Integrative analysis of transcriptomic data related to the liver of laying hens: from physiological basics to newly identified functions

Genome-wide variation study and inter-tissue communication analysis unveil regulatory mechanisms of egg-laying performance in chickens

Egg-laying performance is of great economic importance in poultry, but the underlying genetic mechanisms are still elusive. In this work, we conduct a multi-omics and multi-tissue integrative study in hens with distinct egg production, to detect the hub candidate genes and construct hub molecular networks contributing to egg-laying phenotypic differences. We identifiy three hub candidate genes as egg-laying facilitators: TFPI2, which promotes the GnRH secretion in hypothalamic neuron cells; CAMK2D, which promotes the FSHβ and LHβ secretion in pituitary cells; and OSTN, which promotes granulosa cell proliferation and the synthesis of sex steroid hormones. We reveal key endocrine factors involving egg production by inter-tissue crosstalk analysis, and demonstrate that both a hepatokine, APOA4, and an adipokine, ANGPTL2, could increase egg production by inter-tissue communication with hypothalamic-pituitary-ovarian axis. Together, These results reveal the molecular mechanisms of multi-tissue coordinative regulation of chicken egg-laying performance and provide key insights to avian reproductive regulation.

Supplemental effect of Pediococcus acidilactici CNCM I-4622 probiotic on the laying characteristics and calcium and phosphorus metabolism in laying hens

The close link between intestinal microbiota and bone health ('gut-bone' axis) has recently been revealed: the modulation of the amount and nature of bacteria present in the intestinal tract has an impact on bone health and calcium (Ca) metabolism. Probiotics are known to favorably impact the intestinal microbiota. The objective of this study was to investigate the effect of Pediococcus acidilactici CNCM I-4622 (PA) on laying performance, egg/eggshell quality, Ca metabolism and bone mineralization and resistance in relatively old layers (50 wks old at the beginning of the experiment) during 14 weeks. 480 Hy Line brown layers were divided into 2 groups (CON and PA: 3 layers/rep, 80 rep/group) and fed with a diet formulated to be suboptimal in calcium (Ca) and phosphorus (P) (- 10% of the requirements). The total egg weight was improved by 1.1% overall with PA, related to an improvement of the weight of marketable eggs (+ 0.9%). PA induced a decreased % of downgraded eggs, mainly broken eggs (- 0.4 pts) and FCR improvement (- 0.8% for all eggs, - 0.9% for marketable eggs). PA also led to higher Haugh units (HU: + 7.4%). PA tended to decrease crypt depth after the 14 weeks of supplementation period in the jejunum (- 25.2%) and ileum (- 17.6%). As a consequence, the VH/CD ratio appeared increased by PA at the end of the trial in the jejunum (+ 63.0%) and ileum (+ 48.0%). Ca and P retention were increased by 4 pts following PA supplementation, translating into increased bone hardness (+ 19%), bone cohesiveness (+ 43%) and bone Ca & P (+ 1 pt) for PA-supplemented layers. Blood Ca and P were respectively improved by 5% and 12% with PA. In addition, blood calcitriol and osteocalcin concentrations were respectively improved by + 83% and + 3% in PA group at the end of the trial, compared to CON group. There was no difference between the 2 groups for ALP (alkaline phosphatase) and PTH (parathyroid hormone). PA significantly decreased the expression of the following genes: occludin in the small intestine, calbindin 1 in the ovarian tissue and actin B in the bone. PA therefore improved zootechnical performance of these relatively old layers, and egg quality. The parallel increase in Ca and P in the blood and in the bone following PA supplementation suggests an improvement of the mineral supply for eggshell formation without impacting bone integrity, and even increasing bone resistance.

