Identification and Characterization of Hypothalamic Alternative Splicing Events and Variants in Ovine Fecundity-Related Genes

Zhang, Zhuangbiao; Tang, Jiao; He, Xiaoyun; Di, Ran; Zhang, Xiaosheng; Zhang, Jinlong; Hu, Wenping

doi:10.3390/ani10112111

Cited by 4 publications

(6 citation statements)

References 56 publications

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“…Combined transcriptomic and proteomic analyses have been widely used to study the mechanisms underlying the development of multiple traits in domestic animals. Our study has revealed a weak positive correlation between the transcriptome and proteome following β-CG induction, which is consistent with previous studies. − These findings suggest post-transcriptional regulation of gene expression in β-CG-induced intestinal damage in piglets. In addition, six genes/proteins in the DEGs and DEPs overlapped, including VAT1L, PSAT1, SCD, VDR, PRND, and AHSP.…”

Section: Discussionsupporting

confidence: 92%

Integrated Transcriptome and Proteome Analyses of β-Conglycinin-Induced Intestinal Damage in Piglets

Li,

Zheng,

Yin

et al. 2024

J. Agric. Food Chem.

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β-conglycinin (β-CG) induces intestinal damage in piglets; however, its regulatory mechanisms are not fully understood. This study aimed to investigate the molecular mechanisms by which β-CG regulates intestinal injury in piglets through downstream genes and proteins. Our findings revealed that β-CG significantly reduced villus height while increasing the crypt depth. In addition, we analyzed the transcriptome and proteome of jejunum tissues after the β-CG treatment. In total, 382 differentially expressed genes (DEGs) and 292 differentially expressed proteins (DEPs) were identified between the treatment and the control groups. The expression levels of DEGs and DEPs were validated by using quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Western blotting, respectively. The findings revealed a consistent correlation between their expression levels and transcriptomic and proteomic data. In addition, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DEGs and DEPs revealed their enrichment in oxidation-related GOs, as well as in lysosome-related pathways. A protein−protein interaction (PPI) regulatory network was constructed based on the DEPs. The integration of transcriptomic and proteomic analyses identified six genes that were significantly different at both the transcript and the protein levels. This study provides valuable insights into the molecular mechanisms underlying β-CG-induced intestinal injury in piglets.

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Section: Discussionsupporting

confidence: 92%

Integrated Transcriptome and Proteome Analyses of β-Conglycinin-Induced Intestinal Damage in Piglets

Li,

Zheng,

Yin

et al. 2024

J. Agric. Food Chem.

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“…Melatonin secretion is closely related to oestrous in sheep, and the EEF2 gene induces melatonin secretion from the pituitary gland to participate in the oestrous of sheep [ 69 ]. Zhang et al found that the relative expression of the ASPA gene in the hypothalamus changed significantly during oestrous and was associated with litter size in sheep [ 70 ]. During domestication, several genes associated with the physical characteristics of sheep were artificially selected in a targeted manner.…”

Section: Discussionmentioning

confidence: 99%

Identification of copy number variation in Tibetan sheep using whole genome resequencing reveals evidence of genomic selection

Shi,

Li,

et al. 2023

BMC Genomics

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Background Copy number variation (CNV) is an important source of structural variation in the mammalian genome. CNV assays present a new method to explore the genomic diversity of environmental adaptations in animals and plants and genes associated with complex traits. In this study, the genome-wide CNV distribution characteristics of 20 Tibetan sheep from two breeds (10 Oula sheep and 10 Panou sheep) were analysed using whole-genome resequencing to investigate the variation in the genomic structure of Tibetan sheep during breeding. Results CNVs were detected using CNVnator, and the overlapping regions of CNVs between individual sheep were combined. Among them, a total of 60,429 CNV events were detected between the indigenous sheep breed (Oula) and the synthetic sheep breed (Panou). After merging the overlapping CNVs, 4927 CNV regions (CNVRs) were finally obtained. Of these, 4559 CNVRs were shared by two breeds, and there were 368 differential CNVRs. Deletion events have a higher percentage of occurrences than duplication events. Functional enrichment analysis showed that the shared CNVRs were significantly enriched in 163 GO terms and 62 KEGG pathways, which were mainly associated with organ development, neural regulation, immune regulation, digestion and metabolism. In addition, 140 QTLs overlapped with some of the CNVRs at more than 1 kb, such as average daily gain QTL, body weight QTL, and total lambs born QTL. Many of the CNV-overlapping genes such as PPP3CA, SSTR1 and FASN, overlap with the average daily weight gain and carcass weight QTL regions. Moreover, VST analysis showed that XIRP2, ABCB1, CA1, ASPA and EEF2 differed significantly between the synthetic breed and local sheep breed. The duplication of the ABCB1 gene may be closely related to adaptation to the plateau environment in Panou sheep, which deserves further study. Additionally, cluster analysis, based on all individuals, showed that the CNV clustering could be divided into two origins, indicating that some Tibetan sheep CNVs are likely to arise independently in different populations and contribute to population differences. Conclusions Collectively, we demonstrated the genome-wide distribution characteristics of CNVs in Panou sheep by whole genome resequencing. The results provides a valuable genetic variation resource and help to understand the genetic characteristics of Tibetan sheep. This study also provides useful information for the improvement and breeding of Tibetan sheep in the future.

