Brain alterations in crested versus non-crested breeds of domestic ducks (Anas platyrhynchos f.d.)

Dumbbell-shaped brains of Polish crested chickens as a model system for the evolution of novel brain morphologies

The evolutionary history of vertebrates is replete with emergence of novel brain morphologies, including the origin of the human brain. Existing model organisms and toolkits for investigating drivers of neuroanatomical innovations have largely proceeded on mammals. As such, a compelling non-mammalian model system would facilitate our understanding of how unique brain morphologies evolve across vertebrates. Here, we present the domestic chicken breed, white crested Polish chickens, as an avian model for investigating how novel brain morphologies originate. Most notably, these crested chickens exhibit cerebral herniation from anterodorsal displacement of the telencephalon, which results in a prominent protuberance on the dorsal aspect of the skull. We use a high-density geometric morphometric approach on cephalic endocasts to characterize their brain morphology. Compared with standard white Leghorn chickens (WLCs) and modern avian diversity, the results demonstrate that crested chickens possess a highly variable and unique overall brain configuration. Proportional sizes of neuroanatomical regions are within the observed range of extant birds sampled in this study, but Polish chickens differ from WLCs in possessing a relatively larger cerebrum and smaller cerebellum and medulla. Given their accessibility, phylogenetic proximity, and unique neuroanatomy, we propose that crested breeds, combined with standard chickens, form a promising comparative system for investigating the emergence of novel brain morphologies.

Identification of Genes Associated with Crest Cushion Development in the Chinese Crested Duck

The crest trait is a specific and widely distributed phenotype in birds. However, the shape and function vary in different species of birds. To understand the mechanism of crest formation, the present study used RNA sequencing and weighted gene co-expression network analysis (WGCNA) to identify the crest-cushion-associated genes in the Chinese crested (CC) duck. As a result, 28, 40, 32, 33, and 126 differentially expressed genes (DEGs) were identified between CC and cherry valley (CV) ducks at the embryonic days (E)15, E22, E28, D7 (7 days old), and D42 stages, respectively. In addition, the results of WGCNA show that 3697 (turquoise module), 485 (green-yellow module), 687 (brown module), 205 (red module), and 1070 (yellow module) hub genes were identified in the E15, E22, E28, D7, and D42 stages, respectively. Based on the results of DEGs and WGCNA Venn analysis, three, two, zero, one, and seven genes were found to be associated with crest cushion formation at the E15, E22, E28, D7, and D42 stages, respectively. The expression of all the associated genes and some DEGs was verified by real-time quantitative polymerase chain reaction. In conclusion, this study provided an approach revealing the molecular mechanisms underlying the crested trait development.

RNA-sequence reveals differentially expressed genes affecting the crested trait of Wumeng crested chicken

Wumeng crested chicken has a cluster of slender feathers on its head, and the underlying skull region exhibits an obvious tumor-like protrusion. This is the typical skull structure of crested chickens. The associated regulatory genes are located on autosomes and are incompletely dominant. This trait is related to brain herniation, but the genetic mechanisms of its formation and development are unclear. In this study, RNA sequencing (RNA-Seq) analysis was conducted on 6 skull tissue samples from 3 Wumeng crested chickens with prominent skull protrusions and 3 without a prominent skull protrusion phenotype. A total of 46,376,934 to 43,729,046 clean reads were obtained, the percentage of uniquely mapped reads compared with the reference genome was between 89.73%-91.00%, and 39,795,458-41,836,502 unique reads were obtained. Among different genomic regions, the highest frequency of sequencing reads occurred in exon regions (85.44-88.28%). Additionally, a total of 423 new transcripts and 26,999 alternative splicings (AS) events were discovered in this sequencing analysis. This study identified 1,089 differentially expressed genes (DEGs), among which 485 were upregulated and 604 were downregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that the DEGs were enriched in terms related to signal transduction, cell development, cell differentiation, the lysosome, serine, and threonine metabolism, and the interaction of cytokines with cytokine receptors. Based on the comprehensive analysis of DEGs combined with reported quantitative trait loci (QTLs), the expression of BMP2, EPHA3, EPHB1, HOXC6, SCN2B, BMP7, and HOXC10 was verified by real-time quantitative polymerase chain reaction (qRT-PCR). The qRT-PCR results were consistent with the RNA-Seq results, indicating that these 7 genes may be candidates genes regulating the crested trait.

Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations

BACKGROUND

The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations.

RESULTS

Based on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100-11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R).

CONCLUSIONS

Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.

A joint analysis strategy reveals genetic changes associated with artificial selection between egg-type and meat-type ducks

Egg-type ducks and meat-type ducks are predominantly commercial or indigenous and have been subjected to artificial directional selection. These two duck types differ substantially in body shape, production performance and reproductivity. However, the genetic changes associated with phenotypic differences remain unclear. Here, we compared the two duck types at the genomic and transcriptomic levels. We identified a large number of SNPs and genes in genomic divergent regions in terms of F_ST and θπ values. The corresponding genes were mainly enriched in embryonic development function and metabolic pathway. RNA-seq analysis also revealed differential gene expression in the liver and gonads. The differentially expressed genes were functionally associated with signal transmission and substance metabolism respectively. Furthermore, we found that seven genes were related to differentiation between the two types by both g genome and transcriptome analysis and were plausible candidate genes. These genes were annotated to GO categories of cell development and disease immunity. These findings will enable a better understanding of the artificial selection history of meat and egg ducks and provide a valuable resource for future research on the breeding of these two lineages.

Deciphering the Forebrain Disorder in a Chicken Model of Cerebral Hernia

Cerebral hernia in crested chicken has been characterized as the protrusion of cerebral hemispheres into the unsealed skull for hundreds of years, since Charles Darwin. The development of deformed forebrain (telencephalon) of cerebral hernia remains largely unknown. Here, the unsealed frontal skull combined with misplaced sphenoid bone was observed and potentially associated with brain protuberance. The shifted pallidum, elongated hippocampus, expanded mesopallium and nidopallium, and reduced hyperpallium were observed in seven regions of the malformed telencephalon. The neurons were detected with nuclear pyknosis and decreased density. Astrocytes showed uneven distribution and disordered protuberances in hyperpallium and hippocampus. Transcriptome analyses of chicken telencephalon (cerebral hernia vs. control) revealed 547 differentially expressed genes (DEGs), mainly related to nervous system development, and immune system processes, including astrocyte marker gene GFAP, and neuron and astrocyte developmental gene S100A6. The upregulation of GFAP and S100A6 genes in abnormal telencephalon was correlated with reduced DNA methylation levels in the promoter regions. The morphological, cellular, and molecular variations in the shape, regional specification, and cellular states of malformed telencephalon potentially participate in brain plasticity and previously reported behavior changes. Chickens with cerebral hernia might be an interesting and valuable disease model to further explore the recognition, diagnosis, and therapy of cerebral hernia development of crested chickens and other species.

Whole genome re-sequencing of crested traits and expression analysis of key candidate genes in duck

The crested duck was a duck breed which features a topknot of feathers on the back of their head. In order to explain the reason of crest, we anatomy the head of some crested ducks. The anatomical structures showed that there was a fat body in the head and a hole in the skull. To determine the reason for the formation of the crest, we used whole genome re-sequencing to detect SNPs and InDels in three crested duck and three normal crested duck (without crest). There were 785,202 unique SNPs and 105,596 unique InDels include in crested duck. There were 14,591 SNPs containing genes and 13,784 InDels continuing genes were mapped on BGI_duck_1.0 by BWA 0.7.16a software. We use KEGG and GO to classification the SNP and InDel containing genes function. The PPI network of SNP containing genes and InDels containing genes was constructed by STRING. The result of PPI and KEGG analysis shown that the formation of crest might include feather development, fatty acid deposition, and skull hypoplasia. To determine the regulated of SNP containing genes and InDels containing genes, which related the different trait, of miRNA we used mirmap to predicted target miRNA of those genes. The miRNA-genes network constructed by Cytoscape. In conclusion, the formation of the crest was a complex process. The fatty acid metabolism block, feather growth and skull hypoplasia might lead crest formation. The tissue expression of four candidate genes showed that they were closely related to the formation of the trait, and could be used as important candidate genes to further elaborate the molecular mechanism of their function.

