The Discovery,Boundary Identification And Function Analysis Of Copy Number Variation Based On Genome And Transciptome Sequencing Data

Chinese and foreign pig breeds have great differences in growth,lean meat rate,meat quality,fertility,immunity and stress resistance.The genetic basis for these difference has always been the one focus of animal genetics and breeding research.When using the whole genome re-sequencing data to analyze selected regions during the domestication process of domestic and foreign pigs,it was found that Chinese domestic pigs and European domestic pigs were subjected to different choices during domestication,and there were different copy number variation regions.However,the regions of CNV(copy number variation)based on genome sequence information are too large,and CNV breakpoints or their boundaries are difficult to precisely localize to a single base.Therefore,the difficulty of CNV breakpoint identification may cause the difficulty of verifying the CNV fragment.In our earlier research,the genomes and the transcriptomes of spleen,testis and inguinal lymph nodes of 6 Tongcheng pigs and 6 Large White pigs in PRRSV infection test were deeply sequenced.Based on the information of 12 individual genomes and transcriptome sequences of the two breeds,bioinformatics methods were used.The analysis predicts CNVR on the pig genome.At the same time,combined with transcriptome data,we screened candidate CNVRs overlapping with genes and established methods to identify CNV boundaries,and then used bioinformatics methods to predict CNV function,providing a reliable foundation for further research on CNV.The main results are as follows:(1)Using the LUMPY and CNVnator analysis software to perform CNV discovery on the resequencing data of 6 Tongcheng pigs and 6 Large White pigs,and to find candidate genes for CNV with differences between Large White Pigs and Tongcheng Pigs.Three immune-related genes,16 differentially expressed genes and a pseudogene with an annotation error were identified.(2)The existence of the candidate gene CNVR was verified in 33 Large White Pigs and 33 Tongcheng populations.Among them,there was a 434 bp deletion of Tongcheng population in the TRIM14 gene,and there was no variation in the Large White population.There was a 932 bp deletion in Large white pigs,and Tongcheng pigs were normal;there was a 470 bp deletion in Tongcheng pigs in the STRA8 gene and there was no deletion in Large White pigs.(3)Combining the spleen,inguinal lymph nodes,and testis transcriptome data of 12 individuals,the relationship between CNV and gene expression regulation was analyzed by correlation analysis method.It was found that 19 CNVs affected the expression of 30 genes in inguinal lymph nodes;in spleen 29 CNVs were found to affect the expression of 179 genes;30 CNVs were found to affect the expression of 220 genes in the testis tissue.(4)The breakpoints of CNV on the four genes of TRIM14,PRKCE,STRA8,and HNRNPA2B1 were identified.The experimentally verified CNV breakpoint was consistent with the software LUMPY prediction breakpoint.Through the analysis of the features of the breakpoint region and the variant region sequence,the possible mechanism of CNV production was deduced.In summary,combining the whole genome sequencing data with transcriptome sequencing data of Tongcheng pigs and Large White pigs through bioinformatics methods,we analyzed the differences of CNV between the Tongcheng population and Large White population and selected candidate genes.The CNVRs were successfully verified in the Large White,Tongcheng,Landrace,and Meishan pig populations,and the location of CNV breakpoints were identified,providing materials and laying the foundation for subsequent functional studies.