| To investigate the molecular mechanism of intestinal development of postnatal piglets during suckling and after weaming fed with different weanling diets in this study, two experiments were conducted by using porcine genome array to analyze the transcription profile of piglets during different growth and development stages. The differentially expressed genes were screened and these data were mined. The results were as followings:Experiment 1. Transcription profile of whole-genome for the developmental intestine of suckling pigletsThe intestinal development of postnatal piglets has an important impact on health and growth performance. The transcription profiles of nursing Yorkshire at the age of 0, 3, 8, 14 and 21 days were detected by using porcine genome array (PGA) in this study. The results were as followings:1. The results of PGA during suckling: More than 8000 differentially expressed transcripts in intestine of piglets during suckling were obtained. Series Test Cluster were analyzed for these differential expression genes and 80 profiles were established, among which profiles 66 and 13 were the most significant (P<0.01). This result indicated that the differentially expressed genes in co-expression of these trends are related to the intestinal development during suckling.2. Six differentially expressed genes were selected and quantified by qRT-PCR. Results illustrated the expression patterns of the six genes were similar to those from PGA. The two experimental methods were both positively correlated with correlation coefficient being 0.934±0.025. This result demonstrateed that the microarray technique used in this study is accurate and reproducible.3. Gene Ontology(GO)analysis of the profile 66 indicated that the co-expression genes in this profile were mainly involved in cell cycle and fungal-type cell wall organization. GO of the profile 13 showed that the co-expression genes in this profile were mainly involved in vitamin and ionic transports. Furthermore, there was a significant inflection point on d3 of age, which suggested that d3 of age was a crucial period for piglets.4. Significant pathway analysis of differentially expressed genes in profiles 66 and 13 indicated that the pathways which the differentially expressed genes participated during suckling were mainly PPAR signaling pathway, linoleic acid metabolism and so on. This result suggested that these pathways were important to the intestinal development.5. Construction and analysis of gene regulatory networks (GRNs) initially revealed that there were 20 genes which possessed important regulatory ability (p<0.01), These genes could regulate other genes in GRN.Experiment 2. Effect of different weaning diets on transcription profile of genome-wide in intestine for weanling pigletsThe weanling diets have an obvious impact on the intestinal development. To investigate the impact of different weaning diets on the intestinal development, in the present study, PGA was employed to detect the difference on transcription spectrum of intestine for weanling piglets fed with different diets with or without milk protein.1. Results of PGA: Analysis of expression profiles in genome-wide transcription in weanling piglets fed with the diets with milk protein (treatment 1) was conducted and 370 differentially expressed transcripts were screened. Among these model profiles, there were 26 significant profiles and profiles 5 and 11 were the most significant (P<0.01). Meanwhile, analysis of expression profiles in genome-wide transcription in weanling piglets fed with the vegetable protein without milk protein (treatment 2) showed that 263 differentially expressed transcripts were screened. Series Test Cluster were analyzed for these differential expression genes and 26 significant profiles were obtained, among these model profiles, profiles 3 and 22 were the most significant (P<0.01). This result indicated that the differentially expressed genes in co-expression of these trends are related to the intestinal development of weanling piglets.2. Six differentially expressed genes were selected and quantified by qRT-PCR. Results illustrated that the expression patterns of the six genes were similar to those from PGA. The two experimental methods were both positively correlated with correlation coefficient being 0.902±0.023 and 0.855±0.036. These resultes indicated that the microarray technique used in this study is accurate and reproducible. 3. The co-expression of genes in these significant profiles were assayed using GO: For the treatment 1, it was found from the results of GO that the genes in profile 5 were mainly involved in some biology process such as tachykinin signaling pathway, elevation of Cytosolic calcium ion concentration and so on, while the genes in profile 11 were mainly involved in positive regulation of viral transcription, inflammatory response, histidine metabolic process, cellular metabolic process (p<0.01) and so on. For the treatment 2, the results of GO revealed that the genes in profile 3 were mainly involved in positive regulation of smooth muscle contraction, while the genes in profile 22 were mainly involved in cell growth.4. Pathway analysis: The signal pathways that the differentially expressed genes participated in both treatments were similar, including PPAR signaling pathway, Aminosugars metabolism, T cell receptor signaling pathway and so on. These pathways changed obviously after weanling (p<0.01).5. Construction and analysis of Dynamic-GeneNet of the differentially co-expression genes in significant profiles: Based on DGN model, gene regulatory networks (GRNs) for the genes in profile 5,11,3 and 22 in treatment land 2 were constructed. The GRNs revealed that there were 12 genes and 9 genes which possessed important regulatory ability in GRN. Meanwhile, 9 genes in these two GRNs were found to have changed the regulatory site. We can choose seed genes from sub-networks that have higher rank scores as potential key genes on the intestinal development of piglets.These results highlight some possible candidate genes for developmental intestine of piglets and provide some data on which to base further study of the molecular mechanism of the developmental intestine of piglets.
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