Whole-genome resequencing reveals signatures of selection and timing of duck domestication

Background

The genetic basis of animal domestication remains poorly understood, and systems with substantial phenotypic differences between wild and domestic populations are useful for elucidating the genetic basis of adaptation to new environments as well as the genetic basis of rapid phenotypic change. Here, we sequenced the whole genome of 78 individual ducks, from two wild and seven domesticated populations, with an average sequencing depth of 6.42X per individual.

Results

Our population and demographic analyses indicate a complex history of domestication, with early selection for separate meat and egg lineages. Genomic comparison of wild to domesticated populations suggests that genes that affect brain and neuronal development have undergone strong positive selection during domestication. Our F_ST analysis also indicates that the duck white plumage is the result of selection at the melanogenesis-associated transcription factor locus.

Conclusions

Our results advance the understanding of animal domestication and selection for complex phenotypic traits.

Genomic determinants of epidermal appendage patterning and structure in domestic birds

Variation in regional identity, patterning, and structure of epidermal appendages contributes to skin diversity among many vertebrate groups, and is perhaps most striking in birds. In pioneering work on epidermal appendage patterning, John Saunders and his contemporaries took advantage of epidermal appendage diversity within and among domestic chicken breeds to establish the importance of mesoderm-ectoderm signaling in determining skin patterning. Diversity in chickens and other domestic birds, including pigeons, is driving a new wave of research to dissect the molecular genetic basis of epidermal appendage patterning. Domestic birds are not only outstanding models for embryonic manipulations, as Saunders recognized, but they are also ideal genetic models for discovering the specific genes that control normal development and the mutations that contribute to skin diversity. Here, we review recent genetic and genomic approaches to uncover the basis of epidermal macropatterning, micropatterning, and structural variation. We also present new results that confirm expression changes in two limb identity genes in feather-footed pigeons, a case of variation in appendage structure and identity.

Removal of a Presumed Peripheral Cerebral Cyst via Craniectomy in a Crested Pekin Duck ( Anas platyrhynchos f dom)

A juvenile, male crested pekin duck ( Anas platyrhynchos f dom) was presented for neurologic signs suggestive of cerebellar disease. Physical examination revealed microphthalmia, erratic head movements, and ataxia. Computed tomography scan of the head and neck regions revealed 2 full-thickness skull-bone defects within the caudal portion of the cranium. The cerebellum appeared to be ventrally compressed by a homogeneous, triangular, fluid-attenuating region (0-10 Hounsfield units). A craniectomy was performed, and a presumed peripheral cerebral cyst was removed with suction and gentle dissection. No postoperative complications occurred, and the patient showed clinical improvement for 5 months after surgery. However, after 5 months, the owners elected euthanasia because of poor prognosis after finding the duck minimally responsive in a water enclosure. At necropsy, a thin-walled, epithelial structure was present in meninges and was adhered to the skull at the presumed surgical site.

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.

Brain size, brain composition and intracranial fat bodies in a population of free-living crested ducks (‘Hochbrutflugenten’)

(1) Brain sizes and brain structure volumes of crested specimens from a population of 'Hochbrutflugenten' ducks (HBTcr), living under seminatural conditions, were compared with those of other duck breeds, among them the breed 'Landente' with the same morphological trait, the crest (LEcr). (2) Brains of both HBTcr and LEcr were larger than expected from an allometric comparison with uncrested breeds. (3) Fat bodies invading the skull were observed in both breeds. (4) In LEcr they could be voluminous; after subtraction of their volume from the brain volume, most brain structures measured were allometrically of the same size as in uncrested breeds. (5) In contrast, HBTcr had small fat bodies, and most of their brain structures were allometrically larger than those of the other breeds. (6) A small fat body in the skull does not appear to influence the survival of HBTcr under seminatural conditions.

