Multi-omics Analysis Of Oviduct Screening Reproductive Candidate Genes And Regulatory Networks In Goat

The kidding number is an important economic trait and has a significant impact on the profitability of domestic goats.The Yunshang black goat is a new breed of meat that has been independently bred in China,with excellent genetic traits of both meat production rate and fertility.Several factors affect fecundity,and the present research primarily focuses on the HPG axis.As an important maternal organ,the oviduct is the site of final sperm capacitation,oocyte fertilization,and early embryo development.In this study,twenty female Yunshang black goats with the kidding number records were divided into high-and low-fecundity groups in the follicular(FH vs.FL)and luteal(LH vs.LL)phases,respectively.The RNA-Seq and DIA-based high-resolution mass spectrometry(MS)techniques were employed to identify RNAs and proteins in oviducts,respectively.The main results obtained were as follows:(1)In this study,RNA-seq was used to measure mRNA expression levels in the oviduct.A total of 68,149 mRNA transcripts were identified,and 1,640 and 2,023 differentially expressed mRNAs(DEGs)were obtained in the follicular phase with low-and highfecundity group(FL vs.FH)and luteal phase with low-and high-fecundity group(LL vs.LH),respectively.Enrichment analysis suggested that DEGs were significantly involved in multiple pathways,such as AMPK,PI3K-Akt,Calcium,Insulin,Wnt,and Prolactin signaling pathways and embryonic development pathways.These pathways may directly or indirectly affect goat reproduction.(2)Non-coding RNA(ncRNA)expression profiles were also established.A total of 24,170 novel lncRNAs,4,078 circRNAs,and 1,116 miRNAs transcripts were identified,and differential analysis showed that 271 differentially expressed lncRNAs(DELs),174 differentially expressed circRNAs(DECs)and 25 differentially expressed miRNAs(DEMs)were identified in the FL vs.FH group,and 377 DELs,286 DECs,and 66 DEMs were identified in the LL vs.LH group.Functional analysis showed that the target genes and host genes of these ncRNAs were mainly enriched in reproduction-related pathways,such as embryonic development and transport,gamete maturation,estrogen secretion,cytokinecytokine receptor interactions,TGF-β signaling pathway,and positive regulation of MAPK cascade.(3)Combining whole-transcriptome sequencing data of the same samples,the ceRNA networks were constructed.Dual luciferase reporter assays showed that LNC＿005981 could compete with SMAD3 to bind miR-328-3p,participating in the regulation of embryonic development.In addition,circ＿0021923 could compete with DOT1 L to bind miR-204-3p,which may be an important mechanism for maternal regulation of embryonic development.(4)A total of 5,409 proteins were identified,and WGCNA analysis suggested that the Tan module was highly associated with high fecundity traits.In addition,98 and 167 differentially abundant proteins(DAPs)were identified in the FH vs.FL and LH vs.LL groups,respectively.Functional analysis showed that CAMSAP3,ITGAM,SYVN1,EMG1,ND5,RING1,CBS,PES1,ELP3,SEC24 C,SPP1,and HSPA8 may play key roles as the oviductal factors to communication with gametes or embryos.(5)Integration analysis of proteomics and transcriptomics revealed that the DAPs and DEGs were commonly involved in the metabolic processes at the follicular phase,which may prepare the oviductal microenvironment for gamete reception.Furthermore,the MAP kinase activity,estrogen receptor binding,and angiotensin receptor binding terms were enriched in the luteal phase,which may be actively involved in reproductive processes.Overall,our study explored the genes and proteins related to oviductal function and its connection to the prolificacy trait of goats in the estrous periods.The molecular mechanism that may regulate fecundity trait in the goat was further explained,providing a theoretical basis for revealing the mechanism of multiple kidding numbers in goats and molecular breeding.