Browsing by Author "Fu, Weixuan"
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Item Characterization of a novel chicken muscle disorder through differential gene expression and pathway analysis using RNA-sequencing(BioMed Central Ltd., 2015-05-21) Mutryn, Marie F.; Brannick, Erin M.; Fu, Weixuan; Lee, William R.; Abasht, Behnam; Marie F Mutryn, Erin M Brannick, Weixuan Fu, William R Lee and Behnam Abasht; Mutryn, Marie F.; Brannick, Erin M.; Fu, Weixuan; Abasht, BehnamBackground Improvements in poultry production within the past 50 years have led to increased muscle yield and growth rate, which may be contributing to an increased rate and development of new muscle disorders in chickens. Previously reported muscle disorders and conditions are generally associated with poor meat quality traits and have a significant negative economic impact on the poultry industry. Recently, a novel myopathy phenotype has emerged which is characterized by palpably “hard” or tough breast muscle. The objective of this study is to identify the underlying biological mechanisms that contribute to this emerging muscle disorder colloquially referred to as “Wooden Breast”, through the use of RNA-sequencing technology. Methods We constructed cDNA libraries from five affected and six unaffected breast muscle samples from a line of commercial broiler chickens. After paired-end sequencing of samples using the Illumina Hiseq platform, we used Tophat to align the resulting sequence reads to the chicken reference genome and then used Cufflinks to find significant changes in gene transcript expression between each group. By comparing our gene list to previously published histology findings on this disorder and using Ingenuity Pathways Analysis (IPA®), we aim to develop a characteristic gene expression profile for this novel disorder through analyzing genes, gene families, and predicted biological pathways. Results Over 1500 genes were differentially expressed between affected and unaffected birds. There was an average of approximately 98 million reads per sample, across all samples. Results from the IPA analysis suggested “Diseases and Disorders” such as connective tissue disorders, “Molecular and Cellular Functions” such as cellular assembly and organization, cellular function and maintenance, and cellular movement, “Physiological System Development and Function” such as tissue development, and embryonic development, and “Top Canonical Pathways” such as, coagulation system, axonal guidance signaling, and acute phase response signaling, are associated with the Wooden Breast disease. Conclusions There is convincing evidence by RNA-seq analysis to support localized hypoxia, oxidative stress, increased intracellular calcium, as well as the possible presence of muscle fiber-type switching, as key features of Wooden Breast Disease, which are supported by reported microscopic lesions of the disease.Item Linkage disequilibrium and recent selection signatures in commercial broilers(University of Delaware, 2016) Fu, WeixuanOver the past 70 years, modern breeding programs have significantly improved traits of economical importance in commercial broilers. Due to recent strong selection and large reduction in effective population size in the breeding program, linkage disequilibrium (LD) in broiler population has changed over generations. Characterizing LD is of fundamental importance for implementation of both genome-wide association studies and genomic selection as well as identification of recent selection signatures. Therefore, using a 60K single nucleotide polymorphism (SNP) panel, we firstly estimated LD and haplotype structure in crossbred broiler chickens and their component pure lines and calculated the consistency of LD between these populations. Compared with the pure lines, the crossbred populations consistently showed a lower level of LD, smaller haploblock sizes and lower haplotype homozygosity on autosomes. Furthermore, correlations of LD between markers at short distances were high between crossbred and pure lines (0.83 to 0.94). Our results suggest that using crossbred populations instead of pure lines can be advantageous for high-resolution quantitative trait loci mapping and good persistence of accuracy of genomic breeding values over generations in genomic selection. Secondly, with better understanding of the extent of LD in commercial broiler populations, we applied two statistical methods to detect signatures of positive selection in five elite lines of commercial broiler chickens, including three broiler sire (male) lines and two broiler dam (female) lines. A total of 321 candidate selection regions were detected by both methods, 42 of which were shared by 2 or more purebred lines. Our results provide a genome-wide scan of recent selection signatures in the five purebred lines. We found several candidate genes for recent selection in multiple lines, such as SOX6 (Sex Determining Region Y-Box 6) and cTR (Thyroid hormone receptor beta), which may have been under selection due to their essential roles in growth, development and reproduction in chickens. Most of the candidate genes in selection regions are novel, and as such they should be of great interest for future research into the genetic architecture of traits relevant to modern broiler breeding.