Software Development And Application For The Integration Analysis Of Functional GENE And QTL Data

Functional Genomics uses the information of structural genomics,systematically studies multiple genes and proteins in the organism,and expounds the function of DNA sequences,which represents a new stage of genomic analysis.The study of transcriptomics can reveal the gene expression of organism,study structure variation and discover new gene,and the transcriptome sequencing technique(RNA-seq)uses the next generation sequencing technology,which provides a new research method for the study of transcriptome.Quantitative traits,like other biological traits,are controlled by genes on chromosomes.Research on quantitative traits of livestock and poultry from the level of gene has become a hotspot in animal research field.Single nucleotide polymorphism(SNP)is the most frequently occurring mutation in the genome,and the study of SNP plays an important role in the exploration of genomic structure,the history of gene evolution and the origin of diseases.Functional genomics,QTL mapping for controlling quantitative traits,and SNP analysis have great significance in elaborating the function of gene sequences,improving the economic value of animal products,and exploring the genes related to biological evolution and disease.In their continuous development,the production of a large number of biological data,need to be collected,classified and analyzed,so far,there is no tool to integrate these types of data effectively.In this study,we use the method of developing R package to quickly integrate RNA-seq data,QTL data and SNP data to achieve mutual query,and auxiliary functions.The AnimalGene2QTL package of this study is run in RStudio or R,and you can view Vignette documents and sample documents.By testing the amount of 10000 rows of data,the result is 47.90 seconds.The results show that the operation of the R package is very simple and fast.In terms of accuracy,we compare the R package of this research with the ENSEMBL and Animalgenome Web sites,query 100 ENSEMBL gene corresponding QTL,through statistical view,the results show that there is no difference in the QTL query,r package and site query results exactly the same,the results show that the R-Package query results are very accurate,with very high effectiveness.On the application,in this study,we used Animalgene2QTL package to search for QTL data of Salmonella enteritidis infection-related genes and campylobacter jejuni related genes in poultry.The data related to Salmonella enteritidis infection is 10,000 high quality target genes,the direct correlation traits were screened by 35,942 QTL statistics,then 369 QTLs related to the study data were identified,and the corresponding genes of 369 qtl were obtained by statistics.In the end,we identified 359 genes directly associated with Salmonella enteritis infection.The data of Campylobacter jejuni infection were 101 ENSEMBL genes,and the direct correlation traits were determined by screening 1437 QTL,and the direct correlation gene was finally identified in 39.We can analyze the GO and Pathway of these genes in combination with the original genetic data,not only to be more precise in the results,but also to increase the reliability of the results.