利用液相芯片开展枫泾猪保种遗传鉴定及评估OA

To meet the needs of genetic identification and evaluation in the conservation of Shanghai local pig genetic resources,a 60K single nucleotide polymorphism(SNP)liquid microarray was developed based on genotyping by target sequencing(GBTS)genotyping technology.Through the SNP microarray,the method of genomic breed composition(GBC)identification of Shanghai local pig breeds was established,and genetic assessment of 2 populations of Shanghai Fengjing pigs(259 head of Qinnong breeding population and 105 head of Songlin breeding population)were carried out.The results showed that,based on GBTS genotyping detection technology,a liquid chip for genotyping of Shanghai local pigs'Shenxin No.1'was successfully constructed.It had a good discrimination for pig breed identification and could be used for precise identification and bloodline purity analysis of local pig breeds in Shanghai and its surrounding areas.The test on the Qinnong population and the Songlin population showed that most of individuals in 2 populations had more than 95%GBC,and the linkage disequilibrium analysis showed that the Qinnong population had a faster LD decay,while the Songlin popultion had a higher LD mean value.Genetic analyses showed that the observed and expected heterozygosity of SNP were 0.290 5 and 0.292 0 in the Qinnong population and 0.335 7 and 0.316 0 in the Songlin population,respectively.Based on runs of homozygosity(ROH)of genome,the genomic inbreeding coefficients of Songlin and Qinnong populations were 0.206 4 and 0.245 1,respectively.Several individuals had high inbreeding coefficients,which needed to be eliminated or optimized to reduce the overall inbreeding level of populations.In addition,the kinship of the samples was constructed based on the IBS(identity by descent)matrices,which layed the foundation for the reconstruction of molecular lineage.