Kinglet in the poultry court of Russia: Whole-genome insights into ancestry, genetic variability, selection footprints and candidate genes in a unique local chicken breed relative to other bantam/dwarf breeds

Simple Summary

Rare local chicken breeds, including bantam/dwarf ones, were, at a certain breeding stage, subject to strong selection for a specific appearance for many generations. This led to adaptation to local conditions, disease resistance and preservation of unique breed characteristics, creating genetic divergence between breeds. Assessing the genetic diversity of various native poultry breeds is crucial for their conservation as genetic resources. One of the rare old Russian chicken breeds is the Korolyok, meaning “kinglet” in Russian. Local dwarf chickens were mentioned in the first Russian book on poultry farming published in 1774 and seen by Pallas in Russia at about the same time. Here, we present for the first time the genetic characteristics of this unique local breed compared to five other dwarf/small chicken breeds. Using whole-genome genotyping, we determined descriptive characteristics of genetic diversity and comprehensively assessed the significance of genetic similarities/differences within and between these breeds. A number of intra-breed population structure patterns and selective signatures were found that were associated with the history of the breed’s formation and subsequent breeding, while harboring relevant candidate genes. The low population size of these breeds, as well as their declining reproductive capacity, may indicate the risk of their extinction.

Abstract

Assessing genetic diversity in various native poultry breeds, including bantam/dwarf ones, is instrumental for their conservation as genetic resources, identifying their specific genetic features, and exploring the history of their genetic divergence. Rare chicken breeds are usually carriers of peculiar phenotypic traits, including adaptations to local conditions, disease resistance, and unique performance features. Here, we report for the first time SNP-based genetic characterization of the Russian Korolyok, translated as “kinglet,” relative to five other dwarf/small breeds: Cochin Bantam, Hamburg Bantam Silver Spangled, Polish White-crested Black, Red White-tailed Dwarf and Silkie White. We estimated phenotypes, heterozygosity, inbreeding, effective population size, and runs of homozygosity (ROHs). Some breeds had higher genetic diversity and others showed elevated inbreeding rates in their genomes. With lower effective population sizes (both presently and in the past), rare breeds came from a limited number of ancestors or were under strong selection pressure over many generations. Within 22 ROHs, we identified 26 prioritized candidate genes (GRB10, RPRD1A, APOOL, EAF2, SEMA5, HACD2, GALANT1, DACH2, CHM, POF1B, HDX, SLC15A2, PDIA5, SEC22, NR2F2, ARRDC4, IGF1R, SYNM, TMEM263, etc.). Our data offer whole-genome insights into genetic variability, history, phylogeny, selective sweeps, and candidate genes of a distinct indigenous Russian chicken breed and other bantam/dwarf breeds.