Identification of key genes associated with residual feed intake in small-sized meat ducks through integrated analysis of mRNA and miRNA transcriptomes

As a major producer and consumer of duck meat, China faces industry challenges due to low feed conversion efficiency. Residual feed intake (RFI), a key metric for poultry feed utilization, remains poorly characterized in small-sized meat ducks. We raised 1,000 ducklings with similar initial body weight (BW) under controlled conditions until 63 days of age. RFI was calculated using average daily gain (ADG), average daily feed intake (ADFI), and metabolic body weight (MBW0.75). Thirty high-RFI (HRFI) and thirty low-RFI (LRFI) ducks were selected to evaluate growth performance. Hypothalamic samples from 6 HRFI and 6 LRFI ducks underwent transcriptomic analysis, including differential gene expression, gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway analysis, weighted gene co-expression network analysis, and miRNA target prediction. Results showed that the LRFI group had significantly lower feed intake (FI) and ADFI than the HRFI group (P < 0.05). Compared to low RFI controls, HRFI meat ducks exhibited 45 differentially expressed (DE) miRNAs (6 upregulated and 39 downregulated) and 323 DE mRNAs (133 upregulated and 190 downregulated), enriched in substance and energy metabolism pathways. Weighted gene co-expression network analysis identified ten hub DE miRNAs, including miR-1-3p, miR-10-5p/3p, miR-182-5p/3p, miR-183-5p, miR-263-5p, miR-96-5p, miR-7, and novel-m0108-5p. miRNA-mRNA network analysis revealed 43 DE regulatory pairs, including 15 with negative feedback. Notably, miR-182 targeted and regulated the highest number of DE mRNAs, showing negative feedback interactions with DDC, UPP2, PRSS35, and SLCO1C1. Dual-luciferase reporter assays confirmed the binding of partial genes. Given DDC's role in dopamine and serotonin synthesis, we further validated the miR-182-5p/DDC regulatory relationship through overexpression, interference, and Western blot experiments. This study provides novel insights into the molecular mechanisms underlying feed efficiency in ducks.

Transcriptome analysis reveals key genes and signalling pathways related to residual feed intake in meat-type ducks

The feed utilisation rate is a key factor that affects the economic benefits of meat-type duck breeding. In recent years, residual feed intake (RFI) has been routinely used in poultry breeding as an index for evaluating feed utilisation. However, the genetic mechanism underlying RFI in meat-type ducks remains poorly understood. In the present study, 1 000 meat-type ducks with similar BW were randomly selected to measure BW gain and feed intake from 21 to 42 d of age to assess RFI. Six high- and six low-RFI meat-type ducks were randomly selected for a transcriptome survey of livers. Protein-protein interaction (PPI) network and gene set enrichment (GSEA) analyses were used to elucidate the molecular basis of RFI. We identified 1 297 differentially expressed genes (DEGs) in the LRFI group, of which 686 and 611 were markedly up- and downregulated, respectively. Functional annotation showed that DEGs were mainly enriched in gene ontology terms related to the regulation of biosynthetic and metabolic processes. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed significant enrichment of insulin signalling and multiple pathways related to energy metabolism. Furthermore, the PPI network analysis revealed that PRKACB, PRKAR2A, FYN, PTK2, ITGB1, ESR1, and PIK3CB were primarily related to the biological processes of lipid metabolism, glucose transport, and immunological stress and may affect RFI. Moreover, the GSEA suggested that upregulated genes in the LRFI group were associated with immune, lipid transport, and insulin signalling. ACLY and SLC50A1 were the most markedly upregulated and downregulated DEGs, respectively. In the PPI network, PRKACB, PRKAR2A, and FYN were identified as pivot genes. The aforementioned DEGs were mainly involved in lipid and glucose metabolism and inflammatory response, consistent with the KEGG and GSEA results. Therefore, these results revealed PRKACB, PRKAR2A, and FYN as potentially key genes for improving feed efficiency traits in meat-type ducks. Our results provide insights into the biological basis of RFI in meat-type ducks and will be useful for the selection of meat-type ducks with a greater feed efficiency phenotype in future breeding programmes.

A comprehensive study of liver-gut microbiota and antioxidant enzyme activity mediated regulation of late-laying hens by high and low residual feed intake

Residual feed intake (RFI) is a better indicator of feed efficiency than feed conversion ratio (FCR). It is frequently used to evaluate the efficacy of poultry and livestock feed consumption. Generally, Low RFI (LRFI) is associated with better feed conversion efficiency, whereas high RFI (HRFI) suggests poorer feed conversion efficiency. The study examined the association between microorganisms, tissue and organ functions. The results demonstrated that in contrast to the HRFI group, the LRFI group revealed higher length measurements, the digestive organs' mass, and chest width. The antioxidant indices revealed that the enzymatic activities (catalase and glutathione peroxidase) in the LRFI group were significantly higher than those in the HRFI group. The serum levels of HDLC, AST, and ACTH were identified as potential markers that could affect RFI. The variations between high and low RFI and the function of the liver and cecum microbiota of hens during late laying period were systematically investigated by multiple omics techniques. Through 16S, the most common beneficial microbial population in the gut of LRFI groups, such as Oscillospirales, Ruminococcaceae, and Butyricicoccaceae, has been detected via a microbiome-metabolome association analysis. Through multi-omics analysis, we found that FABP1 and ACSS2 are important regulatory genes affecting RFI. These findings will provide a basis for comprehending the role of gut microbiota in regulating RFI and the molecular mechanism behind the phenotypic changes observed in late-laying hens.

