Siyuan Xing

Domesticated animal meat production and quality are closely related to muscle growth and fat deposition. Fat deposition is determined by adipocyte differentiation and development. Fatness related genes and the regulation of their expression play an important role in fat deposition. In this thesis, I describe chicken breast muscle intramuscular fat (IMF) and abdominal fat (AF) deposition during development. I provide gene expression profiles in breast muscle, liver, and abdominal fat. By using transcriptome analyses to obtain new insights into the correlation between gene expression and fat in chickens, I identified new fatness related candidate genes. The new understanding of gene expression and chicken fat deposition can potentially be used in chicken breeding.

In Chapter 2, I describe the development of a new chicken SNP genotyping array. The SNPs on the array are based on i) whole-genome sequencing from 5 Chinese traditional local breeds and 3 commercial lines, ii) top significant associated SNPs for 15 traits of interest, which were identified using the 60 K chicken SNP array, iii) SNPs from candidate genes e.g., differentially expressed genes for IMF in fast- and slow-growing chickens, iv) SNPs related to feed efficiency, and v) SNPs from a commercial 600 K genotyping array. The genotyping results of the newly developed SNP array in 13 different breeds/lines show a high genotyping rate and the breeds/lines can be clearly distinguished. The SNP array has been utilized for genomic selection in chicken, genome-wide association studies, and to characterize population structure and diversity of different selection lines.

Chapter 3 focuses on a study to identify candidate genes of breast muscle IMF and abdominal fat deposition. Described are the IMF and abdominal fat deposition during development in a slow-growing chicken line. Fat accumulation in breast and abdomen both accelerate from day 56 after hatching. Transcriptome profiling of chicken breast muscle and abdominal fat during developmental stages resulted in the clustering of developmentally dynamic genes. Hub genes affecting these traits were identified e.g., ENSGALG0000004N99S, a candidate for high breast muscle IMF, and CREBPLN, related to low abdominal fat weight. The transcription factor LPMBTLN and the transcription factor co-factors TNIPN, HATN, and BENDS showed a correlation to both high breast muscle IMF and low abdominal fat weight.

The objective of Chapter 4 is to provide a comprehensive understanding of the gene regulation in chicken liver during development. RNA-seq data of liver samples from the embryonic stage to the egg-laying stage, which were derived from slow-growing female chickens, were generated to identify differentially expressed genes between adjacency stages. The differentially expressed genes were enriched in pathways for fatty acid metabolism, biosynthesis of unsaturated fatty acids, fatty acid degradation, and PPAR signalling. To identify hub genes during liver development, a cluster analysis of the developmentally dynamic genes was performed. This resulted in the identification of ACSBG2 as a candidate gene correlated to abdominal fat weight. The ACSBG2 gene overlaps with 2 abdominal fat weight QTLs on chromosome 28.

In chapter 5, we further explore gene expression regulation of IMF and abdominal fat deposition in chicken. We used breast muscle and abdominal fat RNA-seq transcriptome data of high-IMF-low-AF and low-IMF-high-AF chickens from a slow growing dwarf line at marketing time. To avoid external influencing factors, we employed the weighted gene co-expression analysis on the transcriptome data. Two hub genes, ACSMP in breast muscle and CYP2ABN in abdominal fat, were identified which are both significantly positively correlated to IMF and significantly negatively correlated to low abdominal fat weight.

Finally, in chapter 6, the general discussion, I discuss the complexity of chicken IMF genetics. I address the advantages and limitations to study chicken IMF deposition by genotyping arrays. Concerning the correlation between gene expression and fat deposition, the potential usage of RNA-seq on fatness studies is discussed. I end my general discussion by emphasizing the future of chicken fatness traits selection.