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To delineate the RNA expression profiles involved in liver function during maternal effects in broiler breeders (Fig. 1a,b), high-throughput RNA sequencing generated 185.88 GB of clean data from 23 liver samples, encompassing both maternal and offspring stages, specifically embryos at day 19 of gestation and chicks 21 d post-hatch. Each sample contributed 7.9 GB of clean data, with a Q30 base percentage consistently exceeding 91.71% (Table 1). A total of 19,031 genes were identified across the liver samples. Clean reads were aligned to the reference chicken genome using HISAT, resulting in a mapping success rate between 90.83% and 93.35% (Table 1). The identification of differentially expressed genes (DEGs) was grounded on comparative analyses and their expression levels across the various samples. A comprehensive array of DEGs was identified in the liver tissue (Table 2, Supplementary Fig. S1a). Principal component analysis (PCA) was employed to model the distribution and segregation trends among the maternal, embryonic, and offspring comparison groups, illustrating distinct clustering patterns (Fig. 1c). A Venn diagram further emphasized the shared and unique gene expression alterations occurring across the maternal, embryonic, and offspring stages. When considering these stages as distinct entities, pairwise differential expression analyses revealed that the maternal versus embryonic stages exhibited the highest number of differentially expressed genes, followed by the embryonic versus offspring stages, with the least differential expression observed between the maternal and offspring stages (Fig. 1d, e).
Table 1. RNA-seq read statistics.
Sample name Clean_reads Raw_bases Q20 Q30 GC_content HISAT mapped HISAT Uniquely mapped Breeder1 38362812 11040224580 96.53% 93.16% 51.99% 88.5% 75.78% Breeder2 37847708 10940622840 96.28% 92.59% 56.15% 72.49% 52.58% Breeder3 34672132 9846336276 96.52% 93.10% 51.41% 89.35% 77.37% Breeder4 40482362 11592999936 96.48% 93.04% 51.51% 89.92% 76.84% Breeder5 37196291 10296891108 96.86% 93.68% 49.86% 92.12% 82.17% Breeder6 40958805 12072458664 96.59% 93.12% 59.16% 59.57% 32.85% Breeder7 35709829 10510141572 96.47% 92.96% 56.03% 75.07% 55.02% Breeder8 33669242 9914908752 96.79% 93.69% 51.39% 90.98% 78.82% Embryo1 40485557 11654523972 95.90% 91.83% 52.50% 89.67% 74.26% Embryo2 37432078 11069231292 96.48% 93.04% 51.34% 88.79% 74.68% Embryo3 39065142 11126909556 96.26% 92.59% 51.62% 88.44% 75.25% Embryo4 35508865 10322469360 96.30% 92.65% 51.73% 90.69% 77.44% Embryo5 37076246 10837283688 96.46% 92.94% 52.48% 89.48% 74.28% Embryo6 39932521 11473593264 96.23% 92.53% 51.41% 89.88% 77.24% Embryo7 43619518 12556149732 96.36% 92.82% 51.46% 90.88% 76.31% Embryo8 36859302 10562648292 96.14% 92.44% 53.36% 76.34% 58.07% Offspring1 35823274 10444364028 96.48% 93.12% 50.66% 91.04% 78.7% Offspring2 38678468 11108159496 96.39% 92.82% 53.96% 81.18% 63.04% Offspring3 38105455 11117678544 96.33% 92.70% 55.17% 79.53% 62.3% Offspring4 38509142 11038901832 95.75% 91.71% 51.52% 88.96% 74.73% Offspring5 38362812 11040224580 96.53% 93.16% 51.99% 88.5% 75.78% Offspring6 37847708 10940622840 96.28% 92.59% 56.15% 72.49% 52.58% Offspring7 34672132 9846336276 96.52% 93.10% 51.41% 89.35% 77.37% Table 2. Pairwise comparison of up and downregulated DEGs between maternal, embryo and offspring chickens in liver.
Compare group Down Up Total Liver Maternal-vs-Embryo 1540 4569 6109 Embryo-vs-Offspring 1449 4578 6027 Maternal-vs-Offspring 26 38 64 Differential GO analysis of DEGs in the maternal effect process
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To further elucidate the characteristic DEGs involved in the liver's role during maternal effects, the top 10 DEGs in the maternal-embryo and embryo-offspring comparisons were identified, including IGFBP1, ABI3BP, DIO3, PDK4, IGFALS, IGF1, among others (Tables 3 & 4). In addition, 2,090 differentially expressed long non-coding RNAs (LncRNAs) were detected, each longer than 1,000 nucleotides (Supplementary Table S1). The distribution of DEGs in the liver are visually depicted in the volcano plots (Fig. 2a).
Table 3. Maternal-vs-embryo Top 10 DEGs.
