Abstract Background The compromised performance of laying hens in the late phase of production relative to the peak production was thought to be associated with the impairment of intestinal functionality, which plays essential roles in contributing to their overall health and production performance. In the present study, RNA sequencing was used to investigate differences in the expression profile of intestinal functionality-related genes and associated pathways between laying hens in the late phase and peak phase of production. Results A total of 104 upregulated genes with 190 downregulated genes were identified in the ileum (the distal small intestine) of laying hens in the late phase of production compared to those at peak production. These upregulated genes were found to be enriched in little KEGG pathway, however, the downregulated genes were enriched in the pathways of PPAR signaling pathway, oxidative phosphorylation and glutathione metabolism. Besides, these downregulated genes were mapped to several GO clusters in relation to lipid metabolism, electron transport of respiratory chain, and oxidation resistance. Similarly, there were lower activities of total superoxide dismutase, glutathione S-transferase and Na^+/K^+-ATPase, and reductions of total antioxidant capacity and ATP level, along with an elevation in malondialdehyde content in the ileum of laying hens in the late phase of production as compared with those at peak production. Conclusions The intestine of laying hens in the late phase of production were predominantly characterized by a disorder of lipid metabolism, concurrent with impairments of energy production and antioxidant property. This study uncovers the mechanism underlying differences between the intestinal functionality of laying hens in the late phase and peak phase of production, thereby providing potential targets for the genetic control or dietary modulation of intestinal hypofunction of laying hens in the late phase of production. Keywords: Laying hen, Late phase of production, Intestinal functionality, Transcriptome, Lipid metabolism, Energy generation, Oxidation resistance Background Layer industry is one of the key components contributing to sustainable food sources in the world. The late phase of production (defined as a period in which the egg production is less than 90%), accounts for a large part of the whole cycle of layer production, during which laying hens are known to be characterized by the declined production performance and poor egg quality as compared with those at peak production, resulting in a restricted economic benefit of layer production [[33]1, [34]2]. One crucial reason for the compromises of production performance and egg quality of laying hens in the late phase of production could be the corresponding impairment of intestinal functional state [[35]3, [36]4]. The important roles of intestinal functional state have been increasingly recognized in contributing to the overall health and production performance of poultry [[37]5, [38]6], probably because the intestine possesses a wide variety of different physiological functions such as barrier function, immune defense, lipid metabolism, detoxification and neuroendocrine function [[39]6–[40]9], in addition to serving as the principal site for nutrient absorption. Since there was a deterioration of intestinal functioning such as absorption and barrier dysfunction, immune and defense defects in older animals as compared with young animals [[41]10, [42]11], the laying hens in the late and peak phase of production were speculated to display distinct differences in terms of intestinal functioning. This could be supported by the findings that aged laying hens had a destructed intestinal structure and an increased susceptibility of gut mucosal system to lose its integrity, as well as being more vulnerable to intestinal inflammatory