Unusual brain composition in Crested Ducks (Anas platyrhynchos f.d.)--including its effect on behavior and genetic transmission

Crested Ducks (CR) occasionally show intracranial fat bodies. Additionally, behavioral abnormalities such as motor incoordination can be observed. Here, it is shown that a behavioral test helps to identify CR that have a problematical fat body. The ducks were put on their backs, and the time required for them to stand up was measured. Ten CR exhibited suboptimal motor coordination. The appropriateness of this test has been proved in a special breeding program. To investigate the influence of fat bodies on brain composition, an allometrical comparison of 26 CR brains with those of three uncrested duck breeds was done. The fat bodies of CR varied from 0.3% to 41% of total brain volume, but two CR did not show a fat body. CR with motor incoordination show significantly larger fat bodies and require significantly more time in the test than "normal" CR. Total brain volume was significantly larger in CR, but brain volume minus fat body was significantly smaller compared to reference breeds. Cerebellum, apical hyperpallium, tegmentum and olfactory bulb are significantly reduced in CR. Obviously the behavioral deficits cannot be explained by the existence of a fat body, but they could be explained by functionally suboptimal cerebella and tegmenta. Fat body size seems to be a decisive factor. The relationship between fat body and reduced structures is discussed. By breeding with test-selected ducks the hatching rate increased and the number of ducklings with malformations or motor incoordination decreased.

Motor incoordination, intracranial fat bodies, and breeding strategy in Crested ducks (Anas platyrhynchos f.d.)

Some Crested ducks (CR) are burdened with an intracranial fat body that, depending on the size and location, may lead to varying degrees of motor incoordination. A behavioral test is proposed that helps to identify those CR individuals bearing the problematical fat body. The test consists of putting the ducks on their backs and measuring the time required to right themselves. This was repeated 13 times per animal, and means were calculated. The minimum time required was 0.5 s, and the maximum was 62.6 s. Individuals that show motor incoordination need more time than ducks without such problems (14.3 s in contrast to 1.2 s) and exhibit a larger intracranial fat body. Ducks used for breeding should require no more than approximately 1 to 2 s to right themselves. In an allometric comparison with 3 other domestic duck breeds, CR show a significantly smaller brain; specifically, the cerebellum, tegmentum, apicale hyperpallium, and olfactory bulb are reduced. The relationship between fat body and these structures was discussed.

Variations in the morphology, distribution, and arrangement of feathers in domesticated birds

Domesticated birds exhibit a greater diversity in the morphology of their integument and its appendages than their wild ancestors. Many of these variations affect the appearance of a bird significantly and have been bred selectively by poultry and pigeon fanciers and aviculturists for the sake of visual appeal. Variations in feather distribution (e.g., feathering of legs and feet, featherless areas in normally feather-bearing skin) are widespread in chickens and pigeons. Variations in the number of feathers (e.g., increased number of tail feathers, lack of tail feathers) occur in certain pigeon and poultry breeds. Variations in feather length can affect certain body regions or the entire plumage. Variations in feather structure (e.g., silkiness, frilled feathering) can be found in exhibition poultry as well as in pet birds. Variations in feather arrangement (e.g., feather crests and vortices) occur in many domesticated bird species as a results of mutation and intense selective breeding. The causes of variations in the structure, distribution, length and arrangement of feathers is often unknown and opens a wide field for scientific research under various points of view (e.g., morphogenesis, pathogenesis, ethology, etc.). To that extent, variations in the morphology, distribution and arrangement of feathers in domesticated birds require also a concern for animal welfare because certain alleles responsible for integumentary variations in domesticated birds have pleiotropic effects, which often affect normal behaviour and viability.