Idetifying Candidate Genes And Signal Pathways Associated With The PRRSV By Using The Whole-genome Resequencing

The pig diseases especially PRRSV posed considerable threat for the modern pig industry. According to incomplete statistics, the pig diseases caused more than 30%economic loss per year of livestock in developing countries, some even up to 50%, while17% in the developed countries. In developed countries relatively less percentage than developing country, because they give more attention for health care of pigs. Throughout the breeding history of pig disease-resistant in domestic and foreign, it is feasible to foster the resistant individual and improve the resistance of group in breeding project. These not only save the expense of medicine and epidemic prevention, but also conform to the faith of green and healthy breeding.It's been proved that different pig breeds have difference susceptibility of pig PRRSV.The excellent property in majority of Chinese indigenous breeds are resistant disease. Many research reported that Chinese indigenous breeds relatively showed resistant to PRRSV than European pig. There rarely reported the breeding of resistant-PRRSV individual or breeds, so this is a potential way to control and cure PRRSV in future. It should be a long way to find and identify more significant mutation sites for PRRSV. Meanwhile, how to make full use of the whole genome re-sequencing data to find out more valuable information is also the key point in the study of genome re-sequencing.Our research base on the data of Chinese and foreign pig breed whole genome re-sequencing, use bioinformatics methods to identify genome-wide genetic variation information on the X and autosomes of Chinese and foreign pigs, hope to explore more candidate genes, mutation sites and signal pathways for pig diseases research. In our research, all pig breeds were divided into Chinese indigenous breeds and European breeds base on the different resistance to PRRSV, and use the different standard of ?2-Test to find the significant difference candidate genes and mutation sites between Chinese and European pigs. The main results are as follow:(1)The significant difference genes in disease between Chinese and foreign pigs common found by Chi-20 test, Pig QTLdb, OMIM and OMIA databaseFive important genes, including GUSB, GALC, MYH9, SEL1 L and FBN1 can be used as the candidate genes for the research of drug targets and animal models.(2)The significant difference genes and pathways present only in pig response to PRRSV infection between Chinese and foreign pigsSeven important genes and nine mutations: COPS5 with synonymy mutation A1003 G, DARS with synonymy mutation G252 A, P4HA1 with missense mutation A771 C,PSMD12 with one missense mutation A1003 G and two synonymy mutation T1007 A ?T1008A, TLR4 with missense mutations A1027 C,ATP6V1H with synonymy mutation G1080 A.They can be used as the accumulation of candidate genes and caused disease mutation sites for the breeding of resistant-PRRSV.Pathways Enrichment: 60 genes presenting only in pig response were enriched in the pathway of Lysosome, toll-like receptor pathway, Tuberculosis, Chemokine signaling pathway and Epstein-Barr virus infection. These pathways uncertain as the significant difference pathways for immune response between Chinese and foreign pigs, and need more research.(3) The significant difference receptor genes and its mutations for PRRSV between Chinese and foreign pigsSDC2 gene has a missense mutation C243 T, result in the AA changed from Asn to Asp. This mutation can be used to analyse the role of HS in leading PRRSV to host.(4)The significant difference key genes and its mutations for PRRSV between Chinese and foreign pigsMx1 gene have two missense mutations A1241 G and C1652 T, result in AA changed Arg414 Lys and Ala551 Val, They can be used as the candidate caused mutation sites for the resist of PRRSV and flu.