responses relative to the young counterparts [[43]12, [44]13]. It seems that the intestinal hypofunction of laying hens in the late phase of production after having undergone the intensive metabolism at peak production is associated with the aging-related down-regulations of the expression of certain functional molecules in the intestine [[45]14, [46]15], as supported by the finding that the age-related decline in the absorption of nutrients (carbohydrates, lipids and amino acids) was linked to the reduced abundances of their transporters in the intestine of rats [[47]16, [48]17], besides, aging-induced disorder of energy generation in the intestine was responsible by the mitochondrial respiratory chain deficiency, being mediated by the reduced expression of cytochrome c oxidase and succinate dehydrogenase [[49]18]. To date, comprehensive knowledge on the age-related discrepancies of intestinal functions between laying hens at different production stages is poorly understood. And far less is known regarding the differences between the intestinal functions of laying hens in the late phase and peak phase of production at the molecular level. Digital expression profiling using next-generation sequencing promises to reduce or eliminate some weakness of microarrays. As one of the powerful next-generation sequencing techniques, RNA sequencing has expanded knowledge on the extent and complexity of transcriptomes [[50]19]. Application of transcriptomic has been considered as an available method for nutrigenomics and physiological genomics studies in chickens, in order to obtain valuable information about the molecular mechanisms associated with the identification of key genes and pathways for the physiological changes following various treatments [[51]20, [52]21]. In this study, the RNA next-generation sequencing was employed to reveal intestinal differences in transcriptome profiles of laying hens at different laying periods, aiming to identify the important genes and critical pathways associated with the underlying mechanism for differences between the complex intestinal functionality of laying hens in the late phase and peak phase of production, thereby providing potential targets for improving the performance of laying hens in the late phase of production. Results Biochemical indices of the layer intestine The layer intestine from LP group had a reduced (P < 0.05) T-AOC and lower (P < 0.05) activities of T-SOD and GST, along with a higher (P < 0.05) content of MDA as compared with those from PP group (Table [53]1). With regard to the indices associated with energy metabolism, there were reductions (P < 0.05) in Na^+/K^+-ATPase activity and ATP level, concomitant with a decreasing trend (P < 0.10) of the activities of ALP and Ca^2+/Mg^2+-ATPase in the layer intestine of LP group relative to PP group (Table [54]2). Table 1. Comparison of intestinal antioxidant status^1 of laying hens between groups^2 (n = 8) T-SOD (U/mg prot.) GST (U/mg prot.) T-AOC (U/mg prot.) GSH (nmol/mg prot.) MDA (nmol/mg prot.) PP 65.84 ± 10.29^a 106.78 ± 30.97^a 11.80 ± 1.15^a 24.91 ± 8.19 3.33 ± 0.58^b LP 52.99 ± 8.08^b 77.95 ± 20.51^b 8.49 ± 1.18^b 20.69 ± 7.60 4.32 ± 0.74^a P-value 0.015 0.046 < 0.001 0.304 0.010 [55]Open in a new tab ^a,b Values with different superscripts within the same column differ significantly (P < 0.05) ^1 T-SOD total superoxide dismutase, GST glutathione S-transferase, T-AOC total antioxidant capacity, GSH reduced glutathione, MDA malondialdehyde ^2 PP laying hens in the peak phase of production, LP laying hens in the late phase of production Table 2. Comparison of intestinal enzyme^1 activities of laying hens between groups^2 (n = 8) ALP (U/mg prot.) Na^+/K^+- ATPase (U/mg prot.) Ca^2+/Mg^2+- ATPase (U/mg prot.) SDH (U/mg prot.) ATP (μmol/mg prot.) PP 3.45 ± 0.53 1.24 ± 0.32^a 1.19 ± 0.34 12.36 ± 4.82 0.81 ± 0.18^a LP 2.98 ± 0.34 0.89 ± 0.30^b 0.92 ± 0.26 9.99 ± 3.62 0.60 ± 0.18^b P-value 0.074 0.043 0.092 0.285 0.036 [56]Open in a new tab ^a,b Values with different superscripts within the same column differ significantly (P < 0.05) ^1 ALP alkaline phosphatase, SDH succinate dehydrogenase, ATP adenosine triphosphate ^2 PP laying hens in the peak phase of production, LP laying hens in the late phase of production Summary of RNA sequencing data As shown in Table [57]3, RNA-Seq generated more than 40,910,976 raw reads for each library, with an average of 52,873,687 and 49,344,174 paired-end reads for the PP and LP groups, respectively. The GC contents of the libraries were ranged from 49.28 to 50.87%, which were very close to 50%. All the samples had at least 92.04% reads equal to or exceeding Q30. The majority of reads in each library were mapped to the Gallus gallus 5.0 assembly of the chicken genome, and the average mapping rates were 87.79 and 90.87% for PP and LP groups, respectively, which had an average of 84.32 and 87.53%, respectively, of the reads mapped to the chicken genome in an unique manner. Table 3. Characteristics^1 of RNA sequencing reads of the layer intestine (n = 4) Samples^2 GC contents (%) Q30 (%) Total reads Mapped reads Mapping ratio Unique mapping ratio PP1 50.67 92.88 58,014,476 52,888,432 91.16% 87.47% PP2 50.06 92.49 50,793,752 46,281,638 91.12% 87.63% PP 3 50.37 92.89 56,232,772 50,630,631 90.04% 86..52% PP4 50.87 93.19 46,453,748 36,633,802 78.86% 75.66% LP1 49.85 92.35 49,218,916 44,799,521 91.02% 87.79% LP2 49.94 93.40 63,324,840 58,066,099 91.70% 88.36% LP3 49.28 92.04 40,910,976 36,615,172 89.50% 86.26% LP4 50.16 93.35 43,921,962 40,084,927 91.26% 87.70% [58]Open in a new tab ^1GC guanine-cytosine, Q30 the proportion of bases with a Phred quality score greater than 30 ^2PP laying hens in the peak phase of production, LP laying hens in the late phase of production Identification of DGEs between groups There was an obvious difference in gene expression profile of the layer intestine between groups, as revealed by the principal component analysis plot (Additional file [59]1). A total of 294 DGEs were identified in the intestine between groups, including 104 upregulated and 190 downregulated genes in LP group relative to PP group (Fig. [60]1a). Volcano plot visualized the difference in the expression profile of intestinal genes in these two groups (Fig. [61]1b). To confirm the accuracy of RNA sequencing data, we randomly selected 12 genes including 3 upregulated genes (GYS2, INSR and Claudin-2) and 9 downregulated genes (SOD3, FABP1, FABP2, LPL, APOA1, TXN, NDUFS6, GSTM2 and GSTA3). The expression levels of these genes were quantified using RT-PCR, and the results were consistent with the findings obtained by RNA-Seq (Fig. [62]2), suggesting that the RNA sequencing reliably identified differentially expressed mRNAs in the ileal transcriptome. Fig. 1. [63]Fig. 1 [64]Open in a new tab The differentially expressed genes (a) and their visualization by volcano plot (b) of the layer intestine in LP group relative to PP group (n = 4). LP, laying hens in the late phase of production; PP, laying hens in the peak phase of production Fig. 2. [65]Fig. 2 [66]Open in a new tab Validation of the differentially expressed genes (DEGs) by RT-PCR (n = 8). a Comparison (fold change) of the RNA-Seq data of LP group relative to PP group. b Individual variability of validated DGEs in RT-PCR between the PP and LP groups. LP, laying hens in the late phase of production; PP, laying hens in the peak phase of production. Values are means and standard deviations represented by vertical bars. Significance of RT-PCR data was set at P < 0.05, while significance of RNA-seq data was set at false discovery rate (FDR) < 0.05 Functional annotation of DGEs between groups To obtain valuable information for functional prediction of DEGs, searches were made