Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History

Abstract

A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th–19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.

Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka

“…The initial stock of breeds for developing PRW was somewhat more diverse and included chickens of Asiatic (Java Black, Brahma, Cochin White and Cochin Buff), North American (Dominique), and European (White-faced Black Spanish) origins [67]. The unique genetic makeup and diversity peculiarities of USH we established here were well in line with our previous genome-wide surveys of this old Russian breed [62,63] relative to the genomes of CRW, as well as the Orloff Mille Fleur [59,62,[132][133][134][135][136], Russian White [50,51,57,58,[137][138][139][140], and other chicken breeds [132,[141][142][143].…”

“…For each of the above four grandparent lines, 10 male birds were sampled. USH is known as an archaic indigenous breed that manifests cold adaptation and is bred in a confined population with little or no selection pressure [62,63]; it was used as a comparative group in the present investigation.…”

“…In pedigree selection systems, significant genetic markers such as single nucleotide polymorphisms (SNPs) can be identified through the use of DNA chip technology, as well as more novel marker-assisted and genomic selection strategies [31,[47][48][49]. Previously, genome-wide SNP scans have been used efficiently for studying the genetic architecture, diversity, selective footprints, and evolutionary implications in various Russian meat-type and other chicken breeds and lines [50][51][52][53][54][55][56][57][58][59][60][61][62][63]. Whole-genome resequencing approaches can produce even more SNPs that are usable for in-depth analyses of genomic architecture and candidate genes [20,64,65].…”

“…These were CRW (Figure 1a) and PRW (Figure 1b) that are used in a four-way broiler cross developed in Russia. As a comparison group, we chose the primitive dual-purpose and fancy breed named Ushanka (USH; Figure 1c) that has been bred in Russia for a few centuries in a closed population without any strict selection pressure [59,62,63].…”