Analysis Of Shaanxi Characteristic Goat Germplasm And Construction Of Shaanxi Provincial Genetic Resources Database

The special geographical and climatic characteristics,historical origins,and hardworking people of Shaanxi Province have jointly created goat breeds with different body shapes,appearances,and production traits.In this study,three valuable goat breeds in Shaanxi Province,Shaanbei White Cashmere Goat,Guanzhong Dairy Goat and Shaannan White Goat,were taken as the research core,and a total of 288 resequencing data of 12 other domestic goat breeds and wild goats within the goat genus were combined to evaluate the genetic diversity and evolutionary potential of goat breed resources using population genetics and other analysis methods,And trained a breed identification model and constructed a genetic resource database in Shaanxi Province,laying the foundation for more effective protection measures and healthy and sustainable utilization of these resources in the future.The main research content and results are as follows:(1)The average sequencing depth of this study sample was 14.64×,and a total of29,422,980 SNPs were detected.According to the analysis of population structure,the results indicate that Shaanbei White Cashmere Goat and Liaoning Cashmere Goat are clustered together,which is consistent with the breeding history;Guanzhong Dairy Goat form a large cluster with Saanen Goat,Toggenburg Goat,and Tangshan Dairy Goat;The differentiation degree of Shaannan White Goat breed is higher compared to other goat breeds.By expected heterozygosity(He),linkage disequilibrium(LD),observed heterozygosity(Ho),nucleotide diversity(Pi),runs of homozygosity(ROH),and inbreeding coefficient analysis based on ROH,the results showed that the observed heterozygosity of Shaanbei White Cashmere Goat was higher than that of other breeds;The consistency of the Guanzhong Dairy Goat population is good,and there is a high degree of heterozygosity;Compared to other domestic populations,Shaannan White Goat have the highest number of long ROH fragments and the highest inbreeding coefficient,indicating that the protection of Shaannan White Goat is urgent.(2)The frequency of target breed and non target breed were used to preliminarily screen the breed high frequency SNP,and through the random forest(RF)the importance of the SNP was visualized.Finally,the support vector machine(SVM)was used to develop the breed identification model.The validation method used 5 fold cross validation,and the model evaluation indicators used Accuracy,Precision and Recall.The results show that the developed model can effectively distinguish between target and non target breed.(3)Based on LAMP(Linux+Apache+My SQL+PHP)build a genetic resource database in Shaanxi Province.In addition to the three goat breeds mentioned above,the database also includes four genetic resources: Qinchuan Cattle,Guanzhong Donkey,Lueyang Chicken and Chinese Honeybee in Yulin region.The database provides retrieval of mutation and selection signal information,as well as display of breed information,genome assembly status.Interactive tables are implemented through the Data Tables plugin,while maps and data mapping are implemented through the Echarts plugin.The retrieval results of variation data include minor allele frequency,annotation information,and frequency distribution of various breeds and populations.Users of the selection signal module can select different detection methods on the retrieval page,such as Tajima’D,Hp,Pi ratio.The results are mainly displayed in the form of Manhattan diagrams and tables.The genetic resource database constructed in this study provides users with a window to understand important genetic resources in Shaanxi Province,and also provides convenient tools for researchers to explore candidate genes related to economic traits.Database access link is http://animal.omics.pro/code/index.php/Shaanxi/.In summary,this study systematically analyzed the population genetic structure and genetic diversity of Shaanbei White Cashmere Goat,Guanzhong Dairy Goat,and Shaannan White Goat at the whole genome level,and developed a breed identification model using various methods such as machine learning,which has good application value.At the same time,it constructed a genetic resource database in Shaanxi Province,providing reference for further strengthening the protection of genetic resources and scientific and reasonable breeding.