Darwin's Fancy Revised: An Updated Understanding of the Genomic Constitution of Pigeon Breeds

Whole-Genome Sequencing for Identifying Candidate Genes Related to the Special Phenotypes of the Taihu Dianzi Pigeon

The Taihu Dianzi pigeon is a breed native to China, and its special piebalding, crest, and polydactyly phenotypes are the result of artificial and natural selection. Here, we analyzed the genetic differences among three kinds of pigeons with different phenotypes at the genomic level. A selective sweep was conducted based on the fixation index (FST) and nucleotide diversity (π) ratio, and the results revealed that MC1R was related to the formation of the distinctive piebalding of the Taihu Dianzi pigeon. Combined with the results of genome-wide association studies, we identified candidate genes associated with the crest (SMYD and STOX2) and polydactyly (SLC52A3 and ANGPT4). The candidate genes identified in this study and their variants may be useful for understanding the genetic mechanism underlying the special phenotypes of the Taihu Dianzi pigeon. This study provides new insights into the genetic factors that may influence the formation of the special piebalding, crest, and polydactyly characteristics in pigeons.

Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences

The domestic pigeon's exceptional phenotypic diversity was key in developing Darwin's Theory of Evolution and establishing the concept of artificial selection. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia has received considerably less attention. Therefore, questions regarding its domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock doves that represent all currently recognized subspecies and span the species' original geographic distribution. Our dataset includes 3 specimens from Darwin's collection, and the type specimens of 5 different taxa. We characterized their population structure, genomic diversity, and gene-flow patterns. Our results show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons, and suggests gene-flow between the rock dove's sister species C. rupestris, and the ancestor of rock doves after its split from West African populations. These genomes allowed us to propose a model for the evolution of the rock dove in light of the refugia theory. We propose that rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least 1 domestication event in the Levant that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.

Genetic Structure of Racing Pigeons (Columba livia) Kept in Poland Based on Microsatellite Markers

Pigeons played a major role in communication before the invention of the telephone and the telegraph, as well as in wars, where they were used to carry information and orders over long distances. Currently, numerous sports competitions and races are held with their participation, and their breeding is demanding not only for breeders, but also for the birds themselves. Therefore, an analysis of the genetic structure of racing pigeons kept in Poland was undertaken on the basis of 16 microsatellite markers, as well as the evaluation of the microsatellite panel recommended by ISAG. For this purpose, Bayesian clustering, a dendrogram, and Principal Coordinate Analysis were conducted. In addition, statistical analysis was performed. Based on this research, it was observed that racing pigeons are genetically mixed, regardless of their place of origin. Moreover, genetic diversity was estimated at a relatively satisfactory level (Ho = 0.623, He = 0.684), and no alarmingly high inbreeding coefficient was observed (F = 0.088). Moreover, it was found that the panel recommended by ISAG can be successfully used in Poland for individual identification and parentage testing (PIC = 0.639, CE-1P = 0.9987233, CE-2P = 0.9999872, CE-PP = 0.99999999).

Genome-wide investigations reveal the population structure and selection signatures of Nigerian cattle adaptation in the sub-Saharan tropics

Background

Cattle are considered to be the most desirable livestock by small scale farmers. In Africa, although comprehensive genomic studies have been carried out on cattle, the genetic variations in indigenous cattle from Nigeria have not been fully explored. In this study, genome-wide analysis based on genotyping-by-sequencing (GBS) of 193 Nigerian cattle was used to reveal new insights on the history of West African cattle and their adaptation to the tropical African environment, particularly in sub-Saharan region. 

Results

The GBS data were evaluated against whole-genome sequencing (WGS) data and high rate of variant concordance between the two platforms was evident with high correlated genetic distance matrices genotyped by both methods suggestive of the reliability of GBS applicability in population genetics. The genetic structure of Nigerian cattle was observed to be homogenous and unique from other African cattle populations. Selection analysis for the genomic regions harboring imprints of adaptation revealed genes associated with immune responses, growth and reproduction, efficiency of feeds utilization, and heat tolerance. Our findings depict potential convergent adaptation between African cattle, dogs and humans with adaptive genes SPRY2 and ITGB1BP1 possibly involved in common physiological activities.

Conclusion

The study presents unique genetic patterns of Nigerian cattle which provide new insights on the history of cattle in West Africa based on their population structure and the possibility of parallel adaptation between African cattle, dogs and humans in Africa which require further investigations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08512-w.

