The Association Of Whole Blood Transcriptome And Reproductive Hormones In Sheep By EGWAS And EQTL

The dynamic changes of reproductive hormones in blood are of great significance for the evaluation of reproductive performance of livestock.The blood transcriptome is not only used to identify immune related biomarker in many species,but also has been gradually applied in livestock production management in recent years.In order to analyze the relationship between the dynamic time-series expression of sheep whole blood transcriptome and the regulation of reproductive hormones,In-depth analysis of blood transcriptome and expression genotype data from Bamei Mutton Sheep,which will help to improve the new understanding of blood application in the management-assisted of livestock reproductive performance.The main results obtained in this study show as follows:1.The temporal dynamic expression of sheep blood transcriptome was studied.The blood transcriptome of sheep with different litter size was detected in March,April and May,and the differentially expressed genes(DEGs)and differently expressed AS events(DEAS)between groups were analyzed.The results showed that a total of 1417 DEGs and 3332 DEAS genes were detected among different litter size.Compared with the no-lambing group,the gene expression patterns of the single lambing group and the twin lambing group were more similar.DEGs and DEAS genes co-functional enrichment results indicated that blood characterization of litter size was related to oocyte meiosis,hormone regulation and immune response,etc.660 DEGs and 3135 DEAS genes were identified between different time-series.The genes of short time-series expression directly or indirectly affected hormone levels at the functional level.Therefore,it is inferred that sheep blood time-series expression genes may be closely related to hormones.2.Based on results of study one,237 samples were expanded.A weighted gene co-expression network analysis(WGCNA)was constructed,and the association between serum concentrations of follicle-stimulaing hormone(FSH),luteinizing hormone(LH),growth differentiation factor 9(GDF9),bone morphogenetic protein 15(BMP15)and gene dynamic expression,and variation was studied in combination with expression genome-wide association study(e GWAS).The results showed that the DEGs of litter size were distributed more in the red and purple modules.Red and purple gene modules were significantly associated with litter size in the global network.Significant genes associated with e GWAS modules were found mainly on the X chromosome,including COIL,NELFE and GCLM,which were involved in the regulation of oocyte maturation,granulocyte capillary regeneration,seasonal reproduction and immune response.The time-series DEGs were mainly distributed in the yellow and blue gene modules.Yellow and blue gene modules had a higher correlation with hormones in the global network.e GWAS significantly associated genes include CASP9 and SRP68,which were enriched into the oxytocin signaling pathway and affect the hormone regulation process.Next,we applied machine learning approaches to RNA-Seq data sets and prior GWAS database to verify and supplement sample grouping and the functions of global network modules,and the support and feasibility of small sample DEGs in large sample analysis were proved.In conclusion,the co-expression network of sheep reproductive hormones was analyzed at the expression genomic level to provide complementary information for the gene expression and the variation of reproductive hormone temporal physiological state.3.In order to further analyze the deep mechanism of LH/FSH ratio Association in high prolificacy sheep.It was found that the DEGs of different LH/FSH ratios ranged from 50 to 150.These genes affected ribosome,prolactin signaling pathway,gonadotropin signaling pathway,ovarian steroid production,oxytocin signaling pathway,and arachidonic acid metabolism and other pathways related to hormone regulation.A total of 1 823 significant associations and 1 433 e QTL-SNPs involved in yellow and blue gene modules were identified,and the distribution were not homogeneous along each chromosome.A total of 690 genes were affected by e QTL-SNPs.A total of 26 445ASE-SNPs were identified,affecting 4 970 genes,which were homogeneous distributed along each chromosome,confirmed the extensive cis-regulation of gene transcription of the association of LH/FSH ratio and sheep blood.A total of 8 blood biomarkers were selected: PCNX4,FAS,RPL36 AL,JCHAIN,LOC101113346,IQSEC1,RPL21 and RPL8.Most of the these showed expression genotypes allelic imbalance and were thus detectable as affected by at least one e QTL-SNP and two ASE-SNPs.4.To explore the deep mechanism of the influence of growth differentiation factor 9and bone morphogenetic protein 15 in high prolificacy sheep.We compared and correlated the whole blood RNA-Seq of GDF9 and BMP15 at different serum concentrations.The results showed that the concentrations of BMP15 and GDF9 in serum may depend on the endocrine signal exchange by regulating the shared DEGs of RPL23 A,LOC101110403,PAQR5,LOC114116858,LOC114114874 and NAIP.Among them,RPL23 A,PAQR5 and NAIP were directly or indirectly involved in oocyte development and ovarian function.Demonstrating the potential of blood to identify major genes and associated biological processes under the influence of hormones.At the same time,ASE-SNP and e QTL-SNP was widely found in blood regulated of GDF9 and BMP15,and a total of 502 ASE-SNPs were identified,including 58 that were simultaneously associated with e QTL-SNP.Putative blood biomarkers that co-regulate the expression of e QTL-SNP and ASE-SNP of GDF9 and BMP15 include JAK1,IL6 R,ITGA4,GAA,PRKD3,CAMK2 D,TAB2 and IQGAP1,which were obvious imbalance of allele expression in their genotypes.In short,we describe the blood transcriptome and reproductive hormone network atlas,and the deep understanding of the regulatory elements associated with reproductive hormones has demonstrated the potential of blood in identifying marker genes and associated biological processes under the dynamic variation of hormones,as well as any other complex traits for which blood as an appropriate surrogate tissue.