Mechanisms of the effects of turpiniae folium extract on growth performance, immunity, antioxidant activity and intestinal barrier function in LPS-challenged broilers

Turpiniae folium extract (TFE) has shown anti-inflammatory and immunomodulatory effects in broilers. However, its mechanisms remain unclear. The aim of this study is to investigate the underlying mechanisms by which TFE influences growth performance, jejunal morphology, immune function, antioxidant capacity and barrier integrity in broilers challenged with Lipopolysaccharide (LPS). A total of 240 one-day-old female broilers were randomly divided into four groups with six replicates of ten birds each. A 2 × 2 factorial design with TFE (basal diets supplemented with 0 or 500 mg/kg TFE) and LPS challenge (intraperitoneal injection of 1 mg/kg body weight of sterile saline or LPS at 21, 23 and 25 days of age). The trial lasted for 26 days. The results showed that: Prior to the LPS challenge, dietary supplementation with TFE for 21 days increased both average daily gain (ADG) (P = 0.037) and average daily feed intake (ADFI) (P = 0.045) in broilers. During the LPS challenge period, LPS challenge led to a decline in growth performance and a negative impact on intestinal morphology, while TFE supplementation significantly reversed these adverse effects, as evidenced by increases in ADG (P = 0.004), ADFI (P = 0.046), jejunal villus height (VH) (P = 0.035), the villus height to crypt depth ratio (VH/CD) (P = 0.007) and decreases in the feed-to-gain ratio (F/G) (P = 0.025), jejunal crypt depth (CD) (P = 0.049). LPS induced inflammatory responses and oxidative stress in the jejunum, leading to a significant upregulation of pro-inflammatory factor gene and protein expression, and a marked downregulation of anti-inflammatory and antioxidant gene and protein expression. TFE supplementation mitigated these effects by yielding completely opposite results except for the expression of toll-like receptor 4 (TLR4) protein (P = 0.916). LPS negatively regulates the expression of genes and proteins involved in intestinal mucosal barrier function. In contrast, TFE supplementation significantly upregulated the expression of zonula occludens-1 (ZO-1) (P < 0.001) gene and ZO-1 (P < 0.001), occludin (OCLN) (P < 0.001), claudin (CLDN) (P < 0.001) proteins. In conclusion, dietary supplementation with TFE effectively counteracts the intestinal immune and oxidative stress induced by LPS challenge in broilers, improves intestinal mucosal barrier integrity and tissue morphology, and ultimately mitigates the negative impact of LPS on broiler growth performance. This effect may involve the modulation of the Nrf2 and nuclear factor kappa B (NF-κB) signaling pathways.

VANGL2 alleviates inflammatory bowel disease by recruiting the ubiquitin ligase MARCH8 to limit NLRP3 inflammasome activation through OPTN-mediated selective autophagy

Inflammatory bowel disease (IBD) is a chronic and potentially life-threatening inflammatory disease of gastroenteric tissue characterized by episodes of intestinal inflammation, but the underlying mechanisms remain elusive. Here, we explore the role and precise mechanism of Van-Gogh-like 2 (VANGL2) during the pathogenesis of IBD. VANGL2 decreases in IBD patients and dextran sulfate sodium (DSS)-induced colitis in mice. Myeloid VANGL2 deficiency exacerbates the progression of DSS-induced colitis in mice and specifically enhances the activation of NLRP3 inflammasome in macrophages. NLRP3-specific inhibitor MCC950 effectively alleviates DSS-induced colitis in VANGL2 deficient mice. Mechanistically, VANGL2 interacts with NLRP3 and promotes the autophagic degradation of NLRP3 through enhancing the K27-linked polyubiquitination at lysine 823 of NLRP3 by recruiting E3 ligase MARCH8, leading to optineurin (OPTN)-mediated selective autophagy. Notably, decreased VANGL2 in the peripheral blood mononuclear cells from IBD patients results in overt NLRP3 inflammasome activation and sustained inflammation. Taken together, this study demonstrates that VANGL2 acts as a repressor of IBD progression by inhibiting NLRP3 inflammasome activation and provides insights into the crosstalk between inflammation and autophagy in preventing IBD.

Lactiplantibacillus plantarum Ameliorated Morphological Damage and Barrier Dysfunction and Reduced Apoptosis and Ferroptosis in the Jejunum of Oxidatively Stressed Piglets

Oxidative stress induces apoptosis and ferroptosis, leading to intestinal injury of piglets. Lactiplantibacillus plantarum P8 (P8) has antioxidant capacity, but its roles in intestinal apoptosis and ferroptosis remain unclear. Here, 24 weaned piglets were assigned to three treatments: control (Con), diquat injection (DQ), and P8 supplementation + DQ injection (DQ + P8). The results showed that the increased jejunal oxidative stress, jejunal morphology impairment, and barrier dysfunction in the DQ-treated piglets were decreased by P8 supplementation. TUNEL and apoptosis-related gene expressions showed increased jejunal apoptosis of DQ-treated piglets; however, reduced apoptosis was observed in the DQ + P8 group. In addition, the mitochondrial morphology and ferroptosis-related gene expressions indicated elevated jejunal ferroptosis in the DQ-treated piglets, and the DQ + P8 treatment attenuated the ferroptosis. Transcriptome identified various differentially expressed genes (DEGs) between different treatments. KEGG analysis indicated that the DEGs were enriched in the PI3K-AKT, NF-κB, and apoptosis pathways. The expressions of key DEGs and key proteins in the PI3K-AKT and NF-κB pathways were further verified. In summary, our results indicate that P8 supplementation ameliorated jejunal oxidative stress, morphological damage, barrier dysfunction, apoptosis, and ferroptosis in the DQ-treated piglets. Moreover, the beneficial effect of P8 may be related to the regulation of PI3K/AKT and NF-κB pathways.