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

Vertebrate craniofacial morphogenesis is a highly orchestrated process that is directed by evolutionarily conserved developmental pathways.1,2 Within species, canalized development typically produces modest morphological variation. However, as a result of millennia of artificial selection, the domestic pigeon displays radical craniofacial variation within a single species. One of the most striking cases of pigeon craniofacial variation is the short-beak phenotype, which has been selected in numerous breeds. Classical genetic experiments suggest that pigeon beak length is regulated by a small number of genetic factors, one of which is sex linked (Ku2 locus).3-5 However, the genetic underpinnings of pigeon craniofacial variation remain unknown. Using geometric morphometrics and quantitative trait locus (QTL) mapping on an F2 intercross between a short-beaked Old German Owl (OGO) and a medium-beaked Racing Homer (RH), we identified a single Z chromosome locus that explains a majority of the variation in beak morphology in the F2 population. Complementary comparative genomic analyses revealed that the same locus is strongly differentiated between breeds with short and medium beaks. Within the Ku2 locus, we identified an amino acid substitution in the non-canonical Wnt receptor ROR2 as a putative regulator of pigeon beak length. The non-canonical Wnt pathway serves critical roles in vertebrate neural crest cell migration and craniofacial morphogenesis.6,7 In humans, ROR2 mutations cause Robinow syndrome, a congenital disorder characterized by skeletal abnormalities, including a widened and shortened facial skeleton.8,9 Our results illustrate how the extraordinary craniofacial variation among pigeons can reveal genetic regulators of vertebrate craniofacial diversity.

Whole‐genome sequencing reveals the artificial selection and local environmental adaptability of pigeons ( Columba livia )

To meet human needs, domestic pigeons (Columba livia) with various phenotypes have been bred to provide genetic material for our research on artificial selection and local environmental adaptation. Seven pigeon breeds were resequenced and can be divided into commercial varieties (Euro‐pigeon, Shiqi, Shen King, Taishen, and Silver King), ornamental varieties (High Fliers), and local varieties (Tarim pigeon). Phylogenetic analysis based on population resequencing showed that one group contained local breeds and ornamental pigeons from China, whereas all commercial varieties were clustered together. It is revealed that the traditional Chinese ornamental pigeon is a branch of Tarim pigeon. Runs of homozygosity (ROH) and linkage disequilibrium (LD) analyses revealed significant differences in the genetic diversity of the three types of pigeons. Genome sweep analysis revealed that the selected genes of commercial breeds were related to body size, reproduction, and plumage color. The genomic imprinting genes left by the ornamental pigeon breeds were mostly related to special human facial features and muscular dystrophy. The Tarim pigeon has evolved genes related to chemical ion transport, photoreceptors, oxidative stress, organ development, and olfaction in order to adapt to local environmental stress. This research provides a molecular basis for pigeon genetic resource evaluation and genetic improvement and suggests that the understanding of adaptive evolution should integrate the effects of various natural environmental characteristics.

Exterior Evaluation of Selected Breeds of Pigeons: Owls and Frills

Owl and frill pigeons are considered one of the oldest breeds of domestic pigeons and for breeders they mean the embodiment of beauty, pride, elegance and temperament. The common feature of the whole group of owl and frill pigeons is the presence of vertically growing feather adornment—frill and a significant refinement of exterior features on the head. The main goal of this study was to record the current situation in the exhibition sector and to compare the exterior of selected breeds of owl and frill pigeons with the relevant European standard at top breeder’s exhibitions. Altogether 722 short-beaked owl and frill pigeons (Oriental frill, African owl and Turbit) raised by breeders from seventeen European countries were evaluated at five important exhibitions in Europe. The examination of the exterior showed that the most common exterior faults on the body of oriental frills were defects in colour pattern or lacing, poorly developed frill, faults in figure as well as defects in positioning and body posture. Exterior faults observed on the heads of oriental frill included: short top or forehead, defects in shape or length of the beak, as well as defects in its line. In addition to the faults in the oriental frills, there were observed imperfections in the rounding of the head and in the length of the wings and tail in the African owls. Turbits frequently exhibited deficiencies with respect to the length of the top or forehead. The exterior evaluation of owl and frill pigeons for breeders in the future shows the need for systematic elimination of deviations from physiological and physical development with culling of individuals transmitting morphological defects.

A Pilot Study Investigating the Dynamics of Pigeon Circovirus Recombination in Domesticated Pigeons Housed in a Single Loft

Pigeon circovirus (PiCV) infects pigeon populations worldwide and has been associated with immunosuppression in younger pigeons. Recombination is a common mechanism of evolution that has previously been shown in various members of the Circoviridae family, including PiCV. In this study, three groups of pigeons acquired from separate lofts were screened for PiCV, and their genome sequence was determined. Following this, they were housed in a single loft for 22 days, during which blood and cloacal swab samples were taken. From these blood and cloacal swabs, PiCV genomes were determined with the aim to study the spread and recombination dynamics of PiCV in the birds. Genome sequences of PiCV were determined from seven pigeons (seven tested PiCV positive) before they were housed together in a loft (n = 58 sequences) and thereafter from the ten pigeons from blood and cloacal swabs (n = 120). These 178 PiCV genome sequences represent seven genotypes (98% pairwise identity genotype demarcation), and they share >88% genome-wide pairwise identity. Recombination analysis revealed 13 recombination events, and a recombination hotspot spanning the 3′ prime region, the replication-associated protein (rep) gene and the intergenic region. A cold spot in the capsid protein-coding region of the genome was also identified. The majority of the recombinant regions were identified in the rep coding region. This study provides insights into the evolutionary dynamics of PiCV in pigeons kept under closed rearing systems.