A ROR2 coding variant is associated with craniofacial variation in domestic pigeons

Assembly and annotation of 2 high-quality columbid reference genomes from sequencing of a Columba livia × Columba guinea F1 hybrid

Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for columbids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for 2 columbid species, Columba livia and Columba guinea. We simultaneously assembled C. livia and C. guinea genomes from long-read sequencing of a single F1 hybrid individual. The new C. livia genome assembly (Cliv_3) shows improved completeness and contiguity relative to Cliv_2.1, with an annotation incorporating long-read IsoSeq data for more accurate gene models. Intensive selective breeding of C. livia has given rise to hundreds of breeds with diverse morphological and behavioral characteristics, and Cliv_3 offers improved tools for mapping the genomic architecture of interesting traits. The C. guinea genome assembly is the first for this species and is a new resource for avian comparative genomics. Together, these assemblies and annotations provide improved resources for functional studies of columbids and avian comparative genomics in general.

Genome-wide association study of growth traits and validation of key mutations (MSTN c.C861T) associated with the muscle mass of meat pigeons

Selective breeding of meat pigeons is primarily based on growth traits, especially muscle mass (MM). Identification of functional genes and molecular markers of growth and slaughter traits through a genome-wide association study (GWAS) will help to elucidate the underlying molecular mechanisms and provide a theoretical basis for the selective breeding of meat pigeons. The phenotypic data of body weight (BW) and body size (BS) of 556 meat pigeons at 52 and 80 weeks of age were collected. In total, 160 434 high-quality single nucleotide polymorphism sites were obtained by restriction site-associated DNA sequencing. The GWAS analysis revealed that MSTN, IGF2BP3 and NCAPG/LCORL were important candidate genes affecting the growth traits of meat pigeons. IGF2BP3 and NCAPG/LCORL were highly correlated to BW and BS, which are related to overall growth and development, while MSTN was associated with pectoral thickness and BW. Phenotypic association validation with the use of two meat pigeon populations found that the MSTN mutation c.C861T determines the MM. These results provide new insights into the genetic mechanisms underlying phenotypic variations of growth traits and MM in commercial meat pigeons. The identified markers and genes provide a theoretical basis for the selective breeding of meat pigeons.

Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F1 hybrid

Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for colubids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for two columbid species, Columba livia and C. guinea. We simultaneously assembled C. livia and C. guinea genomes from long-read sequencing of a single F1 hybrid individual. The new C. livia genome assembly (Cliv_3) shows improved completeness and contiguity relative to Cliv_2.1, with an annotation incorporating long-read IsoSeq data for more accurate gene models. Intensive selective breeding of C. livia has given rise to hundreds of breeds with diverse morphological and behavioral characteristics, and Cliv_3 offers improved tools for mapping the genomic architecture of interesting traits. The C. guinea genome assembly is the first for this species and is a new resource for avian comparative genomics. Together, these assemblies and annotations provide improved resources for functional studies of columbids and avian comparative genomics in general.

An allelic series at the EDNRB2 locus controls diverse piebalding patterns in the domestic pigeon

Variation in pigment patterns within and among vertebrate species reflects underlying changes in cell migration and function that can impact health, reproductive success, and survival. The domestic pigeon (Columba livia) is an exceptional model for understanding the genetic changes that give rise to diverse pigment patterns, as selective breeding has given rise to hundreds of breeds with extensive variation in plumage color and pattern. Here, we map the genetic architecture of a suite of pigmentation phenotypes known as piebalding. Piebalding is characterized by patches of pigmented and non-pigmented feathers, and these plumage patterns are often breed-specific and stable across generations. Using a combination of quantitative trait locus mapping in F2 laboratory crosses and genome-wide association analysis, we identify a locus associated with piebalding across many pigeon breeds. This shared locus harbors a candidate gene, EDNRB2, that is a known regulator of pigment cell migration, proliferation, and survival. We discover multiple distinct haplotypes at the EDNRB2 locus in piebald pigeons, which include a mix of protein-coding, noncoding, and structural variants that are associated with depigmentation in specific plumage regions. These results identify a role for EDNRB2 in pigment patterning in the domestic pigeon, and highlight how repeated selection at a single locus can generate a diverse array of stable and heritable pigment patterns.

Chicken HOXC8 and HOXC10 genes may play a role in the altered skull morphology associated with the Crest phenotype

One of the most intriguing traits found in domestic chickens is the Crest phenotype. This trait, characterized by a tuft of elongated feathers sprouted from the head, is found in breeds such as Polish chickens and Silkie chickens. Moreover, some crested chicken breeds also exhibit a protuberance in their anterodorsal skull region. Previous studies have strived to identify the causative factors of this trait. This study aimed to elucidate the role of chicken HOXC8 and HOXC10 in the formation of the Crest phenotype. We explored the effect of ectopic expression of HOXC8 or HOXC10 on the chicken craniofacial morphology using the RCAS retrovirus transformation system. Microcomputed tomography scanning was conducted to measure the 3D structure of the cranial bone of transgenic embryos for geometric morphometric analysis. We found that the ectopic expression of HOXC8 or HOXC10 in chicken heads caused mild morphological changes in the skull compared with the GFP-transgenic control group. Geometric morphometric analysis showed that HOXC8 and HOXC10 transgenic groups expressed a mild upward shape change in the frontal region of the skull compared with the control group, which is similar to what is seen in the crested chicken breeds. In conclusion, this study supports findings in previous studies in which HOX genes play a role in the formation of the altered skull morphology related to the Crest phenotype. It also supports that mutations in HOX genes may contribute to intra- and inter-specific variation in morphological traits in vertebrates.