A multitissue transcriptomic analysis reveals a potential mechanism whereby Brevibacillus laterosporus S62-9 promotes broiler growth

Brevibacillus laterosporus S62-9 has been shown to improve broiler growth performance and immunity. In the present study, we aimed to evaluate the effects of B. laterosporus S62-9 on the immunity and lipid metabolism of broilers by means of transcriptomic analysis. A total of 160 1-day-old broilers were randomly allocated to a S62-9 group, the diet of which was supplemented with 106 CFU/g B. laterosporus S62-9 daily, and a control group, which was not. After 42 d of feeding, the broilers in the S62-9 group had higher body mass (7.2%) and feed conversion ratio (5.19%) than the control group. Supplementation with B. laterosporus S62-9 resulted in lower serum total cholesterol and low-density lipoprotein-cholesterol concentrations and higher high-density lipoprotein-cholesterol concentrations. An analysis of the fatty acid composition of the broiler's thigh muscles revealed that the proportions of the unsaturated fatty acids myristoleic acid (C14:1) and arachidonic acid (C20:1) were higher for birds in the S62-9 group. Transcriptomic analysis also showed an upregulation of immunity-related genes in the S62-9 group. Gene Ontology functional enrichment analysis showed that the mitogen-activated protein kinase pathway was enriched in the liver, the defense response was enriched in the duodenum, and immunoglobulin-related entries were enriched in the jejunum of the S62-9 group. Furthermore, the expression of key genes involved in unsaturated fatty acid synthesis (SCD, encoding stearoyl-CoA desaturase) and fatty acid metabolism (HACD2, encoding 3-hydroxyacyl-CoA dehydratase 2) was upregulated in the liver, and the expression of genes associated with fat biosynthesis and accumulation, such as PLIN1, encoding perilipin 1, and FABP4, encoding fatty acid binding protein 4, was upregulated in the ileum of the birds in the S62-9 group. In summary, supplementation with B. laterosporus S62-9 could improve immune defense and the fatty acid metabolism of broiler chickens, thereby enhancing their disease resistance and promoting growth and development.

The role of α7nAchR and PD-L1 in neuroimmune regulation of keloid treatment

Keloid formation, characterized by aberrant fibroproliferation and immune dysregulation, remains a challenging clinical concern. This study aims to elucidate the neuroimmune mechanisms underlying keloid pathogenesis and explores the efficacy of a combined treatment approach involving modulation of the α7 nicotinic acetylcholine receptor (α7nAchR), a key player in neural transmission, and programmed death ligand 1 (PD-L1), an immune checkpoint molecule, for keloid intervention. A key innovation lies in the identification of signal peptide-CUB-EGF-like domain-containing protein 3 (SCUBE3) as a potential target gene influenced by this dual treatment. We elucidate the underlying mechanism, wherein the hypoxic keloid microenvironment fosters an upsurge in SCUBE3 secretion. Subsequently, SCUBE3 forms complexes with TGF-β, initiating the activation of the PI3K/AKT/NF-κB signaling pathway. Notably, SCUBE3 is secreted in the form of exosomes, thereby exerting a profound influence on the differentiation of T cells and macrophages within the keloid milieu. This research not only provides a comprehensive understanding of the molecular mechanisms involved but also offers a promising avenue for the development of targeted therapies to address keloid-associated fibrosis and immune dysregulation. In conclusion, the combined inhibition of α7nAchR and PD-L1 represents a promising therapeutic strategy with SCUBE3 as a pivotal molecular target in the complex landscape of keloid pathophysiology.

Effects of residual feed intake on the economic traits of fast-growing meat ducks

Feed efficiency (FE) is a crucial economic indicator of meat duck production. The objective of this study was to assess the impact of residual feed intake (RFI), defined as the difference between the actual and expected feed intake based on animal's production and maintenance requirements, on the growth performance (GP), slaughter and internal organ characteristics of fast-growing meat ducks. In total, 1,300 healthy 14-day-old male fast-growing meat ducks were housed in individual cages until slaughter at the age of 35 d. The characteristics of the carcass and internal organs of 30 ducks with the highest RFI (HRFI) and the lowest RFI (LRFI) were respectively determined. RFI, the feed conversion ratio (FCR), and average day feed intake (ADFI) were significantly lower in the LRFI group than the HRFI group (P < 0.001), while there were no significant differences in marketing BW or BW gain (BWG) (P > 0.05). The thigh muscle and lean meat yields were higher, and the abdominal fat content was lower (P < 0.001) in the LRFI group, while there were no significant differences in other carcass traits between the groups (P > 0.05). The liver and gizzard yields were significantly higher (P < 0.001) in the LRFI group, while there were no significant differences (P > 0.05) in intestinal length between the groups. RFI was highly positively correlate with FCR and ADFI (P < 0.01), but negatively correlated the yields of thigh muscle, lean meat, liver, and gizzard, and positively correlated with abdominal fat content. These results indicate that selection for low RFI could improve the FE of fast-growing meat ducks without affecting the marketing BW and BWG, while increasing yields of thigh muscle and lean meat and reducing abdominal fat content. These findings offer useful insights into the biological processes that influence FE of fast-growing meat ducks.

