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

Abstract

Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by F_ST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.

Keywords: Russian White breed; SNPs; White Cornish breed; candidate genes; chicken; gene ontology; gene richness; genomic regions; selection signatures.

Figure 1

Two studied chicken breeds: Russian White (a) and White Cornish (b).

Figure 2

Genetic relationships between the Russian White (RW) and White Cornish (WC) chicken populations: (a) a principal component analysis (PCA) plot showing the distribution of RW and WC individuals in the dimensions of two coordinates, i.e., the first (PC1; X-axis) and second (PC2; Y-axis) principal components, with percentage of total genetic variability, which can be explained by each of the two components, being indicated within the parentheses; (b) a Neighbor-Net tree constructed based on the F_ST genetic distances among the studied populations; and (c) an admixture plot representing cluster structure of the studied populations if the number of clusters K = 2.

Figure 3

Descriptive statistics of the runs of homozygosity (ROH) by ROH length class in the breeds of Russian White (RW) and White Cornish (WC) chickens: (a) mean number of ROHs (Y-axis) by ROH length class (X-axis; 0.5–1, 1–2, 2–4, 4–8, 8–16, and >16 Mb); (b) overall mean length of ROHs (Y-axis) by ROH length class (X-axis; >0.5 Mb, >1 Mb, >2 Mb, >4 Mb, >8 Mb, and >16 Mb).

Figure 4

Genomic distribution of F_ST values estimated between the Russian White and White Cornish populations. Values for the X-axis are chicken autosomes (breadth of autosomes corresponds to their length) and those for the Y-axis are F_ST values. SNPs were plotted relative to their positions within each autosome. The threshold, which was estimated as the top 0.1% for F_ST values, is indicated by a horizontal line.

Figure 5

Signatures of selection in the genomes of the studied Russian White (RW) and White Cornish (WC) chicken populations based on the hapFLK statistics. Values for the X-axis are chicken autosomes, and those for the Y-axis are values of statistical significance (−log₁₀ p-values). The blue line indicates threshold of significance at p < 0.01 (i.e., −log₁₀(p) > 2). Magnified plots of the few most representative chromosome areas containing the hapFLK regions are presented above the plot. Values for the X-axis are the genomic positions on corresponding autosome. Each color band corresponds to one haplotype cluster, and the height of a band shows the cluster frequency. Magnified plots for all 15 putative regions identified by hapFLK analysis are presented in Figure S3.