Assessing Genomic Diversity And Signatures Of Selection In Dorper Sheep Using Whole-genome Sequencing And Transcriptome Data

Dorper sheep,a major commercial mutton sheep breed,has played an important role in the breeding of new varieties and improvement of local breeds due to its excellent growth rate,heavy carcasses,outstanding meat quality and hardiness.In China,many studies through purebred and crossbreeding experiments have shown that Dorper sheep have significant advantages in growth rate,slaughter rate and meat quality compared to local breeds such as Small Tail Han,Hu and Tan Sheep.However,the molecular genetic bases of the dominant traits are currently unclear,and there is also a lack of molecular genetic markers that can be applied for early artificial selection.Therefore,in this study,approximately 10X genome resequencing was performed on 20 Dorper sheep to identify genome-wide SNP and InDel variations.By compared the genomes of Dorper with those of the Small Tail Han,Hu and Tan Sheep available in the NCBI database,the selected regions of the Dorper were identified using F_ST,XP-EHH and nSL.Then,we carried out the gene annotation and enrichment analysis.Finally,RNA-seq was used to identify differentially expressed genes associated with growth and meat quality in liver and muscle tissues of 3 Dorper and 3Small Tail Han sheep,and the genes associated with growth advantage in Dorper sheep were screened and validated by RT-q PCR.The main results of this study were as follows:（1）A total of 20273317 high quality SNPs were identified in the genomes of 20Dorper sheep;1963246 InDels,including 844804 insertions and 1118442 deletions.（2）The genomic diversity level of Dorper（P_N=0.9236,H_E=0.2832,H_O=0.2479）was lower than Small Tail Han,Hu,and Tan sheep.The inbreeding degree in the Dorper（Fis=0.1212）was higher than Small Tail Han,Hu,and Tan sheep（3）A total of 397 candidate genes were identified by F_ST,nSL and XP-EHH,including some genes that have been reported to be associated with traits in Dorper sheep,such as meat quality（PPP1R12 and CACHD1）,energy metabolism and growth（LMO7 and RALGAPA2）,adipogenesis（PPARG and CAND2）,body weight（ADSL,PDGFD and PPARG）,etc.Notably,a total of 38 candidate genes were identified by all three methods,indicating that these genes were strongly selected in Doper sheep.Among them,CPT2 and EHBP1 are associated with fat deposition,PDE2A is associated with olfaction.Transcription factors of the KLF12 family are important regulators of adipogenesis.In addition,haplotype analysis of EHBP1 and CERS4 revealed significant differences between Dorper and other local sheep.One missense mutation（EHBP1:rs427725035）and one synonymous mutation（PPARG:rs161286565）were detected in the candidate genes,with significant differences in gene frequencies between Dorper sheep and other local sheep breeds.These candidate genes provide a theoretical basis for the genetic mechanism of growth,meat quality and other traits in Dorper sheep.（4）The number of DEGs identified in both tissues was 2188,with 950 and 1007genes expressed up-and down-regulated in liver,respectively;and 160 and 71 genes up-and down-regulated in muscle,respectively.Some DEGs,such as TGFB1,TGFB3,FABP3 and LPL may be associated with growth and muscle development in Dorper sheep.Some enrichment analysis results were associated with muscle growth and development such as developmental growth（GO:0048589）and myogenic fibres（GO:0030016）.This experiment was further validated using RT-q PCR for eight genes,whose expression patterns were consistent with the RNA-seq results.This study analysed genetic diversity,population structure,genome-wide selection signals,gene expression profiles of liver and muscle tissues and differential genes in Dorper sheep based on high-throughput sequencing technology.The results showed that the genetic background of Dorper sheep is significantly different from that of Small Tail Han,Hu and Tan sheep,and its genetic diversity is lower than that of the other three breeds.Candidate genes and molecular markers associated with dominant traits such as growth and development,fat deposition and carcass traits were obtained.