The Identification Of Copy Number Variation And Small Insertion-Deletion Mutations In Pig Genome And Functional Analysis

The differences of traits like fecundity,growth rate,meat quality,lean meat yield and stress resistance between China and foreign pig breeds are distinct,which become the emphasis of recent genetics and breading research.Rapid advancements in the development of genome structural variation make the exploration of copy number variation(CNV)have become a hot spot,then,insertion-deletion(InDel)which insert small fragment into the genome to cause deletion variation has been discovered in latest studies is considered as an important way of variation to influence the animal traits.The bioinformatics research of CNV and Indel in previous studies has been conducted:a total of 3131 copy number variable regions(CNVRs)in autosomes were identified according to 49 pigs resequencing data of different China and foreign breeds;a great number of exons and alternative splice sites which occurred InDel were discovered by Tongcheng whole genome resequencing data compared with the published 16 China and foreign breeds(populations)resequencing data.On the basis of previous research,the selection,identification and determination of boundary of CNV and Indel were carried out,meanwhile,genotyping and association analysis in Landrace and Large White population were performed.This study aims to provide useful marker for Marker-assisted selection and provide experimental and theoretical basis for further study of CNV and InDel.The main results as follow:(1)We select 28 candidate CNVRs from 3131 CNVRs to validate by QPCR according to the CNV’s mutation types,chromosome location and whether CNV occurs on gene region,24 CNVRs of which have been verified,the verification rate is 86%.(2)Using breakpoint amplification method to detect the populations of Tongcheng pigs and Large White pigs,the results have been shown that IRF1 internal gene could amplify the 15394 bp deletion fragment which is similar to the expectancy and is able to fully match the reference sequence,but reference type and heterozygous genotype are not found.(3)Depending on the size and location of InDel,15 deletion variants in non-exon region were screened out and then were detected in Yorkshire and Tongcheng pigs,futhermore,six InDel variation were successfully identified and selected six Indels which affected genes exon.Deletion of 312 bp in DZIP1L internal gene were found in identification experiments,which deletion of 23 bp in exon 14;300 bp deletion occurred inside the TLK2 gene,wherein the exon 13 loses 12 bp.(4)Genotyping the deletion variants of DZIP1L gene and performing association analysis of boar semen quality traits in Landrace populations.The results demonstrated that a population,as compared with genotype II porcine,genotype DD porcine had more swine ejaculate volume and lower sperm density.TLK2 gene deletion variants were genotyped and association analysis of growth traits was conducted in Yorkshire and Large White population,genotype II and genotype ID distributed wider,whereas genotype DD was less but had a larger corrective loin muscle area to 100 Kg in both populations.(5)In other work,the detection method of transgenic animals and their products component-human lysozyme gene(hLYZ)by qualitative PCR was established,moreover,a national standard-setting work was completed.