Positive effects of rutin on egg quality, lipid peroxidation and metabolism in post-peak laying hens

Excessive fat deposition due to impaired fat metabolism in chickens is a major problem in the poultry industry. Nutritional interventions are effective solutions, but current options are limited. A safe phytochemical, rutin, has shown positive effects in animals, but its effect on lipid metabolism in poultry remains unknown. Hence, this study is to investigate the effects of rutin on egg quality, serum biochemistry, fat deposition, lipid peroxidation and hepatic lipid metabolism in post-peak laying hens. A total of 360 Taihang laying hens (49-week-old) were randomly divided into five groups and fed a basal diet (control group, 0%) and a basal diet supplemented with 300 (0.03%), 600 (0.06%), 900 (0.09%), and 1,200 (0.12%) mg rutin/kg feed, respectively. The results showed that eggshell strength was significantly (p < 0.05) higher in the dietary rutin groups, whereas yolk percentage (p < 0.05), total cholesterol (TC) (p < 0.01) and yolk fat ratio (p < 0.01) decreased linearly (p < 0.05) in the dietary rutin groups. Importantly, dietary rutin reduced serum triglyceride (TG) and TC levels, decreased abdominal lipid deposition and liver index (p < 0.05), and which concomitantly decreased hepatic lipid (TG, TC, and free fatty acid) accumulation (p < 0.05). An increase (p < 0.05) in total antioxidant capacity and superoxide dismutase activity and a decrease (p < 0.05) in malondialdehyde levels were also found. At the same time, the activities of hepatic lipase, acetyl-CoA carboxylase and malic enzyme in the liver were decreased (p < 0.05). Dietary rutin also increased (p < 0.05) the expression of fatty acid oxidation-related genes (carnitine palmitoyl transferase 1, peroxisome proliferator-activated receptor α, farnesoid X receptor). Additionally, it decreased fatty acid synthesis genes (sterol regulatory element binding protein-1c, acetyl-CoA carboxylase α, stearoyl-CoA desaturase 1) (p < 0.05). In conclusion, the addition of rutin (0.06-0.12%) to the diet improved the fat metabolism and increased liver antioxidant capacity in post-peak laying hens, and these positive changes improved egg quality to some extent.

Molecular mechanisms of hypothalamic-pituitary-ovarian/thyroid axis regulating age at first egg in geese

Age at first egg (AFE) has consistently garnered interest as a crucial reproductive indicator within poultry production. Previous studies have elucidated the involvement of the hypothalamic-pituitary-ovarian (HPO) and hypothalamic-pituitary-thyroid (HPT) axes in regulating poultry sexual maturity. Concurrently, there was evidence suggesting a potential co-regulatory relationship between these 2 axes. However, as of now, no comprehensive exploration of the key pathways and genes responsible for the crosstalk between the HPO and HPT axes in the regulation of AFE has been reported. In this study, we conducted a comparative analysis of morphological differences and performed transcriptomic analysis on the hypothalamus, pituitary, thyroid, and ovarian stroma between normal laying group (NG) and abnormal laying group (AG). Morphological results showed that the thyroid index difference (D-) value (thyroid index D-value=right thyroid index-left thyroid index) was significantly (P < 0.05) lower in the NG than in the AG, while the ovarian index was significantly (P < 0.01) higher in the NG than in the AG. Furthermore, between NG and AG, we identified 99, 415, 167, and 1182 differentially expressed genes (DEGs) in the hypothalamus, pituitary, thyroid, and ovarian stroma, respectively. Gene ontology (GO) analysis highlighted that DEGs from 4 tissues were predominantly enriched in the "biological processes" category. Additionally, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that 16, 14, 3, and 26 KEGG pathways were significantly enriched (P < 0.05) in the hypothalamus, pituitary, thyroid, and ovarian stroma. The MAPK signaling pathway emerged as the sole enriched pathway across all 4 tissues. Employing an integrated analysis of the protein-protein interaction (PPI) network and correlation analysis, we found GREB1 emerged as a pivotal component within the HPO axis to regulate estrogen-related signaling in the HPT axis, meanwhile, the HPT axis influenced ovarian development by regulating thyroid hormone-related signaling mainly through OPN5. Then, 10 potential candidate genes were identified, namely IGF1, JUN, ERBB4, KDR, PGF, FGFR1, GREB1, OPN5, DIO3, and THRB. These findings establish a foundation for elucidating the physiological and genetic mechanisms by which the HPO and HPT axes co-regulate goose AFE.

Comparative Transcriptome Analysis Provides Novel Insights into the Effect of Lipid Metabolism on Laying of Geese

Simple Summary

The importance of lipid metabolism in the egg production of poultry has been widely reported. Meanwhile, geese have lower egg production and unique lipid metabolism patterns compared with chicken and duck. It is of great significance to further improve egg laying performance to explore the differences of fat metabolism and the molecular mechanisms in geese with different egg laying performance. This study compared the phenotypic differences of liver and abdominal fat, as well as the transcriptome level differences of liver, abdominal fat, and ovarian stroma among high-, low-, and no-egg production groups. The results reveal that lipid metabolism regulated by the circadian rhythm of the liver may directly or indirectly affect ovarian function through the inflammation and hormone secretion of abdominal fat.

