Comprehensive Variant Discovery In The Pig Genome Using High-depth Sequencing Data

Pig(Sus scrofa)was firstly domesticated around 10,000 years ago,and it is one of the successfully domesticated animals in human history.Owing to the environmental differences in multiple regions,and the establishment of multiple domesticate centers of pigs,extensive phenotypic differences have been accumulated for different pig breeds.The fundamental reason for phenotypic differences is the genetic variations among pigs,in this study,we used high throughput sequencing data to analyze genome-wide genetic variation in pigs,including analyses of structural variants(SV),and construction of whole genome sequence map using de novo method in pigs.The variation of climates in the vast geographical regions of China as well as human activities lead to the emergence of multiple pig breeds,which shows differences in environmental adapation and phenotype.Behide that,it is all about genetic mutation accumulation.Using SV as genetic marker,selective sweep signals have been detected in many other species.Moreover,SV provided higher resolution to distinguish populations and to explain phenotypic variances.Focusing on SV,in the study,we used genome-wide resequencing data of 66 Chinese indigenous pig in high-depth to analyze population differences.Results revealed genetic differentials among different geographical pig groups(the southern Chinese domestic pig group,the northern Chinese domestic pig group,and the Tibetan pig group),and corresponding environmental adaptations.Moreover,the results also suggest domesticate difference between the southern Chinese domesic pig group and the northern Chinese domesic pig group.These findings are of great significance to guide further studies,in respect to the genetic basis of phenotypic differences among Chinese indigenous pigs.Although large amount of variants were detected by resequecing data in high-depth,some genetic information still cannot be effectively captured due to the limitation of resequencing method.In this study,we did high quality de novo assembling of six pig genomes,including Yorkshire,Landrace,Erhualian,Min,Shazilin and Dahuabai pigs.Together with previously released assemblies,we further analyze the genetic differences in different pig breeds.According the comparison of these 17 genomes,the multiple assembling quality indexes of six genomes assembled in this study were mostly higher than assemblies released by previous studies.In the results of variant detection,we detected about 35 million single nucleotide polymorphisms(SNPs)and 32,437 SVs.For SNPs,by incorporating with 40 resequencing data of Chinese and European pigs and genome assemblies,we had validated seven selective regions,which were associated with reproduction and obesity traits.For SVs,we compared different mechods in the detection of these variants,results showed that de novo method can detect insertions more effectively.We further built a core genome of pigs that were highly conserved in all pigs studyed.Among the core genome sequences,for one thing,we detected potential disease related mutants,such as ADRB3 which is associated with obesity risk,and ZNF644 which is associated with myopia,etc.,moreover,we also detected genes with mutations specifically found in pigs compared to other close species,such as SLC2A1 which is involved in glycogen transportation and KDR associated with angiocardiopathy.For another thing,we searched for pig genes that were evolutionarily close to human while harbored specific mutations,which provides a scientific basis for the further research on the bio-medical model of pig.Altogether,the results of the present study were all based on the next generation sequencing data in high-depth.We systematically compared the mode of SV loci distribution in Chinese indigenous pigs using resequencing data,which revealed the important functionality of SVs to the genetic differences.Meanwhile,we used the de novo assembling method to effectively cover the complete information of the whole pig genome,which provides an important basis for the furture study of disease model in pigs.