Study On Breed Characters,Conservation And Utilization Of Saba Pigs Based On Genomic Information

Saba pig is a famous indigenous pig breed in Yunnan province.Among all the indigenous pig breeds in Yunnan province,Saba pig has the highest fertility rate and the largest body size.However,there is still a lack of research on the genetic basis of the superior germplasm characteristics of the Saba pig.There is also a lack of molecular technical guidance on the protection and utilization of this pig breed.Therefore,in this study,we obtained the genome information of the pigs using the reduced genome sequencing technology and carried out studies on the germplasm characteristics,protection and utilization of the Saba pig.The main results are as follows:（1）The status of Saba pig in pig genetic resources.Based on the genome reducing and sequencing method（GGRS）,we sequenced 7 indigenous pig breeds（including Saba pig）from Yunnan province.We also collected the genome sequence data of some other breeds from,Zhejiang province,Jiangsu province,Shanghai province,and the West（Western breeds）.Using this genome sequence data,we performed an analysis of phylogenetic tree,population structure and population admixture and found that Saba pig breed is genetically unique.There was a medium degree of differentiation between Saba pig and the other pig breeds in Yunnan province,and a higher degree of differentiation between Saba pigs and the Western pigs.The genetic distance between Saba pig and Dahe pig was small.Compared with other breeds in Yunnan,the genetic relationship between Saba pig and other pig breeds from Jiangsu,Zhejiang and Shanghai was smaller.（2）Genetic background of important characteristics of Saba pig.We carried out the genome selection signature analysis within and across populations.In the across population analysis,we applied the partial least squares（PLS）method to detect the genetic difference between populations.Furthermore,we developed a method called fast PLS to simplify the computation complexity of PLS.Through simulated and real genotype data,we proved the computational superiority of fast PLS and its higher detection performance compared with the F_STmethod.To carry out functional annotation of the candidate regions,we used the information of human enhancer and diseases and carried out enhancer prediction in the pig genome.We also built a database ETph（enhancer and their targets in pig and human）.Within the Saba population,we found genes（PRL,ADRA1B）and enhancers related to reproduction traits.In the across population analysis,we found 22 unreported genetic markers that were unique to Saba pigs.Using the developed fast PLS method,we detected important genes and pathways associated with growth（IGF1R）,body size（LTBP2）,meat quality（PHKG1,LEP）and reproductive（BMP7）traits.（3）Analysis of conservation of Saba pig.To determine the current conservation status of the Saba pig population,we analysed the genetic diversity and population genetic structure of the breed.Our results showed that the diversity of Yunnan pig breeds was relatively higher than other breeds and Diqing Tibetan pig breed has the highest diversity.To accurately assess this genetic diversity,especially in a small population like ours,we analyzed the expected heterozygosity（H_e）within a breed using an estimation method based on real genetic conditions.We found that we might underestimate H_eif it is estimated under Hardy-Weinberg equilibrium assumption.For the Saba pig breed,we also found out that the population structure and selection of back-up boar at the genome-wide level are effective,however,this is not so when selecting at the reproduction trait level.We suggested that using a phylogenetic tree to select valuable individuals for conservation program based on the genome-wide and trait-specific markers would be more effective.（4）Utilization analysis of Saba pig.Based on the genome-wide and trait-specific markers,we carried out a heterosis prediction analysis between Saba and Western pig breeds.We suggested that the Duroc×Saba and Duroc×（Yorkshire×Saba）could be used as an appropriate matching model of binary and ternary hybridization.Besides,we also analyzed the genetic difference between the parent lines of Diansa pig.We identified some genes and signaling pathways in coat color（KIT）,growth（IGF1R）,reproduction（ESR1,FSHB,BMP7）and meat quality（FTO）among their parents.In summary,in this study,using the genomic information,we explored the genetic characteristics of Saba pig breed and identified some genes associated with body size,fertility and meat quality.We found that Saba pig has high genetic diversity.We also predicted the appropriate hybrid models for this breed.In addition,we proposed a fast PLS method and made use of the comparative genomics technology to predict the pig enhancers.We explored the suitable index for investigating the genetic diversity of a small population.We also suggested that conservation programs should be designed by combining the information of genome-wide and trait-specific markers.These results can not only help us to better understand the genetic background of Saba pig,but also provide a molecular basis for the protection and utilization of this pig.The results of this study will also lay a foundation for follow-up works on pig molecular design and breeding,and provide references for the evaluation,protection and utilization of other indigenous pig breeds.