Analysis Of Genome And SNP Genetic Markers In Rats Of Common Strains

Wistar,Goto-Kakizaki(GK),Brown-Norway(BN)and Sprague-Dawley(SD)are four commonly used rats,which were generally used as animal models in a wide range of studies on drugs and disease mechanisms.Genetic detection technology is one of the important method for monitoring the genetic quality of experimental animals.With the progress of genomics research,single nucleotide polymorphism(SNP)markers have gradually been applied to genetic detection in various experimental animals.Compared with the traditional methods,the use of SNP marker has many significant advantages.Therefore,SNP will become ideal genetic markers in genetic detection of rats.This study has developed two sets of SNP genetic markers for different uses through high-throughput sequencing,bioinformatics technique,Sanger sequencing and DNA pooling method.The specific contents are as follows:(1)First,whole-genome resequencing was performed on Wistar rats and GK rats.The bioinformatics technique was used to align the resequencing results to the BN rat reference genome,and the specific SNPs within the genome range of Wistar rats and GK rats were screened.94,800 and 106,019 homozygous specific SNPs were detected in Wistar and GK rats respectively,of which 56216 SNPs were shared by Wistar and GK rats.There were only 38 SNPs were found to be different genotypes among BN rat reference genomes,Wistar and GK rats.15 of them were selected as the candidate SNPs(Panel1).In addition,for the heterozygous SNPs,1~2 SNPs in each autosome were selected to comprise the second group of 28 candidate SNPs sites(Panel2)to assess the genetic diversity of the rat population.(2)SNPs of Panel1 and their upstream and downstream were further screened by Sanger sequencing.Finally,13 SNP markers that can be used to identify Wistar,GK,BN and SD rats were obtained,which named as SNP4,SNP5,SNP6,SNP9,SNP12,SNP13 and SNP14,SNP16,SNP17,SNP18,SNP19,SNP20 and SNP21.Among them,SNP13 can directly identify Wistar,GK,BN and SD rats.SNP16 and SNP17 can directly identify SD rats,SNP18 and SNP19 can directly identify GK rats,SNP20 and SNP21 can directly identify BN rats,while SNP4,SNP5,SNP6,SNP9,SNP12 and SNP14 can identify GK and BN rats.DNA pool method were used to expand the sample in order to verify the polymorphism of these sites in the population.(3)SNPs of Panel2 and their upstream and downstream were further screened by DNA pool method.Finally,25 SNP markers were obtained which can be used to evaluate the heterozygosity and genetic diversity of these four strains of rats.These SNPs were named snp3,snp4,snp6,snp7,snp8,snp11,snp,snp13,snp16,snp17,snp18,snp21,snp25,snp26,snp27,snp28,snp29,snp30,snp31,snp32,snp33,snp34,snp35,snp36,snp37.The allele frequencies of these 25 SNPs in each strain of rats were estimated.Using the allele frequencies of each strain can assess the genetic diversity of the rat population.