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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

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Author(s):
Boschiero, Clarissa [1, 2] ; Monteiro Moreira, Gabriel Costa [1] ; Gheyas, Almas Ara [3, 4] ; Godoy, Thais Fernanda [1] ; Gasparin, Gustavo [1] ; Sampaio Correa Mariani, Pilar Drummond [1] ; Paduan, Marcela [1] ; Mello Cesar, Aline Silva [1] ; Ledur, Monica Correa [5] ; Coutinho, Luiz Lehmann [1]
Total Authors: 10
Affiliation:
[1] Univ Sao Paulo, Luiz Queiroz Coll Agr ESALQ, Anim Sci Dept, Anim Biotechnol, BR-13418900 Piracicaba, SP - Brazil
[2] Noble Res Inst, 2510 Sam Noble Pkwy, Ardmore, OK 73401 - USA
[3] Univ Edinburgh, Roslin Inst, Dept Genet & Genom, Easter Bush Campus, Edinburgh EH25 9RG, Midlothian - Scotland
[4] Univ Edinburgh, Royal Sch Vet Studies, Easter Bush Campus, Edinburgh EH25 9RG, Midlothian - Scotland
[5] Embrapa Suinos & Aves, BR-89715899 Concordia, SC - Brazil
Total Affiliations: 5
Document type: Journal article
Source: BMC Genomics; v. 19, JAN 25 2018.
Web of Science Citations: 8
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. (AU)

FAPESP's process: 14/21380-9 - Genome wide association studies for fat deposition and carcass yield in chickens
Grantee:Gabriel Costa Monteiro Moreira
Support type: Scholarships in Brazil - Doctorate
FAPESP's process: 15/00616-7 - Identification and characterization of CNVs in chicken genome and association with development of breast muscle
Grantee:Thaís Fernanda Godoy
Support type: Scholarships in Brazil - Doctorate
FAPESP's process: 14/08704-0 - Identification of loci of interest for poultry production
Grantee:Luiz Lehmann Coutinho
Support type: Research Projects - Thematic Grants