Inherited copy number variation in the chicken genome and association with breast muscle traits

Author(s)

Thaís Fernanda Godoy

• Document type: Doctoral Thesis
• Press: Piracicaba.
• Institution: Universidade de São Paulo (USP). Escola Superior de Agricultura Luiz de Queiroz (ESALA/BC)
• Defense date: 2018-03-08

Examining board members

Luiz Lehmann Coutinho; Clarissa Boschiero; Mônica Corrêa Ledur; Gabriel Rodrigues Alves Margarido

• Advisor: Luiz Lehmann Coutinho

Abstract

Copy number variation (CNV) is an important polymorphism that is associated with a wide range of traits in human, wild and livestock species. In chicken, an important source of animal protein and a developmental model organism, CNV is associated with several phenotypes and evolutionary footprints. However, identification and characterization of CNV inheritance on chicken genome lacks further investigation. We screened CNVs in chicken using two distinct populations with known pedigree. In 826 broilers we identified 25,819 CNVs (4,299 deletions and 21,520 duplications) of which 21,077 were inherited, 201 showed no inheritance and 4,541 were classified as de novo CNVs. In 514 F2 animals (layer and broiler cross) we identified 21,796 CNVs (2,254 deletions and 19,543 duplications) of which 18,230 were inherited, 587 not inherited and 2,979 were classified as de novo CNVs. After a strict filtering step to remove potential false positives and negative CNVs, only 220 (4.84%) and 430 (14.43%) de novo CNVs remained in the broiler and F2 populations, respectively. A total of 33.11% (50 out of 151) of the inherited CNVs identified in ten animals were validated by sequencing data. From the validated CNVs, 64% had more than 80% of their size (bp) validated. A total of 59% and 48.8% were classified as novel CNVs regions (CNVRs) in the broiler and F2, respectively. Considering the Bonferroni-corrected p-values for multiple testing and statistically significant p-values ≤ 0.01, we found two CNV segments significantly associated with breast weight, one with breast weight yield, six with breast meat weight, 18 CNV segments with breast meat yield, four with breast filet weight and two with breast yield. These CNV segments that were significantly associated overlapped with 181 protein-coding genes. The CNVseg 300, that was associated with all traits and encompass six CNVRs, overlapped a total of 26 protein-coding genes. Among these genes, the gene MYL1 (Myosin Light Chain 1) is expressed in the fast skeletal muscle fibers, and the genes MLPH (Melanophilin), PRLH (Prolactin Releasing Hormone) and RAB17 (Member RAS Oncogene Family), that were associated with the lavender phenotype (feather blue-grey color) and regulation of homeothermy and the metabolism. The present study improves our knowledge about CNV in the chicken genome and provides insight in the distribution and of different classes of CNVs, i.e. inherited and de novo CNVs, in two experimental chicken populations. In addition, the genome-wide association analyses were the first performed on broiler population with breast muscle traits, that are important characteristics for poultry production. The GWAS results allow us to understand the probably relationship between some genes and CNVRs that are significantly associated with breast muscle traits. (AU)

• 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 Opportunities: Scholarships in Brazil - Doctorate