Integrated transcriptome and microbiome analyses of residual feed intake in ducks during high production period

Residual feed intake (RFI) is a crucial parameter for assessing the feeding efficiency of poultry. Minimizing RFI can enhance feed utilization and reduce costs. In this study, 315 healthy female ducks were individually housed in cages. Growth performance was monitored during the high laying period, from 290 to 325 d of age. The cecal transcriptome and microbiome of 12 ducks with high RFI and 12 with low residual feed intake (LRFI) were analyzed. Regarding growth performance, the LRFI group exhibited significantly lower RFI, feed conversion ratio (FCR), and feed intake (Fi) compared to the HRFI group (p < 0.01). However, there were no significant differences observed in body weight (BW), body weight gain (BWG), and egg mass (EML) between the groups (p > 0.05). Microbiome analysis demonstrated that RFI impacted gut microbial abundance, particularly affecting metabolism and disease-related microorganisms such as Romboutsia, Enterococcus, and Megamonas funiformis. Transcriptome analysis revealed that varying RFI changed the expression of genes related to glucose metabolism and lipid metabolism, including APOA1, G6PC1, PCK1, and PLIN1. The integrated analysis indicated that host genes were closely linked to the microbiota and primarily function in lipid metabolism, which may enhance feeding efficiency by influencing metabolism and maintaining gut homeostasis.

Genes involved in the cholecystokinin receptor signaling map were differentially expressed in the jejunum of steers with variation in residual feed intake

The jejunum is a critical site for nutrient digestion and absorption, and variation in its ability to take up nutrients within the jejunum is likely to affect feed efficiency. The purpose of this study was to determine differences in gene expression in the jejunum of beef steers divergent for residual feed intake (RFI) in one cohort of steers (Year 1), and to validate those genes in animals from a second study (Year 2). Steers from Year 1 (n = 16) were selected for high and low RFI. Jejunum mucosal tissue was obtained for RNA-seq. Thirty-two genes were differentially expressed (PFDR≤0.15), and five were over-represented in pathways including inflammatory mediator, cholecystokinin receptor (CCKR) signaling, and p38 MAPK pathways. Several differentially expressed genes (ALOX12, ALPI, FABP6, FABP7, FLT1, GSTA2, MEF2B, PDK4, SPP1, and TTF2) have been previously associated with RFI in other studies. Real-time qPCR was used to validate nine differentially expressed genes in the Year 1 steers used for RNA-seq, and in the Year 2 validation cohort. Six genes were validated as differentially expressed (P < 0.1) using RT-qPCR in the Year 1 population. In the Year 2 population, five genes displayed the same direction of expression as the Year 1 population and 3 were differentially expressed (P < 0.1). The CCKR pathway is involved in digestion, appetite control, and regulation of body weight making it a compelling candidate for feed efficiency in cattle, and the validation of these genes in a second population of cattle is suggestive of a role in feed efficiency.

Bacillus amyloliquefaciens attenuates the intestinal permeability, oxidative stress and endoplasmic reticulum stress: transcriptome and microbiome analyses in weaned piglets

Endoplasmic reticulum (ER) stress is related to oxidative stress (OS) and leads to intestinal injury. Bacillus amyloliquefaciens SC06 (SC06) can regulate OS, but its roles in intestinal ER stress remains unclear. Using a 2 × 2 factorial design, 32 weaned piglets were treated by two SC06 levels (0 or 1 × 108 CFU/g), either with or without diquat (DQ) injection. We found that SC06 increased growth performance, decreased ileal permeability, OS and ER stress in DQ-treated piglets. Transcriptome showed that differentially expressed genes (DEGs) induced by DQ were enriched in NF-κB signaling pathway. DEGs between DQ- and SC06 + DQ-treated piglets were enriched in glutathione metabolism pathway. Ileal microbiome revealed that the SC06 + DQ treatment decreased Clostridium and increased Actinobacillus. Correlations were found between microbiota and ER stress genes. In conclusion, dietary SC06 supplementation increased the performance, decreased the permeability, OS and ER stress in weaned piglets by regulating ileal genes and microbiota.

RNA-seq transcriptome analysis provides new insights into the negative effects of tannic acid on the intestinal function of Brandt's voles (Lasiopodomys brandtii)

Tannic acid (TA), a significant plant secondary metabolite, is contained in the daily food of Brandt's voles. Its adverse effect on gut function has been shown in earlier research, but the underlying molecular mechanisms remain uncertain. In this study, male Brandt's vole (13 weeks old) were divided into two groups and given 0 (control) or 1,200 (TA-treated) mg•kg-1 TA for 18 days. Then RNA sequencing was used to conduct a thorough transcriptome analysis on the duodenum, jejunum, and ileum of Brandt's voles. Results showed that TA significantly increased serum total cholesterol concentration (P < 0.05) and decreased the nutrient digestibility (P < 0.05) of Brandt's voles. Furthermore, there were 174 differentially expressed genes (DEGs) in the duodenum, 96 DEGs in the jejunum, and 88 DEGs in the ileum between the control and TA-treated groups. Enrichment analysis revealed that many genes associated with bile secretion, fat digestion and absorption, innate immune response, and tight junction such as ABCG2, ABCG8, PEAK1, and IFR2, etc. were altered after TA treatment, which were verified by quantitative real-time PCR. These findings suggested that TA can change the expression of intestinal genes, thereby, altering nutrition metabolism and immunological function, eventually hindering the growth of Brandt's voles. The results of this study provide a theoretical basis for explaining how TA affects the gut function of Brandt's voles at the molecular level.

Heat stress exposure cause alterations in intestinal microbiota, transcriptome, and metabolome of broilers

Introduction

Heat stress can affect the production of poultry through complex interactions between genes, metabolites and microorganisms. At present, it is unclear how heat stress affects genetic, metabolic and microbial changes in poultry, as well as the complex interactions between them.

