RESUMO
The worldwide chicken gene pool encompasses a remarkable, but shrinking, number of divergently selected breeds of diverse origin. This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture, genetic variability, and detailed structure among 49 populations. These populations represent a significant sample of the world's chicken breeds from Europe (Russia, Czech Republic, France, Spain, UK, etc.), Asia (China), North America (USA), and Oceania (Australia). Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism (SNP) chip, a bioinformatic analysis was carried out. This included the calculation of heterozygosity/homozygosity statistics, inbreeding coefficients, and effective population size. It also included assessment of linkage disequilibrium and construction of phylogenetic trees. Using multidimensional scaling, principal component analysis, and ADMIXTURE-assisted global ancestry analysis, we explored the genetic structure of populations and subpopulations in each breed. An overall 49-population phylogeny analysis was also performed, and a refined evolutionary model of chicken breed formation was proposed, which included egg, meat, dual-purpose types, and ambiguous breeds. Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding. In general, whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.
Assuntos
Galinhas , Genoma , Animais , Filogenia , Galinhas/genética , Genômica/métodos , Demografia , Polimorfismo de Nucleotídeo Único , Variação GenéticaRESUMO
Monitoring the genetic diversity of small populations is important with respect to conserving rare and valuable chicken breeds, as well as discovery and innovation in germplasm research and application. Restriction fragment length polymorphisms (RFLPs), the molecular markers that underlie multilocus DNA fingerprinting (MLDF), have historically been employed for this purpose, but over the past two decades, there has been an irreversible shift toward high-throughput single-nucleotide polymorphisms (SNPs). In this study, we conducted a comparative analysis of archived MLDF results and new data from whole-genome SNP genotyping (SNPg) among 18 divergently selected breeds representing a large sample of the world gene pool. As a result, we obtained data that fit the general concept of the phylogenetic distribution of the studied breeds and compared them with RFLP and SNP markers. RFLPs were found to be useful markers for retrospective assessment of changes in the genetic architecture and variability underlying the phenotypic variation in chicken populations, especially when samples from previous generations used for MLDF are unavailable for SNPg. These results can facilitate further research necessary to assess the possibility of extrapolating previous MLDF results to study the long-term dynamics of genetic diversity in various small chicken germplasm populations over time. In general, the whole-genome characterization of populations and breeds by multiple SNP loci will further form the basis for the development and implementation of genomic selection with the aim of effective use of the genetic potential of the domestic gene pool in the poultry industry.