Gene Log2FC p−value Regulation IGFBP1 −3.4921 < 0.0001 down ABI3BP −4.4975 < 0.0001 down MT3 −4.7465 < 0.0001 down DIO3 −4.8438 < 0.0001 down CHRNA7 −5.4058 < 0.0001 down TTLL2 −5.4702 < 0.0001 down NEGR1 −6.8204 < 0.0001 down SREBF2 −2.9490 6.11E-303 down PDK4 −2.8915 3.08E-300 down IRF1 −3.0829 4.15E-299 down IGFBP1, Insulin-like Growth Factor Binding Protein 1; ABI3BP, ABI Family Member 3 Binding Protein; MT3, Metallothionein 3; DIO3, Deiodinase Iodothyronine Type III; CHRNA7, Cholinergic Receptor Nicotinic Alpha 7 Subunit; TTLL2, Tubulin Tyrosine Ligase Like 2; NEGR1, Neuronal Growth Regulator 1; SREBF2, Sterol Regulatory Element Binding Transcription Factor 2; PDK4, Pyruvate Dehydrogenase Kinase 4; IRF1, Interferon Regulatory Factor 1. Table 4. Embryo-vs-Offspring Top 10 DEGs.
Gene Log2FC p−value Regulation MT3 5.1899 < 0.0001 up ABI3BP 4.5664 < 0.0001 up IGFBP1 4.1745 < 0.0001 up HMGCR −3.1252 < 0.0001 down IGFALS −3.7697 < 0.0001 down IGFBP4 −3.8229 < 0.0001 down FASN −5.1979 < 0.0001 down IGF1 −6.3826 < 0.0001 down CDKN2B −6.4335 < 0.0001 down ELOVL2 −6.2947 < 0.0001 down MT3, Metallothionein 3; ABI3BP, ABI Family Member 3 Binding Protein; IGFBP1, Insulin-like growth factor-binding protein 1; HMGCR, 3-Hydroxy-3-Methylglutaryl-CoA Reductase; IGFALS, Insulin-like growth factor-binding protein; acid labile subunit; IGFBP4, Insulin-like growth factor-binding protein 4; FASN, Fatty Acid Synthase; IGF1, Insulin-like growth factor 1; CDKN2B, Cyclin Dependent Kinase Inhibitor 2B; ELOVL2,ELOVL Fatty Acid Elongase 2. Figure 2.
GO enrichment analysis of differentially expressed genes (DEGs). (a) Volcano plot, (b) top 10 GO pathways enriched in DEGs between maternal and embryo stages. The cyan color represents GO's Biological Process (BP) pathways, while the yellow color represents GO's Cellular Component (CC) pathways.
Enrichment analysis was also performed to pinpoint key genes and pathways implicated in the maternal effect. The liver undergoes a functional transition from cell development and differentiation during the embryonic stage to glucose and lipid metabolism and immune function by the 21-d post-hatch stage. Gene Ontology (GO) enrichment analysis revealed significant biological pathways, including those related to multicellular organism development, synaptic transmission (GABAergic), adherens junction organization, cholesterol biosynthetic process, unsaturated fatty acid biosynthetic process, immune response, and the B cell receptor signaling pathway (Fig. 2b, Fig. 3a & b).
Figure 3.
GO functional annotation analysis of embryo vs offspring stages. (a) Enriched functions at the GOBP (Gene Ontology Biological Process) level, (b) enriched functions at the GOCC (Gene Ontology Cellular Component) level.
Expression patterns of developmentally related genes across three stages
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Based on the analysis of RNA expression profiles across the three stages, 20 characteristic genes involved in the regulation of cell proliferation and organ development were successfully identified (Fig. 4). Key genes such as IGF1, IGFBP1, IGFBP2, IGFBP4, IGFALS, and HMGCR were significantly upregulated in the liver tissues of both embryos and offspring, with expression levels being particularly higher in the embryonic stage. Additionally, critical genes regulating lipid metabolism, including FASN, ELOVL2, ELOVL5, ELOVL6, SREBF2, ACACA, and CYP7A1 were also found to be significantly upregulated in the liver of both embryos and offspring. A correlation analysis of characteristic target genes (including LncRNAs) across the three stages was conducted to gain deeper insights into the regulatory patterns of maternal effects (Fig. 5, Supplementary Table S2).
Figure 4.
Expression of DEGs in maternal, embryo, and offspring liver tissues. The red and blue squares represent FPKM values, with darker red indicating higher expression levels. Upregulated DEGs are marked in dark yellow, while downregulated DEGs are shown in white.
Figure 5.
Correlation analysis of DEGs in maternal, embryo, and offspring stages. Pink represents negative correlations, while cyan indicates positive correlations.
Time analysis of liver function across three developmental stages
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Time-series analysis was utilized to explore the DEGs across the maternal-embryo-offspring stages, aiming to delineate the dynamic changes in liver mRNA expression profiles influenced by maternal effects (Fig. 6a). By comparing DEGs with a Q value ≤ 0.05 and an absolute log2|fold change| ≥ 1 across the various stages, the DEGs were organized into six distinct clusters, with expression patterns predominantly following 'high-low-high' and 'low-high-low' trends (Fig. 6b).
