Differential deposition of intramuscular and abdominal fat in chicken

Fat deposition in domesticated chicken has received much attention in modern breeding and poultry production. The aim is for high intramuscular fat (IMF) content for better meat quality and low abdominal fat (AF) for higher feed efficiency. Fatness traits are complex quantitative traits influenced by many variants in the genome some of which are likely to affect gene expression during development. Despite the ever-increasing amount of sequencing data, knowledge of fatness phenotypes and the underlying genes and variants is still limited. In this thesis, a new chicken SNP genotyping array is described based on SNPs segregating in local Chinese breeds and commercial lines. The new array offers potential benefits in breeding programs aimed at increasing both the meat quality and the feed efficiency. Furthermore, I describe the IMF and the AF deposition during development. I explore the transcriptomes of chicken breast muscle, AF, and liver in different stages. More specific, I provide time course transcriptome profiles for breast muscle, AF, and liver in chicken and identify developmentally dynamic genes in the three tissues. Weighted gene co-expression network analysis (WGCNA) results demonstrate that the expression of L3MBTL1, TNIP1, HAT1, and BEND6 genes correlate to both high breast muscle IMF and low AF weight in breast muscle and AF while ACSBG2 gene expression in liver is correlated to high AF weight. I finally provide the transcriptome analysis in breast muscle and AF from high-IMF-low-AF and low-IMF-high-AF chickens at marketing time. The expression of ACSM3 and CYP2AB1 correlate to both high IMF and low AF weight in breast muscle and AF, respectively. Together, I provide a comprehensive overview of gene expression affecting IMF and AF deposition in chicken. The results described in this thesis provide new insights in chicken fat deposition and allow further SNP array updates and improvements on meat quality in the selection process.