Gut-brain bidirectional determination in regulating the residual feed intake of small-sized meat ducks.

The gut-brain axis is essential in maintaining the homeostasis of neuronal system, endocrine system, and intestinal microbiota in both the afferent and efferent directions. This axis is considered to be a key mechanism that regulates feed efficiency (FE). This study aimed to investigate the regulatory mechanisms of gut-brain axis-related genes on the residual feed intake (RFI) in H-strain small-sized meat ducks. A total of 500 ducks with similar initial BW (635.2 ± 15.1 g) were selected and reared in the same experimental facility until slaughter at 42 d of age. RFI was calculated from the average daily gain (ADG), average daily feed intake (ADFI), and metabolic body weight (MBW0.75). Thirty high-RFI (H-RFI) and 30 low-RFI (L-RFI) birds were selected for further evaluation of growth performance, carcass characteristics, and blood biochemical parameter measurements. Six L-RFI and 6 H-RFI birds were then subjected to hypothalamic transcriptomic and cecal microbial sequencing analyses. Results indicated that L-RFI birds exhibited lower production performance (ADFI, FCR, and RFI) and blood biochemical indices (total cholesterol and ghrelin content) compared with H-RFI birds (P < 0.05). Gene expression differed significantly between the L-RFI and H-RFI birds, with 70 upregulated and 50 downregulated genes. The bacterial communities of L-RFI birds showed higher abundances of Bacteroides, Bifidobacterium, and Lactococcus, and lower abundances of Erysipelatoclostridium, Parasutterella, Fournierella, and Blautia compared with H-RFI birds (P < 0.05). Interactive analysis revealed bacterial communities associated with FE were significantly correlated with hypothalamic genes (P < 0.05), for example, Bacteroides was positively correlated with DGKH and LIPT2, while negatively correlated with CAPN9, GABRD, and PDE1A. Bifidobacterium showed significant correlations with ATP2A3, CALHM6, and TMEM121B. Overall, RFI was a crucial indicator of FE, regulated by interactions between brain gene expression and gut microbiota through cAMP signaling, neuroactive ligand-receptor interaction, and calcium signaling pathways. Notably, increased expression of hypothalamic genes and abundance of carbohydrate-utilization microbiota in L-RFI meat ducks improved FE by enhancing energy metabolism and volatile fatty acids absorption.

Iron-Confined CRISPR/Cas9-Ribonucleoprotein Delivery System for Redox-Responsive Gene Editing.

Clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 9 (Cas9) is a promising gene editing tool to treat diseases at the genetic level. Nonetheless, the challenge of the safe and efficient delivery of CRISPR/Cas9 to host cells constrains its clinical applicability. In the current study, a facile, redox-responsive CRISPR/Cas9-Ribonucleoprotein (RNP) delivery system by combining iron-coordinated aggregation with liposomes (Fe-RNP@L) is reported. The Fe-RNP is formed by the coordination of Fe3+ with amino and carboxyl groups of Cas9, which modifies the lipophilicity and surface charge of RNP and alters cellular uptake from primary endocytosis to endocytosis and cholesterol-dependent membrane fusion. RNP can be rapidly and reversibly released from Fe-RNP in response to glutathione without loss of structural integrity and enzymatic activity. In addition, iron coordination also improves the stability of RNP and substantially mitigates cytotoxicity. This construct enabled highly efficient cytoplasmic/nuclear delivery (≈90%) and gene-editing efficiency (≈70%) even at low concentrations. The high payload content, high editing efficiency, good stability, low immunogenicity, and ease of production and storage, highlight its potential for diverse genome editing and clinical applications.

Identification of SNPs in MITF associated with beak color of duck.