Methods

Thus, at 28  days of age a total of 200 Arbor Acres broilers with similar body weights were randomly divided into the control (CON) and heat stress treatment (HS). There were 5 replicates in CON and HS, respectively, 20 per replication. From the 28-42  days, the HS was kept at 31 ± 1°C (9:00-17:00, 8 h) and other time was maintained at 21 ± 1°C as in the CON. At the 42nd day experiment, we calculated the growth performance (n = 8) of broilers and collected 3 and 6 cecal tissues for transcriptomic and metabolomic investigation and 4 cecal contents for metagenomic investigation of each treatment.

Results and discussion

The results indicate that heat stress significantly reduced the average daily gain and body weight of broilers (value of p < 0.05). Transcriptome KEGG enrichment showed that the differential genes were mainly enriched in the NF-kB signaling pathway. Metabolomics results showed that KEGG enrichment showed that the differential metabolites were mainly enriched in the mTOR signaling pathway. 16S rDNA amplicon sequencing results indicated that heat stress increased the relative abundance of Proteobacteria decreased the relative abundance of Firmicutes. Multi-omics analysis showed that the co-participating pathway of differential genes, metabolites and microorganisms KEGG enrichment was purine metabolism. Pearson correlation analysis found that ornithine was positively correlated with SULT1C3, GSTT1L and g_Lactobacillus, and negatively correlated with CALB1. PE was negatively correlated with CALB1 and CHAC1, and positively with g_Alistipes. In conclusion, heat stress can generate large amounts of reactive oxygen and increase the types of harmful bacteria, reduce intestinal nutrient absorption and antioxidant capacity, and thereby damage intestinal health and immune function, and reduce growth performance indicators. This biological process is manifested in the complex regulation, providing a foundational theoretical basis for solving the problem of heat stress.

Combined effect of microbially derived cecal SCFA and host genetics on feed efficiency in broiler chickens

BACKGROUND

Improving feed efficiency is the most important goal for modern animal production. The regulatory mechanisms of controlling feed efficiency traits are extremely complex and include the functions related to host genetics and gut microbiota. Short-chain fatty acids (SCFAs), as significant metabolites of microbiota, could be used to refine the combined effect of host genetics and gut microbiota. However, the association of SCFAs with the gut microbiota and host genetics for regulating feed efficiency is far from understood.

RESULTS

In this study, 464 broilers were housed for RFI measuring and examining the host genome sequence. And 300 broilers were examined for cecal microbial data and SCFA concentration. Genome-wide association studies (GWAS) showed that four out of seven SCFAs had significant associations with genome variants. One locus (chr4: 29414391-29417189), located near or inside the genes MAML3, SETD7, and MGST2, was significantly associated with propionate and had a modest effect on feed efficiency traits and the microbiota. The genetic effect of the top SNP explained 8.43% variance of propionate. Individuals with genotype AA had significantly different propionate concentrations (0.074 vs. 0.131 μg/mg), feed efficiency (FCR: 1.658 vs. 1.685), and relative abundance of 14 taxa compared to those with the GG genotype. Christensenellaceae and Christensenellaceae_R-7_group were associated with feed efficiency, propionate concentration, the top SNP genotypes, and lipid metabolism. Individuals with a higher cecal abundance of these taxa showed better feed efficiency and lower concentrations of caecal SCFAs.

CONCLUSION

Our study provides strong evidence of the pathway that host genome variants affect the cecal SCFA by influencing caecal microbiota and then regulating feed efficiency. The cecal taxa Christensenellaceae and Christensenellaceae_R-7_group were identified as representative taxa contributing to the combined effect of host genetics and SCFAs on chicken feed efficiency. These findings provided strong evidence of the combined effect of host genetics and gut microbial SCFAs in regulating feed efficiency traits. Video Abstract.

Impact of divergence of residual feed intake on triglyceride metabolism-related gene expression in meat-type ducks

Triglyceride (TG) metabolism is a key factor that affects residual feed intake (RFI); however, few studies have been conducted on the related gene expression in poultry. The aim of the present study was to investigate the expression of genes and their associations with RFI in meat-type ducks. Weight gain and feed intake (FI) at an age 21-42 days were measured and the RFI was calculated. Quantitative PCR was used to test the expression of the six identified genes, namely peroxisome proliferator activated receptor γ (PPARγ), glycerol kinase 2 (GK2), glycerol-3-phosphate dehydrogenase 1 (GPD1), glycerol kinase (GYK), lipase E (LIPE), and lipoprotein lipase (LPL) in the duodenum in the high RFI (HRFI) and low RFI (LRFI) groups. The results demonstrated that daily feed intake, feed conversion ratio (FCR), and RFI were markedly higher in HRFI ducks than those in LRFI ducks. Moreover, the levels of expression of PPARγ, GK2, and LIPE were significantly higher in the LRFI group than those in the HRFI group. Correlation analysis showed that PPARγ, GK2, and LIPE were significantly negatively associated with FCR and RFI. Furthermore, gene expression levels were negatively associated with the measured phenotype. The association of GK2 with PPARγ, GPD1, LPL, and LIPE was positive. The relationship between the TG related gene and RFI was further verified to potentially develop pedigree poultry breeding programs. The results of this study suggested that the expression of genes correlated with TG metabolism and transport is up-regulated in the duodenum of ducks with high feed efficiency. PPARγ, GK2, and LIPE are important genes that affect RFI. The results of the present study provide information that could facilitate further explorations of the mechanism of RFI and potential markers at the molecular and cellular levels.

