Study On Population Genetics And Molecular-Assisted Conservation Of Laiwu Pig Based On 80K Chip Data

Laiwu pigs origin from Laiwu City,Shandong provinces,which is a representative indigenous pig breed of China.It is famous as fertility,strong resistance and exceptionally high intramuncular fat content（11.6%）,providing an excellent genetic resource for the genetic improvement of modern commercial pigs.It was reported that the Laiwu pigs introgressed by the European commercial pig breeds.The disordered hybridization and non-standard conservation schemes will increase the introgression of Laiwu population,which may lead to the risk of the loss of germplasm characteristics.All core population individuals（238）were sampled from a sate-supported conservation population and genotyped these pigs using Gene Seek 80K SNP Bead Chip.The aim of this study was to uncover the genetic diversity,population structure,signatures of selection and propose a reasonable conversation strategy.The main results are summarized as follows:（1）The genetic diversity indexes of present Laiwu pigs are better than that of the population 18 years ago.This improvement of the present Laiwu population is due to gene flow from European commercial breeds.（2）The neighbor-joining tree and principal component analysis indicate that,the Laiwu pig populations are clustered together.The present Laiwu pig population is scattered,and many individuals close to the European commercial pig breeds.The admixture analysis reveals that an average 26.75%of present Laiwu pig population are European origin.（3）By estimating the ancestry proportion of each Laiwu pig,the individuals with greater than average ancestry proportions of Chinese local pig breeds were distributed into"purebred",and 10 families were assigned according to their clustering patterns of NJ tree.The individuals with ancestry proportion greater than the mean minus two standard deviations and less than the mean were taken as the population to be purified and assigned into 3 families.Removing the individuals with ancestry proportion less than the mean minus two standard deviations.Integrating with the inbreeding degree of each individual,a classified purification scheme was developed.（4）Selection scans were porformed using two haplotype-derived statistics（ROH and i HH12）and two genetic differentiation-based approaches(F_STand Eigen GWAS).The results detect a list of candidate genes for environmental adaptation,fat deposition,reproduction and growth traits of Laiwu pigs.Altogether,this study not only enrich the knowledges of the formation history of Chinese indigenous pig breeds for people,providing data support for protection and utilization of Laiwu pigs,but also present a reference for the conservation of other local livestock and poultry germplasm resuorces.