| Nature,as an organic whole,is filled with complex interactions.Organisms living inside this organic whole are subjected to a combination of effects from maternal inheritance,epigenetic,pathogen challenge,environmental conditions and other effectors.Global climate change brought a host of damages to the ecological environment;specifically,the increase of average global temperature negatively impacted the producti'vity of livestock industries.Moreover,recent disease outbreaks has changed breeding objectives to have more emphasis on health.Today,a principal mission of the breeding scientists is to focus on how to select and breed more climate-adaptable livestock that are heat and disease resistant.Therefore,we utilized the latest next generation sequencing techniques and characterized the whole transcriptome response to heat and immune stimulation using unique genetic lines.The thesis has three parts:1.RNA-seq technology was used to investigate the effects of acute(35?,3h)and chronic(35?,7h/d,7d)heat stress on the liver transcriptome of 3 wk chickens of a heat-susceptible line,a heat-resistant line,and their 19th generation advanced intercross line.Forty-eight RNA-seq data and analysis suggested that heat stress caused more damage on broiler than Fayoumi in cellular development,energe metabolic process and hormone regulation.Also,acute heat stress had greater impact on chickens than chronic heat stress.And the angiopoietin-like 4 gene was predicted as a candidate gene for improvement of heat tolerance in chickens.This research extends our understanding of the liver response to different heat treatments in distinct genetic chicken lines and provides information necessary for breeding birds to be more resilient to the negative impacts of heat.2.To characterize the response to ALV challenge,we developed a novel methodology that combined four datasets:mRNA expression,mRNA expressions that are associated with regulatory factors miRNA and IncRNA,and ALV gene expression.Specific Pathogen-Free(SPF)layer chickens were infected with ALV-J or maintained as non-injected controls.Spleen samples were collected at 40 days post injection(dpi),and sequenced.The combined analysis of the 4 RNA expression datasets revealed that the defensins gene family plays an important role in the immunosuppression caused by ALV-J.Moreover,the results show ALV infection is detected by pattern-recognition receptors(TLR9 and TLR3)leading to a type-I IFN mediated innate immune response that is modulated by IRF7 and IRF1.Co-expression network analysis of mRNA with miRNA,lncRNA and virus genes identified key elements within the complex networks utilized during ALV response.The integration of information from the host transcriptomic,epigenetic and virus response also has the potential to provide deeper insights into other host-pathogen interactions.3.Taking advantage of the simplicity and controllability of the cell model,we performed an in vitro study with bone marrow derived dendritic cells(BMDC).BMDC from disease resistant-Fayoumi and disease susceptible-Leghorn chickens were stimulated with heat and/or LPS.The cellular results are partial consistence with the in vivo outlined in study 1 above;it identified some critical genes and signaling pathways(such as cAMP pathway),and their interaction networks.Additionally,with the several time points,a tendency chart with related immune mechanism was created.In conclusion,our study focused on two main environmental challenges:high ambient temperature and a neoplastic disease.Using advancement of high-throughput sequence technology,we explored the role of environmental stressor and epigenetic to genetic mechanism.Complexity of experiment design,diversified angles of analysis,doing the best to model and present the complex environment,it helps to character the response of based on genotype and phenotype.Integrating the information with combined analysis of the data,more reliable results will help to guide breeding and provide an effective strategy for future research. |
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