To adjust breeding programs for local, commercial, and fancy breeds, and to implement molecular (marker-assisted) breeding, a proper comprehension of phenotypic and genotypic variation is a sine qua non for breeding progress in animal production. Here, we investigated an evolutionary subdivision of domestic chickens based on their phenotypic and genotypic variability using a wide sample of 49 different breeds/populations. These represent a significant proportion of the global chicken gene pool and all major purposes of breed use (according to their traditional classification model), with many of them being characterized by a synthetic genetic structure and notable admixture. We assessed their phenotypic variability in terms of body weight, body measurements, and egg production. From this, we proposed a phenotypic clustering model (PCM) including six evolutionary lineages of breed formation: egg-type, meat-type, dual purpose (egg-meat and meat-egg), game, fancy, and Bantam. Estimation of genotypic variability was carried out using the analysis of five SNPs, i.e., at the level of genomic variation at the NCAPG-LCORL locus. Based on these data, two generally similar genotypic clustering models (GCM1 and GCM2) were inferred that also had several overlaps with PCM. Further research for SNPs associated with economically important traits can be instrumental in marker-assisted breeding programs.

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Commercial breeds of chickens are staying under strong selection pressure on increasing of production level. Meanwhile aboriginal breeds are conserving unique adaptation traits, helping them to survive in severe climate. Local breeds combining high resistance, but lower productivity traits are widely kept in smallholders of developing countries. Improving of egg traits in such breeds should be done by selection, not crossing with commercial breeds. Aim of our studies was genetic change of QTL loci linked with yolk size (YS) and egg mass (EM) in resource chicken breeds. Studies were done using 293 samples from Pushkin, Rhode-Island, Amroks, Chinese Silk, Yurlow crawl and Russian White (RW) breeds kept in RRIFAGB Collective Use Centre ‘Genetic Collection of Rare and Endangered Chicken Breeds. EM was recorded in age of 30 weeks. YS was evaluated using ultra sound scanner. Genotyping was performed using illumina 60K Chicken Bead Chip. GWAS studies were performed on RW breed. Sufficient associations of EM were found on chromosome 4 (rs14201361, P < 1.6e-5 & GGaluGA152718, P < 3.3e-5). Correlation of YS and EM were calculated within breeds, difference were from 0.29 to 0.65. Haploblocks were analyzed in QTL region on chromosome 11 linked with YS. Due to selection and genetic drift different haplotype blocks were formed in breeds having different YS. Shown results could be used for improving egg traits in aboriginal domestic breeds. Studies were founded by RFFI project 18-016-00114 A.