Population Genetic Analysis Of Tibetan Pig Based On Whole Genome Resequencing

Tibetan pig is one of the characteristic livestock in Qinghai-Tibet Plateau and also the original livestock resource with unique local characteristics.These resources are also an important gene pool.At present,China has paid more and more attention to the protection of local varieties.The Tibetan pig conservation farms,conservation areas and stock farms in China are developing rapidly and the protection of varieties is gradually strengthening.In order to better protect the Tibetan pig,we need to carry out in-depth research on its growth characteristics,genetic,and genetic characteristics,and then formulate more effective protection strategies based on the results of the research.In order to explore the genetic characteristics and domestication origin of Tibetan pig population on the Qinghai-Tibet Plateau,genomic sequencing data were collected from 10 geographically isolated Tibetan pig populations.The 10 populations came from parts of four provinces in China,Tibet,Sichuan,Yunnan and Gansu.They were geographically isolated from each other,and their genetic relationships,contributions to the genetic diversity of the entire Tibetan pig population,and the origin of domestication were unclear.Therefore,in this study,the population principal components of these populations were analyzed by whole genome resequencing technology,and their phylogenetic trees were constructed.Then population differentiation analysis,harmful mutant analysis,and genetic diversity analysis were performed,and genes related to the environmental adaptation of Tibetan pig to the plateau were screened out by GO enrichment from the selective scanning results.Specific research results include:1.The results of population principal component analysis showed that for first principal component,no significant segregation was observed among Tibetan pig populations,while significant differentiation was observed between Tibetan pig and wild boar populations.Regarding the second principal component,it was found that the difference between T1 population and other populations was significant,and the GZT,SCT and YNT populations were similar but had little difference from other populations.2.The results of phylogenetic tree analysis showed that the populations of GZT,SCT and YNT formed a small evolutionary branch,while T1 and T2 were more closely related to the wild boar.3.The results of population differentiation analysis showed that the differentiation values of GZT,SCT and YNT populations were relatively low.The difference was greatest between the GST and T3 populations and smallest between the T2 and TT populations.While the differentiation and genetic distance between TT and other populations were the smallest on average.The average values of differentiation and genetic distance between T3 and other populations were the largest.4.Harmful mutant results showed that the number of harmful mutations in Tibetan pig population ranged from 1606(T3)to 3499(TT),with only 229 cases in all populations.Most of the deleterious mutations were population-specific and ranged from 187(T3)to 652(TT).5.Genetic diversity analysis showed that TT population contributed the most to genetic diversity and allelic diversity,with TT,YNT,T1,SCT and GST populations contributing more than 10%,TT,Aba T and SCT populations contributing more than 10%,and other populations contributing about 9%.6.The results of selective scanning analysis showed that genes such as RXFP1,FZD1,OR1F1,TBX19,MSTN,ESR1,MC1 R,HIF3A and EGLN2 were related to lung development,hard palate development,hair color,hormone metabolism,facial appearance and olfactory perception.The whole genome of 10 Tibetan pig populations in Qinghai-Tibet Plateau was re-sequenced.According to population genetic analysis,it was found that Tibetan pigs living in various regions of Qinghai-Tibet Plateau had slight genetic differentiation.Genes associated with hypoxic adaptation,hair color,hormone metabolism,facial appearance,and olfaction have also been screened.These findings will help to understand the origin and domestication of Tibetan pigs,optimize the protection scheme of Tibetan pig germplasm resources,and lay a foundation for further research on the regulatory genes of environmental adaptive traits of Tibetan pigs.