Abstract

The lower egg production of geese (20~60 eggs per year) compared with chicken and duck limits the development of the industry, while the yolk weight and fatty liver susceptibility of geese was higher than that of other poultry. Therefore, the relationship between lipid metabolism and the laying performance of geese remains to be explored. Phenotypically, we observed that the liver fat content of the high-, low-, and no-egg production groups decreased in turn, while the abdominal fat weight increased in turn. For transcriptional regulation, the KEGG pathways related to lipid metabolism were enriched in all pairwise comparisons of abdominal fat and liver through functional analysis. However, some KEGG pathways related to inflammation and the circadian rhythm pathway were enriched by DEGs only in abdominal fat and the liver, respectively. The DEGs in ovarian stroma among different groups enriched some KEGG pathways related to ovarian steroidogenesis and cell adhesion. Our research reveals that lipid metabolism regulated by the circadian rhythm of the liver may directly or indirectly affect ovarian function through the inflammation and hormone secretion of abdominal fat. These results offer new insights into the regulation mechanisms of goose reproductive traits.

Hepatic glycerolipid metabolism is critical to the egg laying rate of Guangxi Ma chickens

Yolk formation in liver is an important process for egg production in hens. The correlations between egg laying rate decline and liver function changes in Guangxi Ma chickens remain unclear. In this study, a total of 21,750 genes and 76,288 transcripts were identified in the RNA expression profiles isolated from liver tissues of 5 groups of Guangxi Ma chickens divided according to the age and egg laying rate. Numerous differential genes (DEGs) were identified after pairwise comparison among samples, and time series analysis categorization (age-related factors) revealed that down-regulated DEGs with aging were predominantly involved in lipid transportation and metabolic processes in the low egg laying rate groups. Notably, functional enrichment analysis confirmed that DGAT2, LIPG, PNPLA2, LPL, CEL, LIPC, DGKD, AGPAT2, AGPAT1 and AGPAT3 were highlighted as hub genes in glycerolipid metabolism pathway, which may be an essential non-age related factors of egg laying rate by regulating the synthesis of triacylglycerol (TAG) in liver. Finally, we categorized DEGs in Guangxi Ma chickens with different egg laying rate caused by age-related factors and found that DEGs with different expression patterns performing different biological functions. The analysis of DEGs with lower egg laying rate caused by non-age related factors and showed that the transportation of TAG was suppressed. Furthermore, critical genes and pathways involved in the synthesis of TAG in livers were identified, which dynamically regulated the formation of yolk precursors. Our results expanded the knowledge of the molecular mechanisms of the yolk precursor synthesis in chicken livers. The results will be helpful to explore the factors that affect egg laying rate from the perspective of yolk synthesis and provide a theoretical basis for improving the egg production of Guangxi Ma chickens.

Comparative liver transcriptome analysis of duck reveals potential genes associated with egg production

BACKGROUND

Molecular studies on egg production in ducks were mostly focused on brain and ovaries as they are directly involved in egg production. Liver plays a vital role in cellular lipid metabolism. It also plays a decisive role in reproductive organ development, including yolk generation in laying ducks at sexual maturity. However, the precise molecular mechanism involved in the liver-blood-ovary axis in ducks remains elusive.

METHODS AND RESULTS

In this study, we analysed the liver transcriptome of laying (LA), immature (IM) and broody (BR) ducks using RNA sequencing to understand the role of genes expressed in the liver. The comparative transcriptome analysis revealed 82 DEGs between LA and IM ducks, 47 DEGs between LA and BR ducks and 51 DEGs between IM and BR ducks. GO analysis of DEGs, showed that DEGs were mainly involved in cellular anatomical entity, intracellular, metabolic process, and binding. Furthermore, pathway analysis indicated the important role of Wnt signaling pathway in egg formation and embryo development. Our study showed several candidate genes including vitellogenin-1, vitellogenin-2, riboflavin binding protein, G protein subunit gamma 4, and fatty acid binding protein 3 that are potentially related to egg production in ducks.

