Bioinformatics Methods For Paternity Test Of Sheep Breeds In Xinjiang By SNP Markers

In recent years,the continuous development of breeding technology of livestock and poultry population has made great progress in sheep industry in China.However,compared with the developed countries,the sheep industry in China is still in the primary stage and the lag of sheep genetic assessment technology is an important problem in the development of sheep industry in China.The wrong genealogica l records will greatly reduce the accuracy of genetic assessment of sheep and thus slow down the genetic progress of sheep populations.In order to reduce the negative effect of wrong pedigree on genetic breeding and save identification cost,it is urgent to establish an accurate pedigree.In addition to strict production management system,the accurate genealogical record information is more dependent on the confirmation of the relationship between sheeps.Accordingly,the research content of this paper consists of the following two parts:1.Verify the accuracy of the SNP for the paternity test among sheep breeds in different regions of Xinjiang and look for the main factors that affect the accuracy of identification.Research according to SNPs which recommended by the International Sheep Genomics Consortium,through the cumulative probability(CPE)to measure the father ruled out SNPs of paternity test and determine the accuracy of paternity test between Xinjiang Sheep breeds of,the last is validated with the likelihood of the improved pedigree appraisal result.Results show that the recommended by ISGC of SNPs in Xinjiang sheep varieties of paternity test accuracy can achieve 99.9% above,the sheep to the distribution of the parent-child relationship between the individuals.In addition,the minimum allele frequency(MAF)and the number of SNPs were main indicators to determine the accuracy of paternity test.2.An optimization scheme for the parentage test of SNPs of local sheep in Xinjiang was proposed.Based on the genetic characteristics of local sheep breeds in xinjiang,on the basis of quality control and coding of 50 K medium density SNP chip,the Monte Carlo simulation algorithm was used to realize the genotype filling of SNPs.Then,the main component analysis(PCA)was used to filter the redundant markerss and obtain the candidate information.Then,based on greedy algorithm,the optimal information SNPs was obtained by further screening the genetic diversity indexes of MAF,the degree of linkage imbalance between SNPs and the genetic distance;finally,the paternity test effect of SNPs was measured by CPE,and compared with the SNPs published by ISGC and the same number of SNPs randomly selected.At the same time,the genetic diversity of SNPs before and after screening was compared,and the phylogenetic evolution trees of 13 sheep breess in Xinjiang were constructed by NJ method.The experimental results show that,the article adopts the method of optimization of 132 SNPs of combination compared with the other two kinds of marking combinations have higher paternity test effectiveness,CPE can reach more than 99.99%,and greatly reduces the required markers identification number,and has better genetic diversity.In addition,it is found that the set of SNPs can also effectively distinguish the relationship between different sheep breeds.