on standard unigenes in the COG and GO databases. The DEGs between groups were functionally distributed into 21 COG categories (Additional file [67]2). Thereinto, the greatest number of DEGs were assigned to the category of general function prediction only (25.6%), followed by the category of lipid transport and metabolism (9.6%), posttranslational modification, protein turnover, chaperones (8.8%), inorganic ion transport and metabolism (7.2%). When mapped to the GO database, the DEGs were distributed into three major functional categories including biological progress, cellular component and molecular function (Fig. [68]3). The most abundant terms annotated to the DEGs in the category of biological progress were cellular process, single-organism process, and metabolic process. While the most abundant terms among the category of cellular component were cell, cell part, and organelle. Within the category of molecular function, the majority of DEGs were assigned to the subcategories of binding and catalytic activity. Fig. 3. [69]Fig. 3 [70]Open in a new tab Gene oncology (GO) classification of differentially expressed genes in the layer intestine between groups (n = 4) Pathway enrichment analysis of DEGs between groups The upregulated genes in LP group relative to PP group were found to confer little association (Q > 0.05) with any KEGG pathway except for tending to be enriched (Q < 0.10) in the pathway of SNARE interactions in vesicular transport (Table [71]4). Comparatively, the downregulated genes in LP group relative to PP group were enriched (Q < 0.05) in the pathways of peroxisome proliferator-activated receptor (PPAR) signaling pathway (rich factor (RF) = 11.7), oxidative phosphorylation (RF = 8.3), and glutathione metabolism (RF = 13.2) (Table [72]5). In addition, these downregulated genes were tended to be enriched (Q < 0.10) in the pathways of drug metabolism-cytochrome P450 (RF = 13.1), metabolism of xenobiotics by cytochrome P450 (RF = 12.4), and glycine, serine and threonine metabolism (RF = 11.8). Table 4. Pathway analysis (top ten) of upregulated genes of the intestine of laying hens in LP group relative to PP group^1 (n = 4) Pathway name Ko_ID Richment _factor P-value Q-value SNARE interactions in vesicular transport ko04130 19.0 0.005 0.090 Starch and sucrose metabolism ko00500 13.6 0.009 0.175 Cardiac muscle contraction ko04260 9.1 0.002 0.374 Focal adhesion ko04510 4.2 0.032 0.617 ECM-receptor interaction ko04512 6.8 0.034 0.648 Mismatch repair ko03430 15.1 0.064 1 Cell adhesion molecules ko04514 4.6 0.068 1 Adrenergic signaling in cardiomyocytes ko04261 4.5 0.071 1 Hedgehog signaling pathway ko04340 7.4 0.127 1 Gap junction ko04540 3.3 0.267 1 [73]Open in a new tab ^1PP laying hens in the peak phase of production, LP laying hens in the late phase of production Table 5. Pathway analysis (top ten) of downregulated genes of the intestine of laying hens in LP group relative to PP group^1 (n = 4) Pathway name Ko_ID Richment _factor P-value Q-value PPAR signaling pathway ko03320 11.7 < 0.001 0.002 Oxidative phosphorylation ko00190 8.3 < 0.001 0.003 Glutathione metabolism ko00480 13.2 < 0.001 0.009 Drug metabolism - cytochrome P450 ko00982 13.1 0.001 0.059 Metabolism of xenobiotics by cytochrome P450 ko00980 12.4 0.002 0.068 Glycine, serine and threonine metabolism ko00260 11.8 0.002 0.079 Carbon metabolism ko01200 5.5 0.006 0.222 Glyoxylate and dicarboxylate metabolism ko00630 10.7 0.015 0.583 Renal cell carcinoma ko05211 53.7 0.018 0.740 Circadian rhythm ko04710 40.3 0.025 0.984 [74]Open in a new tab ^1PP laying hens in the peak phase of production, LP laying hens in the late phase of production In the PPAR signaling pathway, fatty acid-binding protein 1 (FABP1|FC = 0.38), FABP2 (FC = 0.49), FABP3 (FC = 0.41), FABP5 (FC = 0.69), FABP6 (FC = 0.58), lipoprotein lipase (LPL|FC = 0.56), apolipoprotein A1 (APOA1|FC = 0.56), sterol carrier protein 2 (SCP2|FC = 0.75) and perilipin-1 (PLIN1|FC = 0.59) were lower expressed in LP group relative to PP group (Table [75]6). While the downregulated genes in LP group that mapped to the pathway of oxidative phosphorylation were identified as following: NADH dehydrogenase (ubiquinone) Fe-S protein 6 (NDUFS6|FC = 0.76), NADH dehydrogenase (ubiquinone) 1 alpha subcomplex subunit 1 (NDUFA1|FC = 0.66), NDUFA8 (FC = 0.74), NDUFB2 (FC = 0.69), NDUFB9 (FC = 0.76), ubiquinol-cytochrome c reductase subunit 9 (UQCR9|FC = 0.65), ATP synthase subunit d (ATP5H|FC = 0.72), ATP synthase subunit e (ATP5I|FC = 0.68), ATP synthase subunit f (ATP5J|FC = 0.69), ATP synthase subunit g (ATP5L|FC = 0.66), and V-type proton ATPase subunit G 1 (ATP6V1G1|FC = 0.76). The downregulated genes in LP group that implicated in the pathway of glutathione metabolism were glutathione S-transferase (GST) omega-1 (GSTO1|FC = 0.73), GST mu 2 (GSTM2|FC = 0.59), GST alpha 3 (GSTA3|FC = 0.69) and ornithine decarboxylase 1 (ODC1|FC = 0.68). Remarkably, the downregulated expression of GSTO1, GSTM2 and GSTA3 in LP group also mediated the decreasing trend of the pathways of drug metabolism-cytochrome P450 and metabolism of xenobiotics by cytochrome P450. Table 6. The differentially expressed genes^1 (|fold change| > 1.3 at a false discovery rate < 0.05) that mapped to the enriched pathways (n = 4) KEGG pathways Pathway_ID Differentially expressed genes (Fold change) PPAR signaling pathway ko03320 FABP1 (0.38), FABP2 (0.49), FABP3 (0.41), FABP5 (0.69), FABP6 (0.58), LPL (0.56), APOA1 (0.56), SCP2 (0.75), PLIN1 (0.59) Oxidative phosphorylation ko00190 NDUFS6 (0.76), NDUFA1 (0.66), NDUFA8 (0.74), NDUFB2 (0.69), NDUFB9 (0.76), UQCR9 (0.65), ATP5H (0.72), ATP5I (0.68), ATP5J (0.69), ATP5L (0.66), ATP6V1G1 (0.76) Glutathione metabolism ko00480 GSTA3 (0.69), GSTM2 (0.59), GSTO1 (0.73), ODC1 (0.68) Drug metabolism-cytochrome P450 ko00982 GSTA3 (0.69), GSTM2 (0.59), GSTO1 (0.73) Metabolism of xenobiotics by cytochrome P450 ko00980 GSTA3 (0.69), GSTM2 (0.59), GSTO1 (0.73) Glycine, serine and threonine metabolism ko00260 LOC418544 (0.55), GLDC (0.51), LOC107051323 (0.51) [76]Open in a new tab ^1FABP fatty acid-binding protein, LPL lipoprotein lipase, APOA apolipoprotein A, SCP sterol carrier protein, PLIN perilipin, NDUFS NADH dehydrogenase (ubiquinone) Fe-S protein, NDUFA NADH dehydrogenase (ubiquinone) 1 alpha subcomplex subunit, NDUFB NADH dehydrogenase (ubiquinone) 1 beta subcomplex subunit, UQCR ubiquinol-cytochrome c reductase subunit, ATP5H ATP synthase subunit d, ATP5I ATP synthase subunit e, ATP5J ATP synthase subunit f, ATP5L ATP synthase subunit g, ATP6V1G V-type proton ATPase subunit G, GSTA3 glutathione S-transferase alpha 3, GSTM2 glutathione S-transferase mu 2, GSTO1 glutathione S-transferase omega-1, ODC1 ornithine decarboxylase 1, LOC418544 cystathionine beta-synthase-like isoform, GLDC glycine dehydrogenase, LOC107051323 glycine hydroxymethyltransferase GO clustering analysis of DEGs related to lipid metabolism, energy production and oxidation resistance Since pathway analysis revealed that DEGs were predominantly enriched in the pathways of PPAR signaling pathway, oxidative phosphorylation and glutathione metabolism, the DEGs were subjected to deep-level GO clustering analysis in relation to lipid metabolism, energy generation and oxidation resistance, in order to better understand the network that responsible for the difference between groups. As shown in Table [77]7, there were reductions (Q < 0.05) of the clusters of transport, regulation of intestinal cholesterol absorption, phospholipid efflux, positive regulation of cholesterol esterification, reverse cholesterol transport, ATP synthesis coupled proton transport, hydrogen peroxide catabolic process, and removal of superoxide radicals within the category of biological process