find that selective production of retinoic acid by neck skin potentiates BMP signaling, making neck skin more sensitive than body skin to suppression of feather development. This selective production of retinoic acid by neck skin constitutes a cryptic pattern as its effects on feathering are not revealed until gross BMP levels are altered. This developmental modularity of neck and body skin allows simple quantitative changes in BMP levels to produce a sparsely feathered or bare neck while maintaining robust feather patterning on the body

The Crest Phenotype in Chicken Is Associated with Ectopic Expression of HOXC8 in Cranial Skin

The Crest phenotype is characterised by a tuft of elongated feathers atop the head. A similar phenotype is also seen in several wild bird species. Crest shows an autosomal incompletely dominant mode of inheritance and is associated with cerebral hernia. Here we show, using linkage analysis and genome-wide association, that Crest is located on the E22C19W28 linkage group and that it shows complete association to the HOXC-cluster on this chromosome. Expression analysis of tissues from Crested and non-crested chickens, representing 26 different breeds, revealed that HOXC8, but not HOXC12 or HOXC13, showed ectopic expression in cranial skin during embryonic development. We propose that Crest is caused by a cis-acting regulatory mutation underlying the ectopic expression of HOXC8. However, the identification of the causative mutation(s) has to await until a method becomes available for assembling this chromosomal region. Crest is unfortunately located in a genomic region that has so far defied all attempts to establish a contiguous sequence

Epilepsy Caused by an Abnormal Alternative Splicing with Dosage Effect of the SV2A Gene in a Chicken Model

Photosensitive reflex epilepsy is caused by the combination of an individual's enhanced sensitivity with relevant light stimuli, such as stroboscopic lights or video games. This is the most common reflex epilepsy in humans; it is characterized by the photoparoxysmal response, which is an abnormal electroencephalographic reaction, and seizures triggered by intermittent light stimulation. Here, by using genetic mapping, sequencing and functional analyses, we report that a mutation in the acceptor site of the second intron of SV2A (the gene encoding synaptic vesicle glycoprotein 2A) is causing photosensitive reflex epilepsy in a unique vertebrate model, the Fepi chicken strain, a spontaneous model where the neurological disorder is inherited as an autosomal recessive mutation. This mutation causes an aberrant splicing event and significantly reduces the level of SV2A mRNA in homozygous carriers. Levetiracetam, a second generation antiepileptic drug, is known to bind SV2A, and SV2A knock-out mice develop seizures soon after birth and usually die within three weeks. The Fepi chicken survives to adulthood and responds to levetiracetam, suggesting that the low-level expression of SV2A in these animals is sufficient to allow survival, but does not protect against seizures. Thus, the Fepi chicken model shows that the role of the SV2A pathway in the brain is conserved between birds and mammals, in spite of a large phylogenetic distance. The Fepi model appears particularly useful for further studies of physiopathology of reflex epilepsy, in comparison with induced models of epilepsy in rodents. Consequently, SV2A is a very attractive candidate gene for analysis in the context of both mono- and polygenic generalized epilepsies in humans

Data sharing reveals complexity in the westward spread of domestic animals across Neolithic Turkey

This study presents the results of a major data integration project bringing together primary archaeozoological data for over 200,000 faunal specimens excavated from seventeen sites in Turkey spanning the Epipaleolithic through Chalcolithic periods, c. 18,000-4,000 cal BC, in order to document the initial westward spread of domestic livestock across Neolithic central and western Turkey. From these shared datasets we demonstrate that the westward expansion of Neolithic subsistence technologies combined multiple routes and pulses but did not involve a set 'package' comprising all four livestock species including sheep, goat, cattle and pig. Instead, Neolithic animal economies in the study regions are shown to be more diverse than deduced previously using quantitatively more limited datasets. Moreover, during the transition to agro-pastoral economies interactions between domestic stock and local wild fauna continued. Through publication of datasets with Open Context (opencontext.org), this project emphasizes the benefits of data sharing and web-based dissemination of large primary data sets for exploring major questions in archaeology (Alternative Language Abstract S1)