Genomic Scan For Identification Of Short Stature Candidate Genesin De Bao Pony

The Debao pony, which is restricted to the Guangxi mountains of the southern China, is of particular interest due to its extremely small size and also one of the most ancient pony genetic resources in the world。The short stature size in Debao pony is the resultant of a long-term orientation of human domestication and adaptation to its natural habitat environment. For Debao pony, the short stature size has been an advantageous trait for carrying mountain consignment from one place to another since a long history. It is, therefore, meaningful to perform stature related research on this breed for its efficient multiplication, utilization and protection. Currently, studies on the historical origins and the molecular genetic mechanisms of short stature in the Debao pony rather late, especially at the genomic level reported extremely rare.In this study, we have undergone genome-wide scan using high-density microarray(GeneSeek Equine SNP 65K) to detect selection signals, copy number variation(CNV) study and Genome-wide association related of heightin three Chinese horse breeds, viz., Debao pony(DB),Inner Mongolian horse(MG) and Yili horse(YL) with different body height. We have also integrated50 K microarray genotyped data of 729 individuals from 32 horse breeds from. The present study was conducted for further confirmation of the evolutionary history of Debao pony to understand genetic mechanism and to provide information on molecular genetics basis for short-stature trait.In this study, phylogenetic tree was constructed fromabove three Chinese horse breedswith Przewalski’s horse as out-group. The three breeds were clustered separately in different evolutionary branches.From genetic distancepoint of view, all Chinese breeds are closer to Mongolian breeds. This study provides valuable information on the molecular basis regarding phylogenetic of three Chinese horses.In order to further understand the relationship between population and genetic structure in Chinese breeds and 32 other breeds, we conducted the principal component analys is(PCA) and genetic structure analys is. Chinese horse breeds clustered together with Mongolian and Northern Siberia(Tuva) horse breeds and classified as small-sized and ancient horse breeds.Linkage disequilibr ium analysis also reinforces that Chinese horse breedsbeing ancient breeds.At the same time,the structure analysis revealed obvious separation of Debao pony from the other two Chinese horse breeds( Yili and Mongolian horses) which illustrates that Debao pony have significantly different genetic background compared with other Chinese horse breeds.In this study, we carriedvarious other genome-wide population differentiation analys is such as FSTbased Di analysis, haplotype-based XP-EHH analys is. In association with body height, we conducted genome wide analys is(GWAS)of Debao pony with other Chinese horse breeds. Finally,we detected significant selection s ignals in 523 and 505 candidateSNPs respectively for Di and XP-EHH values on the Debao pony breeds. Based on the correlation with associated body height analysis, both methods screened significant c orrelation with body height for22 SNP loci on Debao pony. Two candidate genes HMGA2,TBX3 are confirmed by gene annotation as significantly associated with body heightin Debao pony. Among identif ied genes, HMGA2 gene which waspreviously in human and equine, whereas we have identif ied novel gene, TBX3 gene for the first timein horses.Moreover, we did not detect the gene flow event between Debao pony and foreign pony breeds. We, therefore, speculate that Debao pony had probably experienced independent domestication process different from other pony breeds found in the world.The results of this study, thus, exhibits different genetic mechanism in Debao pony for short stature in comparison to other foreign pony breeds.This studyprovidesnovel molecular evidence for understanding genetic mechanism for short stature in world pony breeds.The results illustrate that Debao pony breeds dwarf molecular genetic mechanism is possibility different from foreign pony breeds.This study could be provide new molecular evidence for understanding genetic machinism for short stature in world pony breeds.Recent studies have proven that concern only with single nucleotide polymorphisms(SNPs) is not enough for detecting phenotypic differences in DNA mutation.There are important functio nal signif icance of variation in the genome in other forms, such as copy number variation(CNV).We carried polymorphism analysis of copy number variation on Debao pony and other Chinese horse breeds. We have detected only a singlegrowth-related CNVR on chromosome 11.The reasons for less CNVRs with relationship with body size in Debao horse genome might be related to limitation inchip density and/or due to performingonly single analytical method. Advent of higher density chips and/ or re-sequencing technology will support to imply more information on CNVRs with relationship with body size in Debao and other dwarf horse genomeIn summary, we found positive selection sites associated with height in Debao pony which vary from other foreign horse breeds indicating that Debao pony shows potential independent molecular genetics mechanism with respect to short stature.