| Tibetan pigs live in the Qinghai-Tibet Plateau region of China,and are the only plateau type pig breed in China,mainly distributed in Tibet,Sichuan,Yunnan,Gansu and other places.As Tibetan pigs live in the special environment of the plateau,they have undergone long-term evolutionary selection and adaptation,forming their unique germplasm characteristics such as low oxygen adaptation,sensitive reaction,resistance to ultraviolet radiation and strong resistance to adversity.Therefore,the current research on Tibetan pigs is mainly focused on their adaptation to the plateau,different geographical distribution and disease resistance.Now Tibetan pigs are mainly divided into four different groups,namely Sichuan Tibetan pigs,Tibetan pigs,Diqing Tibetan pigs and Hezuo Tibetan pigs,according to the geographical location of growth,but due to the vast area of Qinghai-Tibet Plateau with complex topography,forming a natural geographical barrier,coupled with the establishment of Tibetan pig nature reserve,there is a long-term geographical isolation between different groups of Tibetan pigs,resulting in the unknown population genetic relationship among the four groups of Tibetan pigs at present.Based on this,this study firstly compared the production performance of four Tibetan pig taxa,and then performed whole genome resequencing analysis on 127 Tibetan pigs of different taxa from four Tibetan pig reserves,and explored the population genetic relationship,population structural composition and selection signals of the four Tibetan pig taxa through in-depth analysis and mining of the sequencing data,based on which the population relationship among the four Tibetan pig taxa was revealed,with the following results:1.The production performance of the four Tibetan pig groups differed greatly,with the Diqing Tibetan pig having the largest slaughter weight and the highest slaughter rate of 70%,and the Tibetan pig having the highest lean meat rate and the lowest Sichuan Tibetan pig;the four Tibetan pig groups performed better in meat quality traits such as meat color,p H,marbling score,etc.,and the Sichuan Tibetan pig had the highest intramuscular fat content;the Diqing Tibetan pig showed the highest reproductive performance with large differences,and the remaining The remaining three groups showed relatively consistent performance.2.687.41 Gb of raw data were obtained by whole-genome resequencing of 127 selected Tibetan pigs in four Tibetan pig reserves,with an average sequencing depth of 2.18 x.An average of 2654216,3563965,3496792 and 2989950 single nucleotide polymorphic loci were identified in Tibetan pigs,Sichuan Tibetan pigs,Diqing Tibetan pigs and Hezuo pigs,respectively.3.3191,2968,3259 and 3413 whole genome long pure fragments(ROH)were detected in Tibetan pigs,Sichuan Tibetan pigs,Diqing Tibetan pigs and Hezuo pigs,respectively.The IBS matrix and G matrix were used to explore the kinship of the four Tibetan pig groups,and it was found that the four Tibetan pig groups had high kinship within each group,indicating that inbreeding existed in all four groups.4.The polymorphic marker ratios of the four Tibetan pig taxa were in the range of 0.4288-0.4788,indicating that the four Tibetan pig taxa had moderate levels of genetic polymorphism;the expected heterozygosity and observed heterozygosity analyses indicated that the individuals within the four Tibetan pig taxa were relatively close to each other,and there were also influences of infiltration from other external bloodlines;the linkage disequilibrium analysis found that the decay rates of the four Tibetan pigs were similar,and all had relatively The analysis of linkage disequilibrium showed that all four Tibetan pigs had similar decay rates,which indicated that the Tibetan pigs were less selected and the population was rich in genetic diversity.5.The results of principal component analysis showed that the four Tibetan pig groups showed more obvious population stratification,among which Diqing Tibetan pig and Hezuo pig had more distant genetic relationship with the other two groups,while Sichuan Tibetan pig and Tibetan pig had more similar genetic relationship;according to the phylogenetic tree analysis,the four Tibetan pig groups had four different evolutionary branches and had more distant evolutionary relationship.6.The results of analyzing the ancestral components of the four Tibetan pig groups using Admixture showed that when K=2,the four Tibetan pig groups mainly had two different ancestral components,and when K=4,the four Tibetan pig groups consisted of four different ancestral sources among them,reflecting the ancestral blood origin of these four Tibetan pig groups.7.The analysis of selection signals in Tibetan pigs using four different signal selection methods,θπ,Fst,Tajima’s D and XP-CLR,showed that 19 genes were co-selected by the four methods in the top 5% of selected regions,and the analysis of their biological functions revealed that these genes were mainly involved in DNA repair,immune regulation,cardiovascular circulation The analysis of their biological functions showed that these genes were mainly involved in DNA repair,immune regulation,cardiovascular circulation and other processes,indicating that Tibetan pigs were selected in these aspects during their evolution.However,due to long-term geographical isolation and natural and artificial selection,the four Tibetan pig taxa,namely Sichuan Tibetan pig,Tibetan pig,Diqing Tibetan pig and Hezuo pig,are now genetically distantly related and reflect different evolutionary directions;the results of this study enrich the understanding of the genetic characteristics of Tibetan pig groups in China and provide theoretical references for resource conservation of Tibetan pigs of different types. |
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