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Abdelmanova AS, Dotsev AV, Romanov MN, Stanishevskaya OI, Gladyr EA, Rodionov AN, Vetokh AN, Volkova NA, Fedorova ES, Gusev IV, Griffin DK, Brem G, Zinovieva NA. Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens. Biology (Basel) 2021; 10:biology10090876. [PMID: 34571753 PMCID: PMC8469556 DOI: 10.3390/biology10090876] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 01/14/2023]
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 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.
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Affiliation(s)
- Alexandra S. Abdelmanova
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Arsen V. Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
- K.I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 23 Akademika Skryabina St., 109472 Moscow, Russia
- Correspondence: (M.N.R.); (N.A.Z.); Tel.: +798-57154351 (M.N.R.); +749-67651163 (N.A.Z.)
| | - Olga I. Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (O.I.S.); (E.S.F.)
| | - Elena A. Gladyr
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Andrey N. Rodionov
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Anastasia N. Vetokh
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Natalia A. Volkova
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Elena S. Fedorova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (O.I.S.); (E.S.F.)
| | - Igor V. Gusev
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
- Correspondence: (M.N.R.); (N.A.Z.); Tel.: +798-57154351 (M.N.R.); +749-67651163 (N.A.Z.)
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