Re-sequencing Analysis Reveals The Selection Signatures Of The Pig Genome

Since their domestication about 9,000 years ago,about 300 breeds of pig(Sus scrofa)have been bred globally under natural and artificial selection.Compared with the wild boar,domestic pigs have large differences in heat/cold tolerance,disease resistance,reproduction,coat color and body shape.These differences may be caused by the selection under the evolution and domestication.The selection leaves a distinct feature on the genome,the selection signature.Detecting the selection signature of domestic animal provide an important genetic basis for elucidating the involvement of natural and human technologies in the evolutionary process and their collective influence on the modern animal genome and,in turn,on improved livestock breeding.The Wannan Black pig is a typical Chinese indigenous breed that is disease-resistant,has high fertility,and a crude-feed tolerance,and has been bred in the south of Anhui province by artificial selection for a long time.At the same time,Yucatan miniature pig(YMP),a naturally small breed,has been domesticated in the hot and arid Yucatan Peninsula and has distinct traits,such as gentleness,intelligence,disease resistance,and relative lack of odor.To date,YMP is widely used as a medical model worldwide.This study aims to detect genome variation and identify selection signatures of the two breeds for exploring the genetic basis of its germplasm characteristics.Detecting genome variation and selection signature detection of Wannan black pig:We resequenced the Wannan Black pig(n=20),which yielded 501.52 G of raw data.After mapping these to the S.scrofa reference genome 11.1,an average of 84.74%(～83.44-85.66%)of reads were mapped.The depth of the experimental population ranged from 7.10-11.38 folds with an average of 9.43.A total of 21M SNVs and 5M InDels(2,898,582 inserts and 2,168,624 deletions)were detected across the genome by combining two methods for extracting genetic variation(GATK and Samtools).We performed principal component analysis(PCA),ADMIXTURE,and SNPHhylo analysis using the sequencing data of 28 pigs from 19 subspecies and 20 Wannan black pigs.Regions under selection between the Wannan Black pigs were identified based on two different statistics,i.e.FST and π ratio.This study successfully constructed the genetic variation map of Wannan black pig and a selection signature map at the genome level.Annotation of genes harbored in selected regions revealed that a series of genes were related to disease-resistant,fertility,and a crude-feed tolerance,including gene(BBS4)that regulate retinal and then cause vision changes,which could provide a good explanation that modern pigs have a visual acuity decline compared to the wild boar population.A gene(Zfp36)that regulates host defense against viral infection,and TNFSF15 associated with diarrhea and other genes involved in regulation of reproduction and growth.Detecting X-Chromosome Genetic Variation and Selection Signature in YMP:A total of 168,118 SNPs and 66,892 InDels were detected.Phylogenetic tree analysis showed that YMP and European breeds had a close genetic distance.Based on the Fst and π ratio methods,the selection signature on the X chromosome of YMP were identified.A total of 317 selection regions were found at 0.01 level,which harbored 77 genes,within 55 to 57 Mb and 75 to 80 Mb detecting strongly signature,but there is almost no signature within 46～55 Mb and 58～74 Mb.By annotating selected genes,a series of GO term:reproductive processes","signaling","immune system processes","response to stimuli"and "growth",and KEGG pathway:"immune system","lipid metabolism","digestive system","Energy metabolism","cell growth and apoptosis",and "signal transduction"were identified.Including some associated with adipose development Several(ACSL4,ATP1B4,and TRPC5);and growth-related(DGKK,ATRX,MED 12,TSPYL2,and MTM1).Genes that regulate reproduction are also found:the DIAPH2 gene are associated with premature ovarian failure,the TEX11 gene associated with infertility,and the LDOC1 gene that affects endocrine function in the placenta.As is well known,YMP is associated with relative lack of odor.X-linked hypohidrotic ectodermal dysplasia(XLHED)is a genetic disease characterized by hypoplasia or absence of hair and sweat glands and is caused by variants in the EDA gene encoding ectodysplasin A.Studies have shown that variants in the EDA gene can lead to XLHED in humans,mice,and cattle.A frameshift variant(c.842delT)is a candidate causative variant for the observed XLHED in male puppies.Based on the above results,we can draw the following conclusions:The whole genome sequencing data of the Wannan black pig population,as well as the data of SNP,InDel are valuable resources for researching evolution,domestication or breeding personnel.These data provide a good basis for the development and utilization of Wannan Black Pig.At the same time,according to the selection signal of Yucatan pigs,it provides a certain direction for the study of human hair diseases.