Identification Of Copy Number Variations In The Chicken Genome And Candidate Genes Associated With Feed Efficiency Using Next-generation Sequencing

The current research focuses on the identification of copy number variations and discovery of candidate genes affecting economically important traits in chickens. The rapid advancement of next-generation sequencing has provided a more powerful tool for structural genomics and functional genomics. In this thesis, we performed genome-wide copy number profiling using whole genome sequencing and in-depth duodenal transcriptome survey for feed efficiency using RNA-Seq.Part I Identification of copy number variations using whole genome sequencingCopy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we performed genome-wide CNV analysis in the12diversified chicken genomes based on whole genome sequencing.A total of8,840CNV regions (CNVRs) covering98.2Mb and representing9.4%of the chicken genome were identified, ranging in size from1.1to268.8kb with an average of11.1kb. Sequencing-based predictions were confirmed at high validation rate by two independent approaches, including array comparative genomic hybridization (aCGH) and quantitative PCR (qPCR). The Pearson’s correlation coefficients between sequencing and aCGH results ranged from0.435to0.755, and qPCR experiments revealed a positive validation rate of91.71%and a false negative rate of22.43%. In total,2,214(25.0%) predicted CNVRs span2,216(36.4%) RefSeq genes associated with specific biological functions. Besides two previously accepted copy number variable genes EDN3and PRLR, we also found some promising genes with potential in phenotypic variants. FZD6and LIMS1, two genes related to diseases susceptibility and resistance are covered by CNVRs. The highly duplicated SOCS2may lead to higher bone mineral density. Entire or partial duplication of some genes like POPDC3may have great economic importance in poultry breeding.Our results based on extensive genetic diversity provide a more refined chicken CNV map and genome-wide gene copy number estimates, and warrant future CNV association studies for important traits in chickens.Part II In-depth duodenal transcriptome survey in chickens with divergent feed efficiency using RNA-SeqSince the feed cost is a major determinant of profitability in poultry industry, how to improve feed efficiency through genetic selection is an intriguing subject for breeders and producers. As a more suitable indicator assessing feed efficiency, residual feed intake (RFI) is defined as the difference between observed and expected feed intake based on maintenance and growth. However, the genetic mechanisms responsible for RFI in chickens are still less well appreciated.In this study, we investigated the duodenal transcriptome architecture of extreme RFI phenotypes in the six brown-egg dwarf hens (three per group) using RNA sequencing technology. Among all mapped reads, an average of75.62%fell into annotated exons,5.50%were located in introns, and the remaining18.88%were assigned to intergenic regions. In total, we identified41promising candidate genes by differential expression analysis between the low and high RFI groups. Furthermore, qRT-PCR assays were designed for10randomly chosen genes, and nine (90.00%) were successfully validated. Functional annotation analyses revealed that these significant genes belong to several specific biological functions related to digestibility, metabolism and biosynthesis processes as well as energy homeostasis. We also predicted253intergenic coding transcripts, and these transcripts were mainly involved in fundamental biological regulation and metabolism processes.Our findings provided a pioneering exploration of biological basis underlying divergent RFI using RNA-Seq, which pinpoints promising candidate genes of functional relevance, is helpful to guide future breeding strategies to optimize feed efficiency and assists in improving the current gene annotation in chickens.