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“…All selected ewes were bred in Tianjin (117.2 E, 39.13 N) with full consideration of animal welfare. Experimental animals were treated with vaginal sponges (InterAg Co., Ltd., New Zealand) (progesterone 300 mg, placed twelve days), and the removal time was set as 0 h. Refer to previous research, six ewes (three polytocous sheep and three monotocous sheep) were euthanized at 48 h (follicular phase), and six ewes (three polytocous sheep and three monotocous sheep) at 216 h (luteal phase) [78,79]. After euthanasia, pituitary samples were collected and preserved as soon as possible for subsequent analysis.…”

Section: Ethical Consideration and Samples Collectionmentioning

confidence: 99%

Key mRNAs and lncRNAs of pituitary that affect the reproduction of FecB + + small tail han sheep

Yang,

Tang,

et al. 2024

BMC Genomics

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Background The pituitary directly regulates the reproductive process through follicle-stimulating hormone (FSH) and luteinizing hormone (LH). Transcriptomic research on the pituitaries of ewes with different FecB (fecundity Booroola) genotypes has shown that some key genes and lncRNAs play an important role in pituitary function and sheep fecundity. Our previous study found that ewes with FecB + + genotypes (without FecB mutation) still had individuals with more than one offspring per birth. It is hoped to analyze this phenomenon from the perspective of the pituitary transcriptome. Results The 12 Small Tail Han Sheep were equally divided into polytocous sheep in the follicular phase (PF), polytocous sheep in the luteal phase (PL), monotocous sheep in the follicular phase (MF), and monotocous sheep in the luteal phase (ML). Pituitary tissues were collected after estrus synchronous treatment for transcriptomic analysis. A total of 384 differentially expressed genes (DEGs) (182 in PF vs. MF and 202 in PL vs. ML) and 844 differentially expressed lncRNAs (DELs) (427 in PF vs. MF and 417 in PL vs. ML) were obtained from the polytocous-monotocous comparison groups in the two phases. Functional enrichment analysis showed that the DEGs in the two phases were enriched in signaling pathways known to play an important role in sheep fecundity, such as calcium ion binding and cAMP signaling pathways. A total of 1322 target relationship pairs (551 pairs in PF vs. MF and 771 pairs in PL vs. ML) were obtained for the target genes prediction of DELs, of which 29 DEL-DEG target relationship pairs (nine pairs in PF vs. MF and twenty pairs in PL vs. ML). In addition, the competing endogenous RNA (ceRNA) networks were constructed to explore the regulatory relationships of DEGs, and some important regulatory relationship pairs were obtained. Conclusion According to the analysis results, we hypothesized that the pituitary first receives steroid hormone signals from the ovary and uterus and that VAV3 (Vav Guanine Nucleotide Exchange Factor 3), GABRG1 (Gamma-Aminobutyric Acid A Receptor, Gamma 1), and FNDC1 (Fibronectin Type III Domain Containing 1) played an important role in this process. Subsequently, the reproductive process was regulated by gonadotropins, and IGFBP1 (Insulin-like Growth Factor Binding Protein 1) was directly involved in this process, ultimately affecting litter size. In addition, TGIF1 (Transforming Growth Factor-Beta-Induced Factor 1) and TMEFF2 (Transmembrane Protein With EGF Like And Two Follistatin Like Domains 2) compensated for the effect of the FecB mutation and function by acting on TGF-β/SMAD signaling pathway, an important pathway for sheep reproduction. These results provided a reference for understanding the mechanism of multiple births in Small Tail Han Sheep without FecB mutation.

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Identification and Characterization of Hypothalamic Alternative Splicing Events and Variants in Ovine Fecundity-Related Genes

Cited by 4 publications

References 56 publications

Integrated Transcriptome and Proteome Analyses of β-Conglycinin-Induced Intestinal Damage in Piglets

Integrated Transcriptome and Proteome Analyses of β-Conglycinin-Induced Intestinal Damage in Piglets

Identification of copy number variation in Tibetan sheep using whole genome resequencing reveals evidence of genomic selection

Key mRNAs and lncRNAs of pituitary that affect the reproduction of FecB + + small tail han sheep

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