Combined transcriptome and metabolome analysis reveal key regulatory genes and pathways of feed conversion efficiency of oriental river prawn Macrobrachium nipponense

BACKGROUND

Oriental river prawn Macrobrachium nipponense is an economically important aquaculture species in China, Japan, and Vietnam. In commercial prawn farming, feed cost constitutes about 50 to 65% of the actual variable cost. Improving feed conversion efficiency in prawn culture will not only increase economic benefit, but also save food and protect the environment. The common indicators used for feed conversion efficiency include feed conversion ratio (FCR), feed efficiency ratio (FER), and residual feed intake (RFI). Among these, RFI is much more suitable than FCR and FER during the genetic improvement of feed conversion efficiency for aquaculture species.

RESULTS

In this study, the transcriptome and metabolome of hepatopancreas and muscle of M. nipponense from high RFI low RFI groups, which identified after culture for 75 days, were characterized using combined transcriptomic and metabolomic analysis. A total of 4540 differentially expressed genes (DEGs) in hepatopancreas, and 3894 DEGs in muscle were identified, respectively. The DEGs in hepatopancreas were mainly enriched in KEGG pathways including the metabolism of xenobiotics by cytochrome P450 (down-regulated), fat digestion and absorption (down-regulated) and aminoacyl-tRNA biosynthesis (up-regulated), etc. The DEGs in muscle were mainly enriched in KEGG pathways including the protein digestion and absorption (down-regulated), glycolysis/gluconeogenesis (down-regulated), and glutathione metabolism (up-regulated), etc. At the transcriptome level, the RFI of M. nipponense was mainly controlled in biological pathways such as the high immune expression and the reduction of nutrients absorption capacity. A total of 445 and 247 differently expressed metabolites (DEMs) were identified in the hepatopancreas and muscle, respectively. At the metabolome level, the RFI of M. nipponense was affected considerably by amino acid and lipid metabolism.

CONCLUSIONS

M. nipponense from higher and lower RFI groups have various physiological and metabolic capability processes. The down-regulated genes, such as carboxypeptidase A1, 6-phosphofructokinase, long-chain-acyl-CoA dehydrogenase, et. al., in digestion and absorption of nutrients, and the up-regulated metabolites, such as aspirin, lysine, et. al., in response to immunity could be potential candidate factors contributed to RFI variation for M. nipponense. Overall, these results would provide new insights into the molecular mechanism of feed conversion efficiency and assist in selective breeding to improve feed conversion efficiency in M. nipponense.

Trade-off between feed efficiency and immunity in specialized high-performing chickens

Based on resource allocation theory, ignoring importance of immunity, and focus on growth and feed efficiency (FE) traits in breeding plans may lead to serious weakness in immune system performance. However, in poultry the adverse effects of selection for FE on the immune system are unclear. Therefore, an experiment was conducted to study the trade-off between FE and immunity using a total of 180 high-performing specialized male chickens from a commercial broiler line which were selected over 30 generations for growth (body weight gain, BWG) and FE (residual feed intake, RFI). Birds were reared for 42 d and 5 FE-related traits of the birds in the last week were considered including daily feed intake (DFI), feed conversion ratio (FCR), residual feed intake (RFI), residual BW gain (RG), and residual intake and gain (RIG). For all 180 chickens, immune system performance including humoral immune response, cell-mediated immunity (CMI), and the activity of lysozyme enzyme (L. activity) as innate immunity was measured. After ascending sort of each FE records, 10% of higher records (H-FE: N = 18) and 10% of lower records (L-FE: N = 18) were determined, and immunity between L-FE and H-FE groups were compared. Moreover, L-BWG and H-BWG were analyzed because BWG is one of components in the FE formula. Performance of the immune system was not statistically different for CMI in none of the studied FE groups. Moreover, high and low groups for DFI and BWG were not different regarding the immunity of the birds. Antibody titers against Newcastle disease virus (NDV) were different between low and high groups of FCR, RG, and RIG. Likewise, SRBC-derived antibodies were significantly different between RFI groups. Rather than humoral immunity, RIG had adversely effect on the innate immunity. Results of the present study showed that although RIG is a more appropriate indicator for FE, choosing for high RIG can weaken the performance of the both humoral and innate immune systems, while RFI had fewer adverse effects.

Temporal transcriptome profiling of floating apical out chicken enteroids suggest stability and reproducibility

Enteroids are miniature self-organising three-dimensional (3D) tissue cultures which replicate much of the complexity of the intestinal epithelium. We recently developed an apical-out leukocyte-containing chicken enteroid model providing a novel physiologically relevant in vitro tool to explore host-pathogen interactions in the avian gut. However, the replicate consistency and culture stability have not yet been fully explored at the transcript level. In addition, causes for the inability to passage apical-out enteroids were not determined. Here we report the transcriptional profiling of chicken embryonic intestinal villi and chicken enteroid cultures using bulk RNA-seq. Comparison of the transcriptomes of biological and technical replicate enteroid cultures confirmed their high level of reproducibility. Detailed analysis of cell subpopulation and function markers revealed that the mature enteroids differentiate from late embryonic intestinal villi to recapitulate many digestive, immune and gut-barrier functions present in the avian intestine. These transcriptomic results demonstrate that the chicken enteroid cultures are highly reproducible, and within the first week of culture they morphologically mature to appear similar to the in vivo intestine, therefore representing a physiologically-relevant in vitro model of the chicken intestine.

Identification of biomarkers associated with the feed efficiency by metabolomics profiling: results from the broiler lines divergent for high or low abdominal fat content

Background

Improving feed efficiency (FE) is one of the main objectives in broiler breeding. It is difficult to directly measure FE traits, and breeders hence have been trying to identify biomarkers for the indirect selection and improvement of FE traits. Metabolome is the "bridge" between genome and phenome. The metabolites may potentially account for more of the phenotypic variation and can suitably serve as biomarkers for selecting FE traits. This study aimed to identify plasma metabolite markers for selecting high-FE broilers. A total of 441 birds from Northeast Agricultural University broiler lines divergently selected for abdominal fat content were used to analyze plasma metabolome and estimate the genetic parameters of differentially expressed metabolites.

