Characterization of CNV regions in chicken genomes and association with breast muscle traits

• Grant number: 16/05769-9
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• Start date: June 11, 2016
• End date: June 10, 2017
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Luiz Lehmann Coutinho
• Grantee: Thaís Fernanda Godoy
• Supervisor: Martien A. M. Groenen
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Institution abroad: Wageningen University, Netherlands
• Associated to the scholarship: 15/00616-7 - Identification and characterization of CNVs in chicken genome and association with development of breast muscle, BP.DR

Abstract

The chicken (Gallus gallus) is an important source of animal protein and an important model in genetics research. The characterization of genetic variants and their association with traits of interest are important initial steps to understand the biological pathways controlling these traits. A relevant source of variation in the chicken genome is the number of copies at certain regions (copy number variations - CNVs). CNVs have been shown to be associated with a broad range of phenotypes in several species. We have previously genotyped CNVs in two experimental populations (broiler and F2 population, and their parental generation), composed of 1,896 chickens, using the relative signals and allele frequencies from a high-density chicken SNP array. This project aims to validate the genotyped CNVs with CNVs identified in the parental line with Next Generation Sequencing data. We will also perform a genome wide association study (GWAS) of CNVs with breast muscle weight, and yield in each population. The associated CNVRs will be further characterized by studying their frequency in the studied populations, the genomic location, and the possible overlap with QTLs, genes and biological pathways. The expected results will contribute to a better understanding of the effect of structural variants in the chicken genome and on a number of important economic traits. (AU)