Identification and characterization of CNVs in chicken genome and association with development of breast muscle

• Grant number: 15/00616-7
• Support Opportunities: Scholarships in Brazil - Doctorate
• Effective date (Start): May 01, 2015
• Effective date (End): February 28, 2018
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Acordo de Cooperação: Coordination of Improvement of Higher Education Personnel (CAPES)
• Principal Investigator: Luiz Lehmann Coutinho
• Grantee: Thaís Fernanda Godoy
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Associated research grant: 14/08704-0 - Identification of loci of interest for poultry production, AP.TEM
• Associated scholarship(s): 16/05769-9 - Characterization of CNV regions in chicken genomes and association with breast muscle traits, BE.EP.DR

Abstract

Chicken (Gallus gallus) is considered a biological model among domestic animals, mainly in studies of the genetic basis and phenotypic diversity. Identifying genetic variation is a crucial step towards a better understanding of the molecular mechanisms responsible for traits of biological interest. Copy number variation (CNV) has been extensively studied because it is a widely distributed variant in the genome and contributes significantly to the phenotypic variation in several species. Different technologies can be used for CNVs identification in the genome, such as aCGH, SNP chip and Next Generation Sequencing. In chickens, studies have been performed for this purpose, but only the aCGH methodology has been used and no study has yet been carried out using the high-density chicken SNP chip (600K Affymetrix). Therefore, this study aims to identify, characterize and validate CNVs across the genome of two experimental populations of chickens (broiler and F2 population, and their parental generation) developed by Embrapa Swine and Poultry. The CNVs identified will be associated with breast muscle deposition traits. For that purpose, the following steps will be performed: genotyping of 2,000 animals with HD 600 K chip (Affymetrix) by GeneTitan® Axiom® Affymetrix®; identification of CNVs by two tools (PennCNV and QuantiSNP); determination of CNV regions (CNVRs) and their frequencies in the populations studied using the CNVRuler tool; characterization of CNVRs identified and evaluation of possible overlaps with QTLs and genes, annotation of CNVRs; CNVRs validation using Next Generation Sequencing data in the parental generation of the two populations; and genome association study (GWAS) of CNVRs with breast muscle weight and yield. It is expected that this project will allow the identification of CNVs in the populations studied and the association of some of them to breast muscle development, enabling a better understanding of the structural variants in the chicken genome. (AU)

Scientific publications

(4)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

MONTEIRO MOREIRA, GABRIEL COSTA; BOSCHIERO, CLARISSA; MELLO CESAR, ALINE SILVA; REECY, JAMES M.; GODOY, THAIS FERNANDA; TREVISOLI, PRISCILA ANCHIETA; CANTAO, MAURICIO E.; LEDUR, MONICA CORREA; GUARATINI IBELLI, ADRIANA MERCIA; PEIXOTO, JANE DE OLIVEIRA; et al. A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens. BMC Genomics, v. 19, MAY 21 2018. (14/21380-9, 15/00616-7, 16/00569-1, 14/08704-0)

BOSCHIERO, CLARISSA; MONTEIRO MOREIRA, GABRIEL COSTA; GHEYAS, ALMAS ARA; GODOY, THAIS FERNANDA; GASPARIN, GUSTAVO; SAMPAIO CORREA MARIANI, PILAR DRUMMOND; PADUAN, MARCELA; MELLO CESAR, ALINE SILVA; LEDUR, MONICA CORREA; COUTINHO, LUIZ LEHMANN. Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines. BMC Genomics, v. 19, JAN 25 2018. (14/21380-9, 15/00616-7, 14/08704-0)

MONTEIRO MOREIRA, GABRIEL COSTA; POLETI, MIRELE DAIANA; PERTILLE, FABIO; BOSCHIERO, CLARISSA; MELLO CESAR, ALINE SILVA; GODOY, THAIS FERNANDA; LEDUR, MONICA CORREA; REECY, JAMES M.; GARRICK, DORIAN J.; COUTINHO, LUIZ LEHMANN. Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach. BMC GENETICS, v. 20, n. 1, NOV 6 2019. (14/21380-9, 16/20440-3, 16/00569-1, 14/08704-0, 15/00616-7)

MOREIRA, GABRIEL COSTA MONTEIRO; BOSCHIERO, CLARISSA; MELLO CESAR, ALINE SILVA; REECY, JAMES M.; GODOY, THAIS FERNANDA; PERTILLE, FABIO; LEDUR, MONICA CORREA; MEIRA TAVARES MOURA, ANA SILVIA ALVES; GARRICK, DORIAN J.; COUTINHO, LUIZ LEHMANN. Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken. SCIENTIFIC REPORTS, v. 8, NOV 1 2018. (15/00616-7, 14/08704-0, 14/21380-9, 16/20440-3, 16/00569-1)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

GODOY, Thaís Fernanda. Inherited copy number variation in the chicken genome and association with breast muscle traits. 2018. Doctoral Thesis - Universidade de São Paulo (USP). Escola Superior de Agricultura Luiz de Queiroz (ESALA/BC) Piracicaba.