Genetic Basis Of Miniatures In Debao Horse Based On Genome Assembly And Resequencing Analysis

The Debao(DB)is a famous miniature horse breed found in Debao County in the southwestern Guangxi region of China.It is one of the valuable Chinese local horse genetic resources and has significant tourism,ornamental,and scientific research value.However,there is a lack of genomic and genetic diversity information for the Debao horse,and the genetic basis for its small size trait is still unclear.Therefore,the genetic basis for the formation of the small size trait in the Debao horse was investigated through genome assembly and resequencing analysis.The main findings of this study are as follows:The chromosome assembly of the species might be advantageous for chromosome evolution and functional gene mapping research.Here,a chromosome-level genome assembly of a male Debao horse(Equus caballus)was generated utilizing Illumina Hi Seq,Pac Bio and Hi-C technologies.The Debao horse genome was 2.44 Gb in size,with contig N50 of 34.25 Mb and a scaffold N50 of 88.98 Mb,and a heterozygosity of 0.29%.The repetitive sequences constitute 41.26% of the genome.Ab initio,RNA sequence-based and homology-based predictions was used to identify protein coding genes.A total of21,038 protein-coding genes were identified.Evolutionary analysis tree revealed that Debao(Equus caballus)is more closely related to common horse(Equus caballus),Donkey(Equus asinus),Zebra(Equus quagga)than other species.The detailed Debao horse genome’s chromosomal assembly and annotation resources enhance understanding of its genetic architecture,provide new information for hose comparison genome and evolution studies.Copy number variations(CNVs)are crucial structural genomic variants affecting complex traits in livestock animals.The current study was designed to conduct a com-prehensive comparative copy number variation analysis among three breeds,Debao(DB),Baise(BS),and Warmblood(WB),with a specific focus on identifying genomic regions associated with miniature features in horses.Using whole-genome next-generation resequencing data,18,974 CNVs were identified across 31 autosomes.Among the breeds,we found 4279 breed-specific CNV regions(CNVRs).Baise,Debao,and Warmblood displayed 2978,986,and 895 distinct CNVRs,respectively,with 202 CNVRs shared across all three breeds.After removing duplicates,1545 CNVRs were obtained from 26 horse genomes.Functional annotation reveals enrichment in biological functions,including antigen processing,cell metabolism,olfactory conduction,and nervous system development.Debao horses have 970 genes overlapping with CNVRs,possibly causing their small size and mountainous adaptations.From this study it is found that the genes GHR,SOX9,and SOX11 may be responsible for the miniature features of the Debao horse by analyzing their overlapping CNVRs.Overall,this study offers valuable insights into the distribution patterns of CNVs in the horse genome and the candidate genes responsible for the formation of miniature traits in Debao horse.Signatures of selection analyses are useful to identify genes associated with body measurements particularly wither height,in horses.Comparative population genomics based on whole-genome resequencing data was used to reveal signatures of selection related miniature traits in Debao horse.Four population comparison approaches,Genetic differentiation(Fst),Pooled heterozygosity(Hp),Nucleotide diversity(θπ)and Extended haplotype homozygosity(XP-EHH)were applied to detect genomic signatures of positive selection and identify genomic regions under selection for body sizerelated miniature traits.Phylogenetically,DB was distinct from other horse but closely related to the Baise horse(BS).Despite the fact that the most evolutionary distance was found between the DB and Warmblood(WB)breeds,the DB and BS breeds did not appear to identify in either the phylogenetic structure or the principal component analysis,which indicates that these two Chinese horse breeds may share genetic components.Selective sweep analysis showed two candidate genes,e CATH-3 and NME6,that may be associated with the miniature characteristic in DB.In summary,this study generated Debao horse genome and identified key candidate genes(GHR,SOX9,SOX11,e CATH-3,and NME6)which may regulate miniature traits.Those findings could provide data support and genetic resource for the foundmental study of the genetic basis of miniature traits in horse,and contribute to a conceptual framework for the research and development of genetic resources of local horse breeds in China.