Results

The results identified 124 differentially expressed plasma metabolites (P < 0.05) between the lean line (high-FE birds) and the fat line (low-FE birds). Among these differentially expressed plasma metabolites, 44 were found to have higher positive or negative genetic correlations with FE traits (|r_g| ≥ 0.30). Of these 44 metabolites, 14 were found to display moderate to high heritability estimates (h² ≥ 0.20). However, among the 14 metabolites, 4 metabolites whose physiological functions have not been reported were excluded. Ultimately, 10 metabolites were suggested to serve as the potential biomarkers for breeding the high-FE broilers. Based on the physiological functions of these metabolites, reducing inflammatory and improving immunity were proposed to improve FE and increase production efficiency.

Conclusions

According to the pipeline for the selection of the metabolite markers established in this study, it was suggested that 10 metabolites including 7-ketocholesterol, dimethyl sulfone, epsilon-(gamma-glutamyl)-lysine, gamma-glutamyltyrosine, 2-oxoadipic acid, L-homoarginine, testosterone, adenosine 5'-monophosphate, adrenic acid, and calcitriol could be used as the potential biomarkers for breeding the "food-saving broilers".

Effects of residual feed intake divergence on growth performance, carcass traits, meat quality, and blood biochemical parameters in small-sized meat ducks

Feed efficiency (FE) is a major economic trait of meat duck. This study aimed to evaluate the effects of residual feed intake (RFI) divergence on growth performance, carcass traits, meat quality, and blood biochemical parameters in small-sized meat ducks. A total of 500 healthy 21-day-old male ducks were housed in individual cages until slaughter at 63 d of age. The growth performance was determined for all the ducks. The carcass yield, meat quality, and blood biochemical parameters were determined for the selected 30 high-RFI (HRFI) and 30 low-RFI (LRFI) ducks. In terms of growth performance, the RFI, feed conversion ratio (FCR), and average daily feed intake (ADFI) were found to be significantly lower in the LRFI group (P < 0.01), whereas no differences were observed in the BW and body weight gain (P > 0.05). For slaughter performance, no differences were observed in the carcass traits between the LRFI and HRFI groups (P > 0.05). For meat quality, the shear force of breast muscle was significantly lower in the LRFI group (P < 0.05), while the other meat quality traits of breast and thigh muscles demonstrated no differences (P > 0.05). For blood biochemical parameters, the serum concentrations of triglycerides (TG) and glucose (GLU) were significantly lower in the LRFI group (P < 0.05), while the other parameters showed no differences (P > 0.05). The correlation analysis demonstrated a high positive correlation between RFI, FCR, and ADFI (P < 0.01). The RFI demonstrated a negative effect on the breast muscle and lean meat yields, but a positive effect on the shear force of breast muscle (P < 0.05). Further, the RFI demonstrated a positive effect on the TG and GLU levels (P < 0.05). These results indicate that the selection for low RFI could improve the FE of small-sized meat ducks without affecting the production performance. This study provides valuable insight into the biological processes underlying the variations in FE in small-sized meat ducks.

Revealing Pathways Associated with Feed Efficiency and Meat Quality Traits in Slow-Growing Chickens

Simple Summary

Korat is a new chicken breed with high-protein meat, low fat, and low purine content. However, the effects of improving the breed’s feed efficiency, which would enhance production, on meat quality are unknown. Hence, understanding the genetic architecture underlying feed efficiency and meat quality traits in chicken offers new opportunities toward genetic improvement. Through a weighted gene co-expression network analysis on Korat chickens, the presented results provide new information on the molecular pathways that play important roles in FE and meat quality that could help achieve the optimum feed efficiency while maintaining meat quality in Korat chickens.

Abstract

Here, molecular pathways and genes involved in the feed efficiency (FE) and thigh-meat quality of slow-growing Korat chickens were investigated. Individual feed intake values and body weights were collected weekly to the calculate feed conversion ratios (FCR) and residual feed intake. The biochemical composition and meat quality parameters were also measured. On the basis of extreme FCR values at 10 weeks of age, 9 and 12 birds from the high and the low FCR groups, respectively, were selected, and their transcriptomes were investigated using the 8 × 60 K Agilent chicken microarray. A weighted gene co-expression network analysis was performed to determine the correlations between co-expressed gene modules and FE, thigh-meat quality, or both. Groups of birds with different FE values also had different nucleotide, lipid, and protein contents in their thigh muscles. In total, 38 modules of co-expressed genes were identified, and 12 were correlated with FE and some meat quality traits. A functional analysis highlighted several enriched functions, such as biological processes, metabolic processes, nucleotide metabolism, and immune responses. Several molecular factors were involved in the interactions between FE and meat quality, including the assembly competence domain, baculoviral IAP repeat containing 5, cytochrome c oxidase assembly factor 3, and myosin light chain 9 genes.

The significant influence of residual feed intake on flavor precursors and biomolecules in slow-growing Korat chicken meat

Objective

This study investigated the association between feed efficiency, physicochemical properties, flavor precursors and biomolecules in the thigh meat of Korat (KR) chickens.

