ORIGINAL RESEARCH article
Front. Vet. Sci.
Sec. Livestock Genomics
Volume 12 - 2025 | doi: 10.3389/fvets.2025.1614599
This article is part of the Research TopicGenomic Insights into Sheep and Goat Breeding Efficiency - Volume IIView all 5 articles
Differential Expression Analysis of lncRNA and mRNA in Ovarian Tissues of Pishan Red Sheep and Hu Sheep with Distinct Genotypes During Estrus
Provisionally accepted
Aisima Muhetaer1
Gao Gong1
Yaoyang Ye1Ayipare • Kuxitaer1Mengting Zhu1
Qifa Li2
Xing Du2
Yiming Sulaiman1*- 1Xinjiang Agricultural University, Ürümqi, Xinjiang Uyghur Region, China
- 2Faculty of Animal Science, Nanjing Agricultural University, Nanjing, Liaoning Province, China
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Pishan Red Sheep and Hu Sheep are sheep breeds with exceptional reproductive characteristics. To investigate the similarities and differences in the expression of reproduction-related genes between these two breeds, this study utilized transcriptome sequencing to identify differentially expressed lncRNAs and mRNAs in ovarian tissues during estrus in Hu Sheep and Pishan Red Sheep carrying FecBB+ and FecB++ genotypes. Furthermore, we explored their potential impacts on fertility. Transcriptome sequencing of ovarian tissues generated 204.58 Gb of clean data. Bioinformatics analysis identified 34,651 lncRNAs, with differential expression analysis revealing 1,481 differentially expressed mRNAs and 698 differentially expressed lncRNAs. Differentially expressed RNAs associated with reproductive performance trends were screened through expression trend analysis. Functional enrichment analysis of target genes for these mRNAs and lncRNAs revealed significant enrichment in KEGG pathways such as "Cytokine-cytokine receptor interaction", "Hippo signaling pathway" and "MAPK signaling pathway" Key candidate mRNAs were identified, including GDF9, GRIA4, HOXC9, HOXD3, MAPK8IP3, AMH, ANGPT2, FGF14, MAPK8IP1, MMP9, and BRINP3. Additionally, critical regulatory relationships between lncRNAs and mRNAs were uncovered. For example, MSTRG.61044.1 exhibited high expression in FecB++ genotype Pishan Red Sheep and may act as a hub regulator in follicular selection and hormonal responses by cis-regulating MAPK8IP1 and trans-regulating AMH, CCL25, MSTRG.23016.1 may regulate genes such as MMP9 and ANGPT2, potentially participating in the modulation of the ovarian tissue remodeling microenvironment. In contrast, MSTRG.15154.3 cis-regulates ERBB4 to modulate the granulosa cell proliferation and differentiation process. The specifically highly expressed MSTRG.2677.1 in Hu Sheep may be involved in maintaining ovarian stromal cell homeostasis through trans-regulation of HGF and BRINP3, MSTRG.27015.1 and MSTRG.60286.1 target MAPK8IP3 and PPP3CB respectively, suggesting their potential roles in cell cycle regulation and oocyte maturation. These findings provide important molecular mechanisms and potential regulatory targets for improving reproductive performance in sheep.
Keywords: Pishan red sheep, Hu sheep, Ovary, Transcriptome, Reproductive performance
Received: 19 Apr 2025; Accepted: 01 Sep 2025.
Copyright: © 2025 Muhetaer, Gong, Ye, Kuxitaer, Zhu, Li, Du and Sulaiman. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Yiming Sulaiman, Xinjiang Agricultural University, Ürümqi, 830052, Xinjiang Uyghur Region, China
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