CONCLUSIONS

The study provides valuable information on the genes responsible for egg production and thus, pave the way for further investigation on the molecular mechanisms of egg production in duck.

A Comprehensive Proteome and Acetyl-Proteome Atlas Reveals Molecular Mechanisms Adapting to the Physiological Changes From Pre-laying to Peak-Laying Stage in Liver of Hens (Gallus gallus)

Along with sexual maturity, the liver undergoes numerous metabolic processes to adapt the physiological changes associated with egg-laying in hens. However, mechanisms regulating the processes were unclear. In this study, comparative hepatic proteome and acetyl-proteome between pre- and peak-laying hens were performed. The results showed that the upregulated proteins were mainly related to lipid and protein biosynthesis, while the downregulated proteins were mainly involved in pyruvate metabolism and were capable of inhibiting gluconeogenesis and lactate synthesis in peak-laying hens compared with that in pre-laying hens. With unchanged expression level, the significant acetylated proteins were largely functioned on activation of polyunsaturated fatty acid oxidation in peroxisome, while the significant deacetylated proteins were principally used to elevate medium and short fatty acid oxidation in mitochondria and oxidative phosphorylation. Most of the proteins which involved in gluconeogenesis, lipid transport, and detoxification were influenced by both protein expression and acetylation. Taken overall, a novel mechanism wherein an alternate source of acetyl coenzyme A was produced by activation of FA oxidation and pyruvate metabolism to meet the increased energy demand and lipid synthesis in liver of laying hens was uncovered. This study provides new insights into molecular mechanism of adaptation to physiological changes in liver of laying hens.

Age-related changes in liver metabolism and antioxidant capacity of laying hens

This study aimed to investigate the age-related changes of hepatic metabolism and antioxidant capacity of laying hens at 3 different ages. A total of 192 Hy-line Brown laying hens were assigned into 3 groups: 1) 195-day-old (D195 group); 2) 340-day-old (D340 group); 3) 525-day-old (D525 group). Each group replicated 8 times with 8 hens at the same age. Higher activity of aspartate aminotransferase and lower contents of total protein and globulin were observed in the serum of 525-day-old hens in comparison with their 195-day-old counterparts (P < 0.05). The 525-day-old hens accumulated higher contents of total cholesterol and triglyceride in the liver than 195-day-old birds. Additionally, compared with hens from D195 or D340 group, 525-day-old birds exhibited a lower circulating estradiol level (P < 0.05). For antioxidant capacity, birds in the D525 group showed a higher malondialdehyde concentration in both serum and liver as compared with D195 or D340 group (P < 0.05). The 525-day-old hens also exhibited lower glutathione peroxidase activities in both serum and liver when compared with 195-day-old birds (P < 0.05). Simultaneously, there was a decline of hepatic superoxide dismutase activity in the D525 group in comparison with D195 group (P < 0.05). Compared with 195-day-old counterparts, 340-day-old birds upregulated the mRNA abundance of nuclear factor erythroid-2 related factor 2 and glutathione peroxidase 1 in the liver (P < 0.05). In contrast, hens from D525 group showed the downregulation of hepatic nuclear factor erythroid-2 related factor 2, NAD(P)H quinone dehydrogenase 1, and superoxide dismutase 1 when compared with D340 group (P < 0.05). These results indicated that increasing age can adversely affect liver metabolism and function of laying hens.

RNA-sequence reveals differentially expressed genes affecting the crested trait of Wumeng crested chicken

