Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

“…A higher value of F ROH inbreeding coefficient, which was observed in RW chickens (0.195 vs. 0.172) ( Table 2 ), may reflect the origin of the studied RW population from a small number of founders [ 11 ]. A slight excess of heterozygotes observed in the RW population may be a consequence of a lower selection pressure and selection for a variety of breeding traits [ 15 , 18 ] as compared to WC [ 23 ]. Genetic drift can be considered another possible reason that led to a significant deviation in the number of heterozygotes among RW chickens as compared to that expected under Hardy–Weinberg equilibrium.…”

“…As a result of the long-term selection for critically low temperatures, the RS phenotypes were characterized by exceptional cold tolerance of neonatal chicks; their snowy-white down at day-old presumably caused by a recessive mutant gene, sw, for snow-white down [14,15]; and elevated resistance to a few neoplastic diseases, such as Marek's disease, leukemia, and carcinomas [11]. The current RG population was more recently derived from the RS as a result of a one-time telic crossing with White Leghorns in 2006 not selected further for cold tolerance and subjected to random mating in 2000-2013 [12,[16][17][18].…”

“…The latter, in turn, was distinguished by more numerous monomorphic markers and longer linkage disequilibrium (LD) regions as well a greater number of runs of homozygosity (ROHs), their greater mean length, and a higher ROH-based inbreeding coefficient. The RG population had the smallest LD values and the largest effective population size [ 12 , 17 , 18 ]. In an additional GWAS using the Illumina Chicken 60K SNP iSelect BeadChip, nine SNPs were reported in the RG population that demonstrated significant associations with egg production traits and coincided with ROHs [ 21 ].…”

“…[ 23 , 24 , 25 , 26 ]. In Russia, a few WC crossbred strains are maintained in the RRIFAGB gene pool collection and have been explored in the genome-wide scanning studies using the Illumina BeadChip [ 17 , 18 ]. They demonstrated a reduced genetic diversity because of small population size, and lower ROH metrics due to crossbreeding effects [ 17 ].…”

“…Several genome-wide studies have been undertaken to detect the genomic footprints of artificial selection in large numbers of chicken breeds (e.g., [ 37 , 38 , 39 , 40 , 41 ]). Despite the initial chicken genome research efforts undertaken so far at the RRIFAGB [ 17 , 18 ], a comparative in-depth search for selection sweeps in chicken breeds of Russian origin at the genome-wide level have not been carried out and would be much anticipated.…”