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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.)

SNP and INDEL detection in a QTL region on chicken chromosome 2 associated with muscle deposition

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Author(s):
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Godoy, T. F. [1] ; Moreira, G. C. M. [1] ; Boschiero, C. [1] ; Gheyas, A. A. [2, 3] ; Gasparin, G. [1] ; Paduan, M. [1] ; Andrade, S. C. S. [1] ; Montenegro, H. [4] ; Burt, D. W. [2, 3] ; Ledur, M. C. [5] ; Coutinho, L. L. [1]
Total Authors: 11
Affiliation:
[1] Univ Sao Paulo, ESALQ, Dept Zootecnia, BR-13418900 Sao Paulo - Brazil
[2] Univ Edinburgh, Dept Genet & Genom, Roslin Inst, Roslin EH25 9PS, Midlothian - Scotland
[3] Univ Edinburgh, Royal Sch Vet Studies, Roslin EH25 9PS, Midlothian - Scotland
[4] Univ Sao Paulo, ESALQ, Dept Genet, BR-13419900 Sao Paulo - Brazil
[5] Embrapa Suinos & Aves, BR-89700000 Concordia, SC - Brazil
Total Affiliations: 5
Document type: Journal article
Source: ANIMAL GENETICS; v. 46, n. 2, p. 158-163, APR 2015.
Web of Science Citations: 8
Abstract

Genetic improvement is important for the poultry industry, contributing to increased efficiency of meat production and quality. Because breast muscle is the most valuable part of the chicken carcass, knowledge of polymorphisms influencing this trait can help breeding programs. Therefore, the complete genome of 18 chickens from two different experimental lines (broiler and layer) from EMBRAPA was sequenced, and SNPs and INDELs were detected in a QTL region for breast muscle deposition on chicken chromosome 2 between microsatellite markers MCW0185 and MCW0264 (105849-112649kb). Initially, 94674 unique SNPs and 10448 unique INDELs were identified in the target region. After quality filtration, 77% of the SNPs (85765) and 60% of the INDELs (7828) were retained. The studied region contains 66 genes, and functional annotation of the filtered variants identified 517 SNPs and three INDELs in exonic regions. Of these, 357 SNPs were classified as synonymous, 153 as non-synonymous, three as stopgain, four INDELs as frameshift and three INDELs as non-frameshift. These exonic mutations were identified in 37 of the 66 genes from the target region, three of which are related to muscle development (DTNA, RB1CC1 and MOS). Fifteen non-tolerated SNPs were detected in several genes (MEP1B, PRKDC, NSMAF, TRAPPC8, SDR16C5, CHD7, ST18 and RB1CC1). These loss-of-function and exonic variants present in genes related to muscle development can be considered candidate variants for further studies in chickens. Further association studies should be performed with these candidate mutations as should validation in commercial populations to allow a better explanation of QTL effects. (AU)

FAPESP's process: 12/15294-7 - IDENTIFICATION OF POLYMORPHISMS IN A REGION OF THE CHICKEN CHROMOSOME 2 ASSOCIATED WITH MUSCLE DEPOSITION
Grantee:Thaís Fernanda Godoy
Support type: Scholarships in Brazil - Master