Comparative Analysis Of Differential Alternative Splicing In Liver And Spleen Tissues Between Yunnan Humped Cattle And Holstein Cattle

Domestic cattle are divided into ordinary cattle（Bos taurus）and zebu（Bos indicus）.They not only have obvious differences in appearance,but also have obvious differences in many physiological processes.Therefore,revealing the molecular differences between the two the mechanism is of great significance.Relevant studies have shown that alternative splicing is ubiquitous in all multicellular eukaryotes,including plants and animals,and they are an important mechanism for enhancing the structure and functional diversity of transcriptional genomes and proteins.However,there are not many researches on alternative splicing in domestic cattle.Therefore,this study selected healthy Yunnan Humped cattle with similar age and no close relatives（the results of mitochondrial sequencing and gene chip sequencing identified that this study used Yunnan Humped cattle as pure Breeding zebu）and Holstein cattle,and reared in the same environment for2 months.After slaughter,liver tissues and spleen tissues of Yunnan Humped cattle and Holstein cattle were selected（5 biological replicates for each tissue）for a total of 20 Samples.Use the Illumina Hi Seq TM 2500 sequencing platform to perform paired-end high-throughput sequencing,and then perform further analysis operations on the obtained transcriptome sequencing data.This study is divided into four comparison groups:analysis of differential alternative splicing between liver tissue and spleen tissue of Yunnan Humped cattle,analysis of differential alternative splicing between liver tissue and spleen tissue of Holstein cattle,liver tissue of Yunnan Humped cattle and Holstein cattle liver analysis of differential alternative splicing of tissues,analysis of differential alternative splicing of spleen tissues of Yunnan Humped cattle and Holstein cattle.In order to find the relationship between their tissue differences and alternative splicing and the relationship between breed differences and alternative splicing,and to find differentially spliced genes related to cattle immunity,disease and growth traits.The main findings are as follows:1.In the analysis of differential alternative splicing between liver tissue and spleen tissue of Yunnan Humped cattle,a total of 830 differential alternative splicing events and362 differentially spliced genes were detected.Among them,the most frequent alternative splicing event is skipped exons（skipped exons,SE）,the least occurrence of alternative splicing events is mutually exclusive exons（mutually exclusive exons,MXE）.In the analysis of differential alternative splicing between liver and spleen tissues of Holstein cattle,a total of 986 alternative splicing events and 402 differentially spliced genes were detected.Among them,SE is the most frequent alternative splicing event,and the least occurrence of alternative splicing events is MXE.In the differential alternative splicing analysis of Yunnan Humped cattle liver tissue and Holstein cattle liver tissue,a total of1592 alternative splicing events and 556 differentially spliced genes were detected;among them,the most frequent alternative splicing event is the variable 3’ Site（alternative3’splice site,A3SS）,the least occurrence of alternative splicing events is MXE.In the analysis of differential alternative splicing between Yunnan Humped cattle spleen tissue and Holstein cattle spleen tissue,a total of 1,235 alternative splicing events and 515 differentially spliced genes were detected.Among them,SE is the most frequent alternative splicing event,and the least occurrence of alternative splicing events is MXE.Based on the analysis of differential alternative splicing in the four groups,the most frequently occurring alternative splicing events in the three groups are all SE,and the number of differentially spliced genes that all have SE alternative splicing events in the four groups is the largest.2.The analysis of differential alternative splicing between liver tissue and spleen tissue of Yunnan Humped cattle and the research of differential alternative splicing between liver tissue and spleen tissue of Holstein cattle found that alternative splicing does exist in different tissues.Chi-square analysis of the results of differential alternative splicing between Yunnan Gaofeng cattle tissues and that of Holstein cattle tissues,its significance P value is 0.0671（P>0.05）,which means that the tissue differences of alternative splicing between different varieties may be similar.3.In the analysis of differential alternative splicing between Yunnan Humped cattle liver tissue and Holstein cattle liver tissue,a total of 556 differentially spliced genes were detected,of which 55 genes are involved in diseases,immune-related GO functions and KEGG pathways.Among them,SERPINF2,F2,C3,C4 A,C1S,MBL2,C5,CFH,CFB,MASP2,MBL1,CFI and FGG participate in multiple GO functions or KEGG pathways related to diseases and immunity;In the differential alternative splicing analysis of Yunnan Humped cattle spleen tissue and Holstein cattle spleen tissue,a total of 515 differentially spliced genes were detected.Through GO-KEGG functional enrichment analysis,61 genes were found to be involved in disease and immune-related GO functions.And KEGG pathway,where ZAP70,STOML2,FYN,CD247,MEF2 C,PTPN6,ITGB2,ITGAL,FCGR3 A,PTK2B,GRB2,BID,SOS2,CD86,VCAM1,LOC534578,CTNNB1 and CTTN participate in multiple GO functions or KEGG pathways.These genes related to cattle metabolism,immunity,disease and growth traits can provide a new molecular basis for cultivating cattle breeds with excellent traits.In summary,this study compares and analyzes the differences between Yunnan Humped cattle and Holstein cattle and the differences between breeds from the perspective of alternative splicing,in order to further understand the relationship between tissue differences and alternative splicing,as well as breed differences and alternative splicing.The relationship provides a new scientific basis;and some related differentially spliced genes have been screened,which provides a new scientific basis for understanding the difference in traits between cattle and a new molecular basis for cultivating cattle breeds with excellent traits.