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Unveiling comparative genomic trajectories of selection and key candidate genes in egg-type Russian White and meat-type White Cornish chickens

Abdelmanova, Alexandra S., Dotsev, Arsen V., Romanov, Michael N., Stanishevskaya, Olga I., Gladyr, Elena A., Rodionov, Andrey N., Vetokh, Anastasia N., Volkova, Natalia A., Fedorova, Elena S., Gusev, Igor V., and others. (2021) Unveiling comparative genomic trajectories of selection and key candidate genes in egg-type Russian White and meat-type White Cornish chickens. Biology, 10 (9). Article Number 876. ISSN 2079-7737. E-ISSN 2079-7737. (doi:10.3390/biology10090876) (KAR id:90048)

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Official URL
https://doi.org/10.3390/biology10090876

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.

Item Type: Article
DOI/Identification number: 10.3390/biology10090876
Uncontrolled keywords: selection signatures; genomic regions; candidate genes; gene ontology; gene richness; chicken; SNPs; Russian White breed; White Cornish breed
Subjects: Q Science > QH Natural history > QH426 Genetics
Q Science > QH Natural history > QH75 Conservation (Biology)
S Agriculture > SF Animal culture
Divisions: Divisions > Division of Natural Sciences > Biosciences
Signature Themes: Food Systems, Natural Resources and Environment
Depositing User: Mike Romanov
Date Deposited: 06 Sep 2021 12:40 UTC
Last Modified: 10 Sep 2021 09:46 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/90048 (The current URI for this page, for reference purposes)
Abdelmanova, Alexandra S.: https://orcid.org/0000-0003-4752-0727
Dotsev, Arsen V.: https://orcid.org/0000-0003-3418-2511
Romanov, Michael N.: https://orcid.org/0000-0003-3584-4644
Stanishevskaya, Olga I.: https://orcid.org/0000-0001-9504-3916
Gladyr, Elena A.: https://orcid.org/0000-0002-5210-8932
Vetokh, Anastasia N.: https://orcid.org/0000-0002-2865-5960
Volkova, Natalia A.: https://orcid.org/0000-0001-7191-3550
Fedorova, Elena S.: https://orcid.org/0000-0002-1618-6271
Griffin, Darren K.: https://orcid.org/0000-0001-7595-3226
Brem, Gottfried: https://orcid.org/0000-0002-7522-0708
Zinovieva, Natalia A.: https://orcid.org/0000-0003-4017-6863
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