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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.)

Identification of selection signatures involved in performance traits in a paternal broiler line

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Author(s):
Costa Almeida, Octavio Augusto [1] ; Monteiro Moreira, Gabriel Costa [1] ; Rezende, Fernanda Marcondes [2] ; Boschiero, Clarissa [3] ; Peixoto, Jane de Oliveira [4] ; Guaratini Ibelli, Adriana Mercia [4] ; Ledur, Monica Correa [4] ; de Novais, Francisco Jose [1] ; Coutinho, Luiz Lehmann [1]
Total Authors: 9
Affiliation:
[1] Univ Sao Paulo, Luiz de Queiroz Coll Agr ESALQ, Piracicaba, SP - Brazil
[2] Univ Fed Uberlandia, Uberlandia, MG - Brazil
[3] Noble Res Inst, Ardmore, OK - USA
[4] Embrapa Suinos & Aves, Concordia, SC - Brazil
Total Affiliations: 4
Document type: Journal article
Source: BMC Genomics; v. 20, JUN 3 2019.
Web of Science Citations: 0
Abstract

BackgroundNatural and artificial selection leads to changes in certain regions of the genome resulting in selection signatures that can reveal genes associated with the selected traits. Selection signatures may be identified using different methodologies, of which some are based on detecting contiguous sequences of homozygous identical-by-descent haplotypes, called runs of homozygosity (ROH), or estimating fixation index (F-ST) of genomic windows that indicates genetic differentiation. This study aimed to identify selection signatures in a paternal broiler TT line at generations 7th and 16th of selection and to investigate the genes annotated in these regions as well as the biological pathways involved. For such purpose, ROH and F-ST-based analysis were performed using whole genome sequence of twenty-eight chickens from two different generations.ResultsROH analysis identified homozygous regions of short and moderate size. Analysis of ROH patterns revealed regions commonly shared among animals and changes in ROH abundance and size between the two generations. Results also suggest that whole genome sequencing (WGS) outperforms SNPchip data avoiding overestimation of ROH size and underestimation of ROH number; however, sequencing costs can limited the number of animals analyzed. F-ST-based analysis revealed genetic differentiation in several genomic windows. Annotation of the consensus regions of ROH and F-ST windows revealed new and previously identified genes associated with traits of economic interest, such as APOB, IGF1, IGFBP2, POMC, PPARG, and ZNF423. Over-representation analysis of the genes resulted in biological terms of skeletal muscle, matrilin proteins, adipose tissue, hyperglycemia, diabetes, Salmonella infections and tyrosine.ConclusionsIdentification of ROH and F-ST-based analyses revealed selection signatures in TT line and genes that have important role in traits of economic interest. Changes in the genome of the chickens were observed between the 7th and 16th generations showing that ancient and recent selection in TT line may have acted over genomic regions affecting diseases and performance traits. (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: 16/00569-1 - Imputation and genome-wide association analysis using haplotypes for abdominal fat in chickens
Grantee:Gabriel Costa Monteiro Moreira
Support type: Scholarships abroad - Research Internship - 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