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© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.

Abstract

Simple Summary

The 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.

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.

Details

Title
Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens
Author
Abdelmanova, Alexandra S 1 ; Dotsev, Arsen V 1   VIAFID ORCID Logo  ; Romanov, Michael N 2   VIAFID ORCID Logo  ; Stanishevskaya, Olga I 3 ; Gladyr, Elena A 1   VIAFID ORCID Logo  ; Rodionov, Andrey N 1 ; Vetokh, Anastasia N 1   VIAFID ORCID Logo  ; Volkova, Natalia A 1   VIAFID ORCID Logo  ; Fedorova, Elena S 3 ; Gusev, Igor V 1 ; Griffin, Darren K 4   VIAFID ORCID Logo  ; Brem, Gottfried 5 ; Zinovieva, Natalia A 1   VIAFID ORCID Logo 

 L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; [email protected] (A.S.A.); [email protected] (A.V.D.); [email protected] (E.A.G.); [email protected] (A.N.R.); [email protected] (A.N.V.); [email protected] (N.A.V.); [email protected] (I.V.G.) 
 School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK; [email protected]; K.I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 23 Akademika Skryabina St., 109472 Moscow, Russia 
 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; [email protected] (O.I.S.); [email protected] (E.S.F.) 
 School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK; [email protected] 
 Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria; [email protected] 
First page
876
Publication year
2021
Publication date
2021
Publisher
MDPI AG
e-ISSN
20797737
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2576382226
Copyright
© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.