Figure 6.
Time analysis of liver expression profiles across maternal, embryo, and offspring stages. (a) Workflow diagram of the time analysis. (b) Cluster analysis of DEGs across the three stages, showing six distinct clusters.
In Cluster 1, KEGG pathway enrichment analysis revealed a significant association with the 'Toll-like receptor signaling pathway', where key characteristic genes included TLR2, TLR4, TLR5, MyD88, and NF-κB. The 'Lysosome' pathway was also enriched, with CTSD (Cathepsin D) and LAMP1 (Lysosomal Associated Membrane Protein 1) identified as pivotal genes, alongside the 'C-type lectin receptor signaling pathway'. Furthermore, the Gene Ontology (GO) categories in this cluster were significantly enriched for activities such as GTPase activator activity, actin filament binding, small GTPase binding, and protein tyrosine kinase activity (Fig. 7a−c).
Figure 7.
Analysis of DEGs in the 'high-low-high' expression pattern (Cluster 1). (a) KEGG enrichment analysis of DEGs. (b) GOMF (Gene Ontology Molecular Function) enrichment analysis of DEGs. (c) GOCC (Gene Ontology Cellular Component) enrichment analysis of DEGs.
In Cluster 2, KEGG analysis highlighted enrichment in the 'Neuroactive ligand-receptor interaction' pathway, with GABRA identified as a characteristic gene, as well as in the 'Calcium signaling pathway' and 'ECM-receptor interaction'. GO categories in this cluster were enriched in functions such as 'Calcium ion binding', 'nucleotide binding', 'synapse', 'neuron projection', 'glutamatergic synapse', and 'microtubule cytoskeleton', with TUBB, MAPs, and KIFs identified as key genes (Supplementary Table S3). The remaining four clusters also displayed enrichment in GO categories related to metabolism, development, and immune function, reflecting dynamic processes that occur throughout the maternal-embryo-offspring transition (Fig. 8a−c, Supplementary Fig. S1b).
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This study, by comparing liver gene expression profiles among breeder hens, chicken embryos, and offspring broilers, has highlighted the pivotal role of maternal effects in embryonic development. Significantly differentially expressed genes such as IGFBP1, ABI3BP, and DIO3, were identified which are crucial for glucose metabolism, lipid metabolism, and cytoskeletal reorganization. Time analysis revealed two primary gene expression patterns: 'high-low-high' and 'low-high-low'. The former pattern, associated with immune function, includes genes like LAMP1 and CTSD that are highly expressed in breeder hens and offspring broilers, indicating enhanced immune activity. The latter pattern includes genes such as GABRA and TUBB, which are highly expressed in chicken embryos, supporting neural network formation and cytoskeletal reorganization. In summary, maternal effects influence the expression of key genes in embryonic development through epigenetic regulation. Understanding this mechanism is crucial for improving broiler production performance. Future research should focus on exploring the relationship between maternal nutrition and epigenetics to optimize feeding strategies for breeder hens.
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About this article
Cite this article
Gao M, Chen Y, Fan H, Chen S, Wang H, et al. 2024. Transgenerational effects on the gene transcriptome of chicken liver. Animal Advances 1: e003 doi: 10.48130/animadv-0024-0003
Transgenerational effects on the gene transcriptome of chicken liver
- Received: 16 August 2024
- Revised: 10 September 2024
- Accepted: 27 September 2024
- Published online: 31 October 2024
Abstract: Chickens are important breeding animals and models for biomedical research, particularly due to their oviparous nature, which makes it an ideal subject for studying maternal effects. This study employs RNA-Seq to conduct a comprehensive analysis of the transcriptomics of the poultry liver, with a focus on maternal transgenerational effects. Samples were examined from broiler breeders, E19 embryos, and 21-day-old offspring, identifying 2,753 DEGs. GO analysis revealed significant enrichment of differentially expressed RNAs in functions such as actin filament binding and lysosomal activity. KEGG analysis identified pathways associated with endocytosis and Toll-like receptor signaling, displaying a high-low-high expression pattern across the broiler breeders, embryos, and offspring, which is closely linked to immune function regulation. Conversely, the Neuroactive ligand-receptor interaction and Calcium signaling exhibited a low-high-low expression pattern, which is intimately associated with organogenesis, and embryonic development. Additionally, based on DEGs, genes such as IGF1, IGFBP, FASN, and ELOVL were identified, which are significantly expressed in embryos and are crucial for development and lipid metabolism regulation. In summary, the present research provides a valuable transcriptional regulatory network for studying maternal effects on liver tissue development in broiler breeders, laying a foundation for further exploration of the molecular mechanisms underlying maternal effects.
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Key words:
- RNA-seq /
- Maternal effect /
- Liver /
- Embryo development /
- Broiler breeder