Methods

The feed intake and body weight of individual male KR chickens were recorded from 1 to 10 weeks old to calculate the individual residual feed intake (RFI) of 75 birds. At 10 weeks of age, chickens with the 10 highest (HRFI) and lowest RFI (LRFI) were slaughtered to provide thigh meat samples. The physicochemical properties (ultimate pH, water holding capacity [WHC], drip loss) and flavor precursors (guanosine monophosphate, inosine monophosphate (IMP), adenosine monophosphate and inosine) were analyzed conventionally, and Fourier transform infrared spectroscopy was used to identify the composition of biomolecules (lipids, ester lipids, amide I, amide II, amide III, and carbohydrates) and the secondary structure of the proteins. A group t-test was used to determine significant differences between mean values and principal component analysis to classify thigh meat samples into LRFI and HRFI KR chickens.

Results

The physicochemical properties of thigh meat samples from LRFI and HRFI KR chickens were not significantly different but the IMP content, ratios of lipid, lipid ester, protein (amide I, amide II) were significantly different (p<0.05). The correlation loading results showed that the LRFI group was correlated with high ratios of lipids, lipid esters, collagen content (amide III) and beta sheet protein (rg loading >0.5) while the HRFI group was positively correlated with protein (amide I, amide II), alpha helix protein, IMP content, carbohydrate, ultimate pH and WHC (rg loading >0.5).

Conclusion

The thigh meat from chickens with different RFI differed in physiochemical properties affecting meat texture, and in the contents of flavor precursors and biomolecules affecting the nutritional value of meat. This information can help animal breeders to make genetic improvements by taking more account of traits related to RFI.

Differential gene expression in duodenum of colored broiler chicken divergently selected for residual feed intake

Feed constitutes about 70% of the total expenditure of poultry production. Maximizing the feed efficiency in juvenile period is essential to achieve low production cost. The efficiency of feed utilization was measured by RFI (residual feed intake) by calculating the difference between an individual animal's observed and its expected feed intake. The expression of genes influencing low and high RFI is required to know the basic molecular mechanism influencing feed efficiency. The present study aimed to estimate the RFI (0-5 week) in a population of indigenously developed colored broiler sire line chicken. The duodenum sample of high and low-RFI broiler chicken was used for microarray analysis. Duodenum exhibited 1030 differentially expressed genes after analysis. Out of total DEGs, 461 genes were downregulated and 569 were upregulated. The fold change of differentiallly expressed genes varies from - 162.6 to 1549.28. A subset of genes was validated by qRT-PCR and results were correlated well with microarray data. In functional annotation study of DEGs, 89 biological processes, 30 cellular components, and 29 molecular functions were identified. Study of the important differentially expressed genes and the related molecular pathways in the population may hold the potential for future breeding strategies for augmenting feed efficiency.

Symposium review: Decomposing efficiency of milk production and maximizing profit

The dairy industry has focused on maximizing milk yield, as it is believed that this maximizes profit mainly through dilution of maintenance costs. Efficiency of milk production has received, until recently, considerably less attention. The most common method to determine biological efficiency of milk production is feed efficiency (FE), which is defined as the amount of milk produced relative to the amount of nutrients consumed. Economic efficiency is best measured as income over feed cost or gross margin obtained from feed investments. Feed efficiency is affected by a myriad of factors, but overall they could be clustered as follows: (1) physiological status of the cow (e.g., age, state of lactation, health, level of production, environmental conditions), (2) digestive function (e.g., feeding behavior, passage rate, rumen fermentation, rumen and hindgut microbiome), (3) metabolic partitioning (e.g., homeorhesis, insulin sensitivity, hormonal profile), (4) genetics (ultimately dictating the 2 previous aspects), and (5) nutrition (e.g., ration formulation, nutrient balance). Over the years, energy requirements for maintenance seem to have progressively increased, but efficiency of overall nutrient use for milk production has also increased due to dilution of nutrient requirements for maintenance. However, empirical evidence from the literature suggests that marginal increases in milk require progressively greater marginal increases in nutrient supply. Thus, the dilution of maintenance requirements associated with increases in production is partially overcome by a progressive diminishing marginal biological response to incremental energy and protein supplies. Because FE follows the law of diminishing returns, and because marginal feed costs increase progressively with milk production, profits associated with improving milk yield might, in some cases, be considerably lower than expected.

Transcriptome analysis reveals mechanism underlying the differential intestinal functionality of laying hens in the late phase and peak phase of production

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.

Studying the variations in differently expressed serum proteins of Hainan black goat during the breeding cycle using isobaric tags for relative and absolute quantitation (iTRAQ) technology

The Hainan black goat is a high-quality local goat breed in Hainan Province of China. It is resistant to high temperatures, humidity, and disease. Although the meat of this breed is tender and delicious, its reproductive performance and milk yield are low. In this study, isobaric tags for relative and absolute quantitation (iTRAQ) technology was used to analyze the differentially expressed proteins in the serum of female Hainan black goats during the reproductive cycle (empty pregnant, estrus, gestation, and lactation). The pathway enrichment analysis results showed that most of the differentially expressed proteins between each period belonged to the complement and coagulation cascades. Analysis of the differential protein expression and function revealed seven proteins that were directly associated with reproduction, namely pre-SAA21, ANTXR2, vWF, SFRP3, β4GalT1, pre-IGFBP2 and Ran. This study revealed the changing patterns of differentially expressed proteins in the reproductive cycle of the Hainan black goat. pre-SAA21, ANTXR2, vWF, SFRP3, β4GalT1, pre-IGFBP2, and Ran were identified as candidate proteins for mediating the physiological state of Hainan black goats and regulating their fertility. This study elucidated the changes in expression levels of differentially expressed proteins during the reproductive cycle of Hainan black goats and also provides details about its breeding pattern.