Genome Analysis Of Litter Size Trait And Transcriptome Analysis Of Follicular Development Of Jining Grey Goat

As one famous local breed in China,Jining grey goat has been selected into the national animal and poultry record for its high reproductive capacity,and could be served as an ideal animal model for the study of reproductive performance in goats.As an important domesticated animal,the research of genetic diversity on goats has been relatively lagging.In 2017,the novel reference genome of goat with high quality has been published in the journal of Nature Genetics,which is based on the third-generation sequencing technology,and would provide a reliable basis for people to better understand,mine and study the important functional genes in goat from genome aspect.Another,at present,people’s cognition of the internal molecular regulation mechanism and gene regulation network of reproductive traits in goat is still relatively lacking.In recent years,the rapid development of single-cell sequencing technology has provided new ideas for exploring genome-wide gene regulation networks at the cellular level,and revealing the fate determination of cell differentiation and functional transcription.Based on the above facts,this study selected Jining grey goat,an excellent local goat breed in China,as the research object,aiming to find the genetic variation and new molecular markers associated with the litter size trait of goats with the genome resequencing technology,thus revealing the genetic basis of litter size trait from the perspective of goat genome.At the same time,single cell sequencing technology was adopted to explore the gene expression and regulation network of oocytes and granulosa cells during follicular development,and through comparative analysis,the germ cell developmental rule of individuals with different reproductive capacity was revealed,which would contribute to improving animal production performance by artificial intervention.The main results were as follows:1.Through whole genome sequencing,large amount of genetic variations in Jining grey goats were identified.At the same time,due to the comparative analysis with Asian wild goats and domestic goats with low litter size,many novel candidate genes associated with reproductive performance in goat,including KIT,ESR1,STIM1,SLC26A2,SPIRE2,etc.,were found.These genes likely undergo selection in the process of evolution and artificial breeding for goat,as well as important molecular markers of goat reproductive performance.In addition,the signal pathway,including ERK,germ cell meiosis and intrauterine embryo development may be the important factors that affect evolution of litter size in goat.2.With the associated analysis of litter size(LS)of Jining grey goats,the selective sweep analysis of different litter size groups of Jining grey goats was performed.42 potential candidate genes related to LS,including KIT,KCNH7 and KMT2 E in LS2 group,and PAK1,PRKAA1 and SMAD9 in LS3 group were identified.Enrichment analysis also showed that programmed cell death in cell development,steroid metabolism and insulin pathway were probably involved in the evolutionary selection of LS in Jining grey goats.3.Using single cell RNA sequence(sc RNA-seq)technology,the transcriptional map of granulosa cells of Jining grey goats in follicular development was successfully constructed.It was found that transcriptional activities related to cell cycle and DNA replication were active in early stage of granulosa cell development,and in late stage,the signaling of steroid metabolism and IGF-like growth factor were enhanced.At the same time,the differences in granulosa cell development of individuals with different litter size groups were mainly reflected by functional transcription in the early and late stages.4.Through the analyses between oocytes and granulosa cells by sc RNA-seq,a batch of marker genes that can be used to identify oocytes and granulosa cells were identified.According to the different stages of follicular development,some functional transcriptional activities in oocytes and granulosa cells coupled with developmental stage were screened.5.Through the interactions analysis between oocytes and granulosa cells mediated by ligand-receptor,the molecular mechanism and regulation of NOTCH,TGF-β signaling pathways and gap junction during follicular development in goat were interpreted in detail,by comparison of dynamic signals expression in human,the special regulatary pattern of these pathways in the process of follicular development in goat was revealed.