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.

An analysis of the maxillary beak shape variation between 2 pure layer lines and its relationship to the underlying premaxillary bone, feather cover, and mortality

Beak shape varies considerably within and between intact-beak laying hens, and aspects of beak shape appear to be heritable. As an alternative to beak treatment (an effective method of reducing damage from severe feather pecking (SFP)), this variation could be used to genetically select hens whose beak shapes are less apt to cause damage. To be able to select certain phenotypes, the beak shape variation that exists within laying hen flocks must first be characterized. The objectives of this study were to 1) describe the maxillary beak shape variation in 2 pure White Leghorn layer lines with intact beaks using geometric morphometrics to analyze images, and 2) examine the beak shape's relationship to the premaxillary bone, feather cover, and mortality. A lateral head image was taken of each hen (n = 710), and 20 landmarks were placed along each image's dorsal and ventral margins of the maxillary beak. Landmark coordinates were standardized by Procrustes superimposition, and the covariation was analyzed by principal components analysis and multivariate regression. Feather cover was scored at 3 ages and mortality was monitored throughout the production cycle. Three principal components (PCs) explained 83% of the maxillary beak shape variation and the first PC partially separated the 2 lines. Maxillary beak shapes ranged from long and narrow with pointed tips to short and wide with more curved tips. Moderate correlations were found between the maxillary beak and premaxillary bone shape (rs = 0.44) and size (rs = 0.52). Line A hens had better feather cover than Line B at all ages. Line A hens also had less total and cannibalism-related mortality than Line B (10.7 and 0.4% vs. 16.7 and 2.4%, respectively). Beak shape may be one factor contributing to the observed differences in feather cover and mortality. The results suggest that distinct maxillary beak phenotypes within each line could be selected to help reduce SFP damage and improve bird welfare.

An allelic series at the EDNRB2 locus controls diverse piebalding patterns in the domestic pigeon

Variation in pigment patterns within and among vertebrate species reflects underlying changes in cell migration and function that can impact health, reproductive success, and survival. The domestic pigeon (Columba livia) is an exceptional model for understanding the genetic changes that give rise to diverse pigment patterns, as selective breeding has given rise to hundreds of breeds with extensive variation in plumage color and pattern. Here, we map the genetic architecture of a suite of pigmentation phenotypes known as piebalding. Piebalding is characterized by patches of pigmented and non-pigmented feathers, and these plumage patterns are often breed-specific and stable across generations. Using a combination of quantitative trait locus mapping in F2 laboratory crosses and genome-wide association analysis, we identify a locus associated with piebalding across many pigeon breeds. This shared locus harbors a candidate gene, EDNRB2, that is a known regulator of pigment cell migration, proliferation, and survival. We discover multiple distinct haplotypes at the EDNRB2 locus in piebald pigeons, which include a mix of protein-coding, noncoding, and structural variants that are associated with depigmentation in specific plumage regions. These results identify a role for EDNRB2 in pigment patterning in the domestic pigeon, and highlight how repeated selection at a single locus can generate a diverse array of stable and heritable pigment patterns.

The non-canonical Wnt receptor Ror2 is required for cartilage cell polarity and morphogenesis of the craniofacial skeleton in zebrafish

Non-canonical/β-catenin-independent Wnt signaling plays crucial roles in tissue/cell polarity in epithelia, but its functions have been less well studied in mesenchymal tissues, such as the skeleton. Mutations in non-canonical Wnt signaling pathway genes cause human skeletal diseases such as Robinow syndrome and Brachydactyly Type B1, which disrupt bone growth throughout the endochondral skeleton. Ror2 is one of several non-canonical Wnt receptor/co-receptors. Here, we show that ror2-/- mutant zebrafish have craniofacial skeletal defects, including disruptions of chondrocyte polarity. ror1-/- mutants appear to be phenotypically wild type, but loss of both ror1 and ror2 leads to more severe cartilage defects, indicating partial redundancy. Skeletal defects in ror1/2 double mutants resemble those of wnt5b-/- mutants, suggesting that Wnt5b is the primary Ror ligand in zebrafish. Surprisingly, the proline-rich domain of Ror2, but not its kinase domain, is required to rescue its function in mosaic transgenic experiments in ror2-/- mutants. These results suggest that endochondral bone defects in ROR-related human syndromes reflect defects in cartilage polarity and morphogenesis.

Auriculocondylar syndrome 2 results from the dominant-negative action of PLCB4 variants

Auriculocondylar syndrome 2 (ARCND2) is a rare autosomal dominant craniofacial malformation syndrome linked to multiple genetic variants in the coding sequence of phospholipase C β4 (PLCB4). PLCB4 is a direct signaling effector of the endothelin receptor type A (EDNRA)-Gq/11 pathway, which establishes the identity of neural crest cells (NCCs) that form lower jaw and middle ear structures. However, the functional consequences of PLCB4 variants on EDNRA signaling is not known. Here, we show, using multiple signaling reporter assays, that known PLCB4 variants resulting from missense mutations exert a dominant-negative interference over EDNRA signaling. In addition, using CRISPR/Cas9, we find that F0 mouse embryos modeling one PLCB4 variant have facial defects recapitulating those observed in hypomorphic Ednra mouse models, including a bone that we identify as an atavistic change in the posterior palate/oral cavity. Remarkably, we have identified a similar osseous phenotype in a child with ARCND2. Our results identify the disease mechanism of ARCND2, demonstrate that the PLCB4 variants cause craniofacial differences and illustrate how minor changes in signaling within NCCs may have driven evolutionary changes in jaw structure and function. This article has an associated First Person interview with the first author of the paper.