Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/34601
Appears in Collections:Aquaculture Journal Articles
Peer Review Status: Refereed
Title: Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines
Author(s): Boschiero, Clarissa
Moreira, Gabriel Costa Monteiro
Gheyas, Almas Ara
Godoy, Thaís Fernanda
Gasparin, Gustavo
Mariani, Pilar Drummond Sampaio Corrêa
Paduan, Marcela
Cesar, Aline Silva Mello
Ledur, Mônica Corrêa
Coutinho, Luiz Lehmann
Contact Email: almas.gheyas@stir.ac.uk
Keywords: Fat deposition
Fst
Genetic variants
Next generation sequencing
INDEL
Selection signatures
SNP
Poultry
Issue Date: 2018
Date Deposited: 15-Oct-2022
Citation: Boschiero C, Moreira GCM, Gheyas AA, Godoy TF, Gasparin G, Mariani PDSC, Paduan M, Cesar ASM, Ledur MC & Coutinho LL (2018) Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines. BMC Genomics, 19 (1), Art. No.: 83. https://doi.org/10.1186/s12864-018-4444-0
Abstract: Background Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection. Results A total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development. Conclusions In this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common genetic variants from a Brazilian broiler and a white egg layer line that can be used for genomic studies involving association analysis with phenotypes of economic interest to the poultry industry.
DOI Link: 10.1186/s12864-018-4444-0
Rights: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Licence URL(s): http://creativecommons.org/licenses/by/4.0/

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