Analysis Of Gene Expression Profiles And Construction Of Network For Key Genes Associated With Inosine Monophosphate In Chicken Muscles

Chinese local chicken breeds Rugao Yellow chicken and exotic breeds Recessive White chicken were selected as the object of study, in order to study genes expression changes of Rugao Yellow chicken and Recessive white chicken from the overall level at different growth times and the growth and development mechanism, which is of great significance for understanding the molecular mechanisms of chicken muscle growth and development.In this study, gene expression profiles of2,4,6,8,10,12weeks of age Rugao Yellow chicken and2,6,10,12weeks of age Recessive White chicken muscle tissues were studied respectively by cDNA microarrays and differentially expressed genes of2,12weeks of age of two kinds of chickens were screened to investigate the intrinsic link of different expression genes and their possible molecular biology and laws of the muscle tissues between two experimental groups, differential genes biological functions were classified by GO, in order to provide a theoretical basis further study.Meat flavor is one of the most important aspects of the meat quality in chicken, many evidences indicated that Inosine Monophosphate （IMP） is one of the key components for meat flavor. The process of the synthesis and metabolism for IMP is very complicated, on the basis of Rugao Yellow chicken microarray data, the Perl language and the Pearson coefficient equation were used for solving the linear correlation of related genes, Cytoscape software was combined to generate genes network diagram of IMP, regulation network of IMP genes and its related genes was built based on the KEGG database at last, the genes functions of this regulation network were classified by Cytoscape and GO. IMP genes include PPAT, PAICS, GARS, AIRS, GART, ATIC, ADSL and AMPD. The purpose of building a regulation network is that the model was screened based on RNA levels on the basis of molecular hybridization, the IMP genes expression difference and the mechanism of interaction were revealed at the transcriptional level in the IMP synthesis pathway; the regulation network model of IMP was built in different spatial and temporal expression with RNA-mediated in order to understand function of cells, tissues from the molecular level and clarify molecular mechanism of different spatial and temporal expression for our local chicken flavor substance-IMP and provide a theoretical basis for industrial development. The main results were as follows:1. Comparison at different growth stages of same chicken breeds（1） The gene expressions of Rugao Yellow chicken and Recessive White chicken muscle were analyzed in different periods （2w-12w） by GeneChip. The expression profiles of13,379differentially expressed genes were obtained, Rugao Yellow chicken, compared to2weeks^P<0.001),114genes were up-regulated,127genes down-regulated, when it was4weeks old,116genes were up-regulated,101genes down-regulated, when it was6weeks old,130genes were up-regulated,110genes down-regulated, when it was8weeks old,136genes were up-regulated,118genes down-regulated, when it was10weeks old,94genes were up-regulated,114genes down-regulated, when it was12weeks old, the data analysis showed that at6weeks8and10weeks, the number of up-regulated genes were significantly more than the number of down-regulated genes, at4and12weeks, the number of up-regulated genes were significantly less than down-regulated genes; Recessive white chickens, compared to2weeks（P<0.001）,72genes were up-regulated,51genes down-regulated, when it was4weeks old,42genes were up-regulated,30genes down-regulated, when it was10weeks old,44genes were up-regulated,34genes down-regulated, when it was4weeks old, the data analysis showed that at the three time points, the number of up-regulated genes were significantly more than the number of down-regulated genes.（2） Different genes were divided into12categories, the correlation coefficients were concentrated in the between0and1, Rugao Yellow chicken, the correlation coefficient between Class6and Class7was1, the correlation coefficient between Class3and Class7, Class4and Class8were0; Recessive white chicken, the correlation coefficient between Class1and class2, Class6and3,7,11were0, the correlation coefficient between Class6and class5,10. Class8and12were1, the correlation coefficient of different genes in Recessive white chicken were generally higher than that in Rugao Yellow chicken in growth and development process 2. Gene expression in different periods （2w,12w）（1） GeneChip was used to construct gene expression profile in order to screen differentially expressed genes of muscle tissue in Rugao Yellow chicken and Recessive white chicken and investigate the molecular mechanism related with muscle tissue traits between the two groups, respectively.208differentially expressed genes （P<0.001） were screened out, of which108are known genes,94up-regulated,114down-regulated for Rugao Yellow chicken;78differentially expressed genes （P<0.001） were screened out, of which39were known genes,44up-regulated,34down-regulated for Recessive white chicken, which were involved in growth, molecular mechanism, immune system process, biosynthetic process, cell communication, protein synthesis and degradation were screened out. Meanwhile, some genes among all these differentially expressed genes that had no annotation in GenBank were screened out; they were presumed to be unknown new genes. At the same time, the results were verified by real-time quantitative PCR and proteomic technology, indicating that microarray results were reliable. The roles that they may play in chicken growth and development, energy metabolism needed to be clarified later.（2）6differentially expressed genes were screened out in the process of growth and development of Rugao Yellow chickens,1differentially expressed gene was screened out in the process of growth and development of Recessive white chickens, RCJMB04₂4e12（NM₂05120） was involved in the process of growth and development in Rugao Yellow chicken and Recessive white chicken, the expression of which was the lowest at4weeks old in Rugao Yellow chicken, while continued to decline in Recessive white chicken, suggesting that it may be a candidate marker of early growth traits in chicken, another five genes related growth-related differences in Rugao Yellow chicken were:HOPX, CCNB2, DDR2, ADD1and IGF1had a certain impact on the growth and development, HOPX was highly expressed, gene expression tendency of to CCNB2, DDR2, ADD1remained gentle, IGF1was lowly expressed.3、Construction of IMP genes regulatory networksThe Perl language and the Pearson coefficient equation were used for solving the linear correlation of related genes, Cytoscape software was combined to generate genes network diagram of IMP, regulation network of IMP genes and its related genes was built based on the KEGG database at last, the genes functions of this regulation network were classified by Cytoscape and GO. （1）Correlation between IMP related genes were analyzed, when correlation coefficients were greater than or equal to0.75, genes included:PPAT, PAICS, ADSL, AMPD, ATIC, GART, AIRS and GARS, when correlation coefficient greater than or equal to0.80, genes included: PPAT, ATIC, AMPD, GART, AIRS, GARS, when correlation coefficient greater than or equal to0.85, genes included:PPAT, AMPD, GART, AIRS, GARS, when correlation coefficient greater than or equal to0.90, genes included:AMPD, GART, AIRS, GARS, conclusion between AMPD and GARS-AIRS-GART composite gene was the highest, the PPAT followed.（2） Expressions of8key IMP genes were analyzed in Rugao Yellow chicken:AMPD and ADSL genes may play major roles and AMPD was a positive regulatory role. Expression trend between GART and GARS, AIRS, AMPD was the opposite, but it could be obtained by the correlation coefficient model that conclusion between AMPD and GARS-AIRS-GART composite gene was the highest, it can be seen that8key IMP genes may have a positive or a negative correlation.（3） Expression of AMPD of AIRS and GARS were upward trend while IMP contents were highest at6and10weeks, which may showed a positive correlation; expression of PPAT, ADSL and GART were downward trend that may be negatively correlated.（4） Comparison of network regulation based on GeneChip and KEGG:GART, PAICS, ADSL, ATIC and AMPD played roles in IMP network regulation of Rugao Yellow chicken, while regulatory role of PPAT, AIRS and GARS were lowly expressed, this reason may be related to the genetic background of the different breeds.