Wumeng crested chicken has a cluster of slender feathers on its head, and the underlying skull region exhibits an obvious tumor-like protrusion. This is the typical skull structure of crested chickens. The associated regulatory genes are located on autosomes and are incompletely dominant. This trait is related to brain herniation, but the genetic mechanisms of its formation and development are unclear. In this study, RNA sequencing (RNA-Seq) analysis was conducted on 6 skull tissue samples from 3 Wumeng crested chickens with prominent skull protrusions and 3 without a prominent skull protrusion phenotype. A total of 46,376,934 to 43,729,046 clean reads were obtained, the percentage of uniquely mapped reads compared with the reference genome was between 89.73%-91.00%, and 39,795,458-41,836,502 unique reads were obtained. Among different genomic regions, the highest frequency of sequencing reads occurred in exon regions (85.44-88.28%). Additionally, a total of 423 new transcripts and 26,999 alternative splicings (AS) events were discovered in this sequencing analysis. This study identified 1,089 differentially expressed genes (DEGs), among which 485 were upregulated and 604 were downregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that the DEGs were enriched in terms related to signal transduction, cell development, cell differentiation, the lysosome, serine, and threonine metabolism, and the interaction of cytokines with cytokine receptors. Based on the comprehensive analysis of DEGs combined with reported quantitative trait loci (QTLs), the expression of BMP2, EPHA3, EPHB1, HOXC6, SCN2B, BMP7, and HOXC10 was verified by real-time quantitative polymerase chain reaction (qRT-PCR). The qRT-PCR results were consistent with the RNA-Seq results, indicating that these 7 genes may be candidates genes regulating the crested trait.

Expression characteristics and regulatory mechanism of Apela gene in liver of chicken (Gallus gallus)

Apela, a novel endogenous peptide ligand for the G-protein-coupled apelin receptor, was first discovered and identified in human embryonic stem cells in 2013. Apela has showed some biological functions in promoting angiogenesis and inducing vasodilatation of mammals by binding apelin receptor, but little is known about its expression characteristics and regulatory mechanism in chicken. In the present study, the coding sequences of Apela in chicken was cloned. The evolution history and potential function of Apela were analyzed. Subsequently, the spatiotemporal expression characteristics of chicken Apela were investigated. Furthermore, the regulatory mechanism of Apela mRNA responsing to estrogen was explored by in vitro and in vivo experiments. The results showed that the length of the CDs of Apela mRNA was 165 bp and encoded a protein consisting of 54 amino acids residues with a transmembrane domain in chicken. The Apela was derived from the same ancestor of Apelin, and abundantly expressed in liver, kidney and pancreas tissues. The expression levels of Apela in the liver of hens were significantly higher at the peak-laying stage than that at the pre-laying stage (p ≤ 0.05). The Apela mRNA levels were significantly up-regulated in primary hepatocytes treated with 17β-estradiol (p ≤ 0.05), and could be effectively inhibited by estrogen receptor antagonists MPP, ICI 182780 and tamoxifen. It indicated that chicken Apela expression was regulated by estrogen via estrogen receptor α (ERα). In individual levels, both the contents of TG, TC and VLDL-c in serum, and the expression of ApoVLDLII and Apela in liver markedly up-regulated by 17β-estradiol induction at 1mg/kg and 2mg/kg concentrations (p ≤ 0.05). This study lays a foundation for further research on Apela involving in hepatic lipid metabolism.

Comparative Analysis of Metabolites in the Liver of Muscovy Ducks at Different Egg-Laying Stages Using Nontargeted Ultra-High-Performance Liquid Chromatography-Electrospray Mass Spectrometry-Based Metabolomics

Liver plays an important physiological function in the synthesis of yolk materials during egg laying in birds. Liver metabolite profiles of Muscovy ducks at different egg-laying stages from the perspective of nontargeted metabolomics were analyzed in this study. Twelve Muscovy ducks were selected at pre-laying (22 weeks, TT group), laying (40 weeks, FT group), and post-laying (60 weeks, ST group) stages, resulting in 36 hepatic metabolite profiles by using ultra-high-performance liquid chromatography-electrospray mass spectrometry. A total of 324 differential metabolites (156 increased and 168 decreased) in FT as compared to the TT (FT/TT) group and 332 differential metabolites (120 increased and 212 decreased) in ST as compared to the FT (ST/FT) group were screened out. Metabolic pathways enriched in FT/TT and ST/FT groups were mainly amino acid metabolism, glycerophospholipid metabolism, nucleotide metabolism, and vitamin metabolism. The amino acid metabolism pathways were upregulated in the FT/TT group and downregulated in the ST/FT group (P < 0.05). The glutathione and ascorbic acid abundances were downregulated, and the choline abundance was upregulated during egg laying (P < 0.05). The liver provides amino acids, lipids, nucleotides, vitamins, and choline, and so on, which are essential materials for yolk precursor synthesis. The decrease in the abundance of glutathione and ascorbic acid indicates that Muscovy ducks might be in a relatively stable physiological state during egg laying.