Integrated Analysis of mRNAs and Long Non-Coding RNAs Expression of Oviduct That Provides Novel Insights into the Prolificacy Mechanism of Goat (Capra hircus)

Abstract

Artificial directional selection has replaced natural selection and resulted in trait differences across breeds in domestic animal breeding. However, the molecular mechanism by which the oviduct regulates litter size remains largely elusive in goats during the follicular phase. Accumulating data have linked lncRNAs to reproductive activities; however, little is known about the modulation mechanism in the oviduct. Herein, RNA-seq was used to measure mRNA and lncRNA expression levels in low- and high-fecundity goats. We observed distinctive differences in mRNA and lncRNA in terms of different kidding numbers and detected the differential expression of 1640 mRNA transcripts and 271 lncRNA transcripts. Enrichment analysis of differentially expressed mRNAs (DEGs) suggested that multiple pathways, such as the AMPK, PI3K–Akt, calcium signaling pathway, oocyte meiosis, ABC transporter, and ECM–receptor interaction pathways, directly or indirectly affected goat reproduction. Additionally, coexpression of differentially expressed lncRNAs (DEL)-genes analysis showed that XLOC_021615, XLOC_119780, and XLOC_076450 were trans-acting as the DEGs ATAD2, DEPDC5, and TRPM6, respectively, and could regulate embryo development. Moreover, XLOC_020079, XLOC_107361, XLOC_169844, XLOC_252348 were the trans-regulated elements of the DEGs ARHGEF2 and RAPGEF6, and the target DEGs CPEB3 of XLOC_089239, XLOC_090063, XLOC_107409, XLOC_153574, XLOC_211271, XLOC_251687 were associated with prolificacy. Collectively, our study has offered a thorough dissection of the oviduct lncRNA and mRNA landscapes in goats. These results could serve as potential targets of the oviduct affecting fertility in goats.

Identification of long noncoding RNAs downregulated specifically in ovarian high‐grade serous carcinoma

“… 52 AMPK is reported to be involved in autophagy of granulosa cells and oocytes, which regulates follicle development, 53 and AMPK in the fallopian tube may contribute to embryonic development, spermatocyte DNA damage repair, and ovarian steroid hormone production. 54 …”

Characterization and Comparative Analysis of Whole-Transcriptome Sequencing in High- and Low-Fecundity Chongming White Goat Ovaries during the Estrus Phase

“…Cortisol and steroid hormones are known to regulate ovarian cell proliferation, apoptosis, folliculogenesis, and folliculogenesis [41]. Animal multifertility is closely related to the occurrence and development of follicles, especially directly related to the number of ovulatory dominant follicles [42]. In another study on the regulation of follicular development in black goats, it was also found that the conversion of progesterone and testosterone occurs in the process of ovarian steroidogenesis, which is one of the most important hormonal pathways known for follicular maturation [10].…”

Integrative Proteomics and Transcriptomics Profiles of the Oviduct Reveal the Prolificacy-Related Candidate Biomarkers of Goats (Capra hircus) in Estrous Periods

“…Previous work has started uncovering the amounts of protein and mRNA expression in the same sample to better understand probable molecular mechanisms and identify reliable biomarkers of specific biological processes [ 24 , 74 ]. In this study, we utilized transcriptomic data generated in the oviduct from the same tissue sample, which we previously published [ 75 , 76 ], to complement the proteomic analysis. Comparing the two phases, our transcriptomics and proteomics results showed that many more transcripts can be identified than proteins in the oviduct.…”

“…High-throughput RNA sequencing (RNA-seq) was conducted following our previously published studies [ 75 , 76 ] and using the same oviduct samples as in protein extraction. Briefly, total RNAs from the 20 oviduct tissues in follicular and luteal phases were extracted by TRIzol reagent (Invitrogen, Carlsbad, CA, USA), respectively.…”