Abstract
Simple SummaryThe search for genomic regions of putative selective signaling is instrumental in obtaining information about selection history in various species and populations. Domestic animals are subject to long-term artificial selection that leaves certain footprints in their genomes one can explore using genome-wide SNP screen. We examined here genomes of two contrasting chicken breeds, the native egg-type Russian White and meat-type White Cornish. Using three statistics, we identified genomic regions under putative selection, both breed-specific and shared between two breeds, that harbor key candidate genes for economically important traits. Our findings will be useful in further understanding selection history and genomic diversity in domestic chickens that would be pivotal in their productive breeding.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 FST 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.
Highlights
Since the middle of the last century, the poultry industry has focused on the exploitation of a few highly specialized, productive lines selected for egg or meat production traits
The Russian White (RW) chickens were characterized by significantly lower level of genetic diversity assessed by the level of unbiased expected heterozygosity (UHE = 0.339 vs. 0.383, p < 0.001) and allelic richness (AR = 1.937 vs. 1.982, p < 0.001) as compared to the White Cornish (WC) breed
The negative value of the inbreeding coefficient UFIS indicates a slight excess of heterozygotes in the RW population (UFIS = –0.016), while the WC breed showed a slighter deficiency of heterozygotes (UFIS = 0.009) than it would be expected under Hardy–Weinberg equilibrium (Table 1)
Summary
Since the middle of the last century, the poultry industry has focused on the exploitation of a few highly specialized, productive lines selected for egg or meat (broiler) production traits. In the chicken (Gallus gallus; GGA), this has led to a drastic decline in the number and population size of native breeds that were extensively used for agricultural production in the past. Two main evolutionary lineages of domestic chickens are represented by egg-type and meat-type breeds [9]. One of the distinctive native egg-type chicken breeds is the Russian White (RW), developed for egg production in the former USSR in 1929–1953 by crossing local low-productive hens with White Leghorn roosters of Danish, British, and American origins [10]. Before 1965, the RW was a major chicken breed employed for egg production in the USSR. In 1975, the number of RW chickens was 29.73 million heads; there was a dramatic drop by 1980 to 4.4 million [10], with a further essential population reduction in later years
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