Identification Of Structural Variations Associated With Breed Formation And Local Adaptation In Chinese Indigenous Pigs Using Whole-Genome Sequencing

Structural Variation(SV)is an important type of genomic mutation that aredifferent from single nucleotide polymorphism(SNP).In recent years,the fast-developing high-throughput sequencing technology has allowed researchers to study the distribution of SV and its potential roles on population genetics and complex phenotypic traits.A large number of researches have proved that SV has great effects on individuals' phenotypes such as disease susceptibility in humans,and commercial traits in agricultural animals and plants.Chinese indigenous pigs are known for their large genetic diversity,good meat quality,high reproduction rate and disease resistance.However,as far as we know,there is no systematic research focusing on the impacts of SV on breed formation and local adaptation of Chinese indigenous pigs.Based on the previous research of our laboratory,this study investigate whole genome sequence data of 64 Chinese pigs with coverage of 25 x generated by Illumina Hiseq 2000 platform.These pigs represented 10 breeds and 6 Chinese wild boars which consisted of Tibetan pigs,Southern Chinese pigs(Bamaxiang,Luchuan and Wuzhishan)and Northern Chinese pigs(Min,Hetao,Laiwuhei).The alignment to the pig reference genome was carried out by using the softwares BWA,Samtools and GATK.Based on the BAM files,SVs were detected using read-depth and read-pair methods by CNVnator and Break Dancer,respectively.We then analyzed the length and population frequency of SVs,as well as their relevance to breed formation and local adaptation of Chinese indigenous pigs.The results showed that:1)The general discerption of the result: The total number of SVs we detected was 288,431,in which 70% were short insertions with length between 100 bp and 400 bp.We also identified 35,850 deletions,9824 CNV Gain and 13,954 CNV Loss mutations.All the SVs aggregately covered 563.29 Mb region thataccounts for 20.1% of pig genome.At individual level,the SVs covered an average of 200 Mb genomic region.The SVs detected in this study have 35.57% to 61.06% overlap with results from independent studies by other groups.2)The correlation analysis between SVs and SNPs: Based on the previous work of our laboratory which applied GATK and SOAPsnp to call 37 million SNPs in the 64 pigs.We then assess the association between SVs and SNPs using Spearman correlation coefficientreveal the.For each SV,association value was calculated with the SNPs in its 1Mb flanking regions.At threshold of,69.2% SVs were associated with a least one s SNP at threshold of r2>0.5;however at threshold of r2>0.8,only 15.3% of SVs were evidenced to associate with a least on SNP in their flanking region.These results showed that many of SV were not in strong linkage disequilibrium with their nearby SNPs,this underline the importance ofdirectly study the impacts of SV on individuals.3)Results of breed-specific SVs: We define Breed-specific SVs as SVs with frequency >50% in a specific breed,an absent in the rest breeds,these SVs could be under positive selection during breeding formation..At this threshold,we detected 186 breed specific SVs.For example,in Tibetan pigs(Tibetan Gansu)we identified a 781 bp deletion on Chromosome 6.This deletion located between two genes ST6GALNAC3 and ST6GALNAC5.These genes were involved into the process of Ganglioside which was proved to reduce the level of cerebral edema,a common high altitude illness.Besides,we identified genes such as ABI1,KIT and TYROBPwhich could associate with small body size of Southern Chinese pig breeds.4)Results of local adaptation related SVs: To identify SVs that may affect the local adaptation of different breeds,we divided all 64 pigs into three groups(pleateau pigs,Southern China pigs and Northern China pigs)based on their geographic distribution.We detected 609 SVs associate with location adaptation of pigs.For instance,we found a 2kb deletion on Chromosome 13 in Tibetan population which was near DDPA2 and DDPA4.These two genes were proved to be crucial in the development process of lung.5)SVs enriched on SSCX: Among the 609 local-adaptation specific SVs there were 503(82.6%)SVs related to cold and hot climate adaptation,341 of them were on Chromosome X between 50 Mb and 65 Mb,which was in agreement with our previous study.GO analysis showed that these SVs may affect neuron and synaptic process.In conclusion,our study will provide new insights for the research of structural variation and its potential roles on the breed formation and local adaptation of Chinese indigenous pig breeds.