Differences In Genomic Selection Signals And DNA Methylation Between Dairy Sheep And Mongolian Sheep

China has many indigenous sheep breeds.Region specific breed like Mongolian sheep are well adapted to their local environment and have good production performance.The introduced dairy sheep breeds like East Friesian and DairyMeade have good milking and reproduction production performance,but their adaptation in Inner Mongolia are relatively poor.Revealing of the underlying genetic mechanisms related to the environmental adaptations and production traits of Mongolian sheep has important theoretical and practical significance for the protection of Mongolian sheep and the breeding of new sheep breeds which are well adapted to the Inner Mongolia environment.In current study,we performed whole-genome sequencing?WGS?with an average depth of 12.29x on 85 sheep?23 Mongolian sheep,7 Small-Tail Han sheep,2East Friesian sheep,46 DairyMeade sheep,and 7 hybrid sheep?.With the integration of 97 sheep WGS data?66 Mongolian series sheep,30 Tibetan series sheep,and one Asiatic mouflon?from public database,we used the latest reference genome?Oar_rambouillet_v1?and constructed genetic variation maps of Dairy sheep,Mongolian series sheep and Tibetan series sheep,analyzed the genetic relationships among the three populations,and identified the genomic selection regions and candidate genes under long-term natural and artificial selection.Moreover,whole-genome bisulfite sequencing with an average depth of 20.78x were conducted on 12muscle and 10 tail-fat tissues of Dairy sheep and Mongolian sheep.We then mapped the genome-wide DNA methylation patterns of the muscle and tail-fat tissues of Dairy sheep and Mongolian sheep at single-nucleotide resolution and identified the differentially methylated genes.The main results were as follows:1.Through the population structure analysis,Dairy sheep were mainly from two ancestral groups Mongolian series sheep had the highest nucleotide diversity,indicating that they had the richest genetic resource pool.2.A group of immune-associated genomic regions in Dairy,Mongolian series,and Tibetan series sheep were found under selection,but distributed in different populations,which indicated that each population may has characteristic immune regulatory mechanisms.The C-type lectin receptor signaling pathway was closely related to disease resistance in Mongolian series sheep and mainly contained selected genes SRC,TPR1,CYLD and PAK1.IL-5 and IRF1 were selected in Dairy sheep and closely related to allergic diseases and immunomodulatory responses,respectively.3.The Ca²⁺signaling pathway was significantly enriched in the selected genomic regions of Mongolian series sheep,which contained selected genes ITPKB,GNAQ,TPR1 and ATP2A3,and may play important roles in their local adaptations.4.The genes LOC101117953,BMP2 and PDGFD,which are closely related to tail-fat development,were identified in Mongolian sheep.RXFP2 which related to horn type and development was identified in Dairy sheep.CERS1,CRYBB3 and DMBT1were under selection in Mongolian series sheep and closely related to neural signal transduction,vision and mucosal immunity,respectively.On chromosome X,AR and OPHN1 were under selection and closely related to male fertility and neurodevelopment.5.The whole-genome DNA methylation landscapes of Mongolian sheep and Dairy sheep were mapped.Mongolian sheep and Dairy sheep had similar DNA methylation dynamics in muscle and tail-fat tissue.Generally,tail-fat tissue had higher methylation level than muscle tissues.The GC content of the promoter region gradually decreased from the transcription start site to the flanking region and subsequently stabilized,and it was negatively correlated with DNA methylation levels.6.In tail-fat and muscle tissues,the calcium/calmodulin-dependent protein kinase type II?gene?CAMK2D?showed differential DNA methylation levels in different regions of the intron,which may closely relate to the fat and muscle metabolism.In this study,we scanned shared and specific genome-wide genomic selection signals among Mongolia series,Tibetan series and Dairy sheep and analyzed the genetic variants contained in these regions.We also compared the DNA methylation differences between Mongolian sheep and Dairy sheep on a genome-wide scale.These results may provide important theoretical guidance for the protection of Mongolian sheep and breeding of new dairy sheep breeds for Inner Mongolia.