in LP group as compared to PP group. In terms of the category of cellular component, the layer intestines from LP group had less (Q < 0.05) clusters of very-low density lipoprotein particle and mitochondrial proton-transporting ATP synthase complex than those from PP group. Within the category of molecular function, we detected downregulated (Q < 0.05) clusters of lipid binding, transporter activity, phosphatidylcholine-sterol O-acyltransferase activator activity, cholesterol transporter activity, hydrogen ion transmembrane transporter activity, glutathione transferase activity, and antioxidant activity in LP group as compared with PP group. Table 7. Gene oncology (GO) clustering analysis of differentially expressed genes^1 (|fold change| > 1.3 at a false discovery rate < 0.05) in relation to lipid metabolism, energy production and oxidation resistance (n = 4) GO terms GO_ID Differentially expressed genes (fold change) P-value Q-value Biological Process  Transport GO:0006810 FABP6 (0.58) 0.010 0.010  Regulation of intestinal cholesterol absorption GO:0030300 APOA1 (0.56), APOA4 (0.52) < 0.001 0.004  ATP synthesis coupled proton transport GO:0015986 ATP5H (0.72), ATP5I (0.68), ATP5L (0.66) < 0.001 0.006  Phospholipid efflux GO:0033700 APOA1 (0.56), APOA4 (0.52) < 0.001 0.011  Positive regulation of cholesterol esterification GO:0010873 APOA1 (0.56), APOA4 (0.52) < 0.001 0.021  Hydrogen peroxide catabolic process GO:0042744 PRDX1 (0.74), APOA4 (0.52) < 0.001 0.035  Reverse cholesterol transport GO:0043691 APOA1 (0.56), APOA4 (0.52) < 0.001 0.035  Removal of superoxide radicals GO:0019430 PRDX1 (0.74), APOA4 (0.52) < 0.001 0.047 Cellular Component  Mitochondrial proton-transporting ATP synthase complex GO:0000276 ATP5H (0.72), ATP5I (0.68), ATP5L (0.66) < 0.001 < 0.001  Very-low density lipoprotein particle GO:0034361 APOA1 (0.56), APOA4 (0.52) 0.001 0.035 Molecular Function  Lipid binding GO:0008289 FABP1 (0.38), FABP2 (0.49), FABP3 (0.41) 0.004 0.009  Transporter activity GO:0005215 FABP6 (0.58) 0.008 0.008  Antioxidant activity GO:0016209 APOA4 (0.52), FABP1 (0.38) 0.001 0.008  Phosphatidylcholine-sterol O-acyltransferase activator activity GO:0060228 APOA1 (0.56), APOA4 (0.52) < 0.001 0.002  Glutathione transferase activity GO:0004364 GSTA3 (0.69), GSTM2 (0.59), GSTO1 (0.73) < 0.001 0.005  Hydrogen ion transmembrane transporter activity GO:0015078 ATP5H (0.72), ATP5I (0.68), ATP5L (0.66) < 0.001 0.007  Cholesterol transporter activity GO:0017127 APOA1 (0.56), APOA4 (0.52) < 0.001 0.027 [78]Open in a new tab ^1FABP fatty acid-binding protein, APOA apolipoprotein A, ATP5H ATP synthase subunit d, ATP5I ATP synthase subunit e, ATP5J ATP synthase subunit f, ATP5L ATP synthase subunit g, PRDX1 peroxiredoxin-1, GSTA3 glutathione S-transferase alpha 3, GSTM2 glutathione S-transferase mu 2, GSTO1 glutathione S-transferase omega-1 Discussion PPAR signaling pathway is a key regulator of metabolism of the intestine [[79]22], which together with the liver are considered as important sites for lipid metabolism [[80]7]. In the present study, the lipid metabolism-related genes such as FABP1, FABP2, FABP3, FABP5, FABP6, LPL and APOA1 that mapped to PPAR signaling pathway were downregulated in LP group relative to PP group. FABP multigene can code for diversified kinds of FABPs such as liver-type FABP (encoded by FABP1), intestinal-type FABP (encoded by FABP2), heart-type FABP (encoded by FABP3), epidermal-type FABP (encoded by FABP5), and ileal-type FABP (encoded by FABP6) [[81]23]. These proteins display high-affinity binding for fatty acids and other hydrophobic ligands, facilitating the transport of lipids to the specific compartments of cells for storage or oxidation [[82]24]. Although FABPs share a highly conserved structure, each of them has its own sequence and exhibits distinct affinity for ligand preferences [[83]25]. Specifically,