Application Of Whole Genome Analysis In Core Group Breeding Of Dongliao Black Pigs

Breeding of local pig breeds is an important part of the development of livestock and poultry industry in China.Dongliao black pig is a famous indigenous breed in Jilin Province,which has good adaptability,cold resistance and rough feeding tolerance.In this study,the genetic structure and genetic diversity of Dongliao black pig population were analyzed,the pedigree was constructed using the SNPs,and the genomic breeding values of litter size traits were estimated.The results may help to the systematic breeding and breed standardization of Dongliao black pigs,and provide the research basis and core breeding group for new breed breeding.A total of 937 Dongliao black pigs were evaluated for body shape and appearance,and 765 pigs（42 boars and 723 sows）that met the breeding criteria were screened out.The ear tissue samples were collected,DNA was extracted,and SNP genotyping was performed using SNP 50 K chip of "Zhong xin yi hao".The chip data of Dongliao black boars were combined with the resequencing data of 13 other Chinese and foreign pig breeds（6 Chinese pig breeds,5 Western pig breeds,European boar breeds,and Asian boar breeds）,a total of 410 samples,and the Plink software was used for quality control.The GCTA,ADMIXTURE,MEGA and other software were used to analyze the principal component,phylogenetic tree and genetic diversity.Based on the data of 765 Dongliao black pigs,the genetic distance between individuals was calculated and the molecular pedigree was constructed.Population genetic parameters and breeding values were estimated and core sows were selected based on the data of litter size traits of Dongliao black pigs.The results are as follows:1.The results of principal component analysis,admixture analysis and phylogenetic tree analysis showed that the Dongliao black pig is the most similar to the northeast folk pig,which was mixed with Berkshire in the early stage and Duroc in the recent stage.The results of genetic diversity analysis showed that the genetic diversity of Dongliao black pigs was rich,and the observed heterozygosity value and marker polymorphism ratio value were 0.377 and 0.981,respectively,which were conducive to gene mining and purification and breeding of characteristic and dominant traits.2.The genetic distance（1-IBS）between individuals was calculated.Most of the individuals had moderate genetic relationships,and the average genetic distance within the population was 0.28.The paired genetic distance was used to construct molecular pedigree,the population was divided into 22 families,and corresponding selection schemes were developed for subsequent breeding.3.The genetic parameters of litter size traits were estimated by using a repeatability model.The estimated heritability of total number born and number born alive were 0.108 and 0.075,and the repeatability was 0.208 and 0.156,respectively.The estimated breeding values of total number born ranged from-1.584 to 1.307,and the estimated breeding values of number born alive ranged from-1.086 to 0.898.The core breeding groups were selected according to the breeding values.Conclusion:Genomic data analysis showed that the Dongliao black pig is the most similar to the northeast folk pig,which was mixed with Berkshire in the early stage and Duroc in the recent stage.The population had rich genetic diversity.By constructing molecular genealogy,the Dongliao black pig population was divided into 22 families,and the selection scheme was formulated.The heritability estimates of total number born and number born alive of Dongliao black pig population were low,and the breeding core group was established according to the breeding value.