Introduction: Beak color-a pigment-related trait-is an important feature of duck breeds. Recently, little research has addressed genetic mechanism of the beak colors in poultry, whereas the process and the regulation factors of melanin deposition have been well described. Methods: To investigate the genetic mechanism of beak colors, we conducted an integrated analysis of genomic selection signatures to identify a candidate site associated with beak color. For this, we used black-billed (Yiyang I meat duck synthetic line H1, H2, H3&HF) and yellow-billed ducks (Cherry Valley ducks and white feather Putian black duck). Quantitative real-time PCR and genotyping approaches were used to verify the function of the candidate site. Results: We identified 3,895 windows containing 509 genes. After GO and KEGG enrichment analysis, nine genes were selected. Ultimately, MITF was selected by comparing the genomic differentiation (FST). After loci information selection, 41 extreme significantly different loci were selected, which are all located in intron regions of MITF and are in almost complete linkage disequilibrium. Subsequently, the site ASM874695v1:10:g.17814522T > A in MITF was selected as the marker site. Furthermore, we found that MITF expression is significantly higher in black-beaked ducks than in yellow-beaked ducks of the F2 generation (p < 0.01). After genotyping, most yellow-billed individuals are found with homozygous variant; at the same time, there are no birds with homozygous variant in black-billed populations, while the birds with homozygous and heterozygous variant share the same proportion. Conclusion: MITF plays a very critical role in the melanogenesis and melanin deposition of duck beaks, which can effectively affect the beak color. The MITF site, ASM874695v1:10:g.17814522T > A could be selected as a marker site for the duck beak color phenotype.

Combine with RNA-seq Reveals the Effect of Melatonin in the Synthesis of Melanin in Primary Melanocytes of Silky Fowls Black-Bone Chicken.

(1) Background: It was found that the melanin of black-bone chicken has various effects such as scavenging DPPH free radicals and anti-oxidation, and the synthesis of melanin is affected by various factors including hormones. In addition, several studies have found that melatonin affects the melanoma cell synthesis of melanin, which has not been reported in chicken primary melanocytes; so, relevant studies were conducted. (2) Methods: In this study, chicken primary melanocytes were isolated and characterized, and then melanocytes were treated with different concentrations of melatonin to investigate the effects of melatonin on melanin synthesis in chicken melanocytes in terms of melanin synthesis-related genes, melanin content, and tyrosinase activity, and combined with RNA seq to detect the change in gene expression level of chicken melanocytes after melatonin treatment. (3) Results: We isolated and characterized primary melanocytes, and indirect immunofluorescence assay results showed positive melanocyte marker genes. RT-qPCR results showed that melatonin decreased the expression of melanin synthesis-related genes. In addition, melatonin reduced the melanin content and decreased the tyrosinase activity of melanocytes in the treated group. A total of 1703 differentially expressed genes were screened by RNA-seq, and in addition, in the KEGG results, the signaling pathway associated with melanin synthesis, and the mTOR signaling pathway were enriched. (4) Conclusions: Melatonin could decrease the synthesis of melanin in chicken primary melanocytes.

The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation.

The Chinese crested (CC) duck is a unique indigenous waterfowl breed, which has a crest cushion that affects its survival rate. Therefore, the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability. In the present study, we first generated a chromosome-level genome of CC ducks. Comparative genomics revealed that genes related to tissue repair, immune function, and tumors were under strong positive selection, indicating that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic stability of CC ducks. We also assembled a Chinese spot-billed (Csp-b) duck genome, and detected the structural variations (SVs) in the genome assemblies of three ducks (i.e., CC duck, Csp-b duck, and Peking duck). Functional analysis revealed that several SVs were related to the immune system of CC ducks, further strongly suggesting that genetic compensation in the anti-tumor and immune systems supports the survival of CC ducks. Moreover, we confirmed that the CC duck originated from the mallard ducks. Finally, we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation. Overall, the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.

Circ_PIAS1 Promotes the Apoptosis of ALV-J Infected DF1 Cells by Up-Regulating miR-183.

(1) Background: circRNAs are closed circular molecules with covalent bonds generated by reverse shearing, which have high stability and have different manifestations in different tissues, cells, or physiological conditions and play important roles in various disease processes and physiological processes. In addition, circ_PIAS1 has been screened out and verified, and the bioinformatics analyzed in previous studies. In this study, we investigated the function of circ_PIAS1 and studied its role in ALV-J infection to provide a basis for the role of circRNA in ALV-J infection. (2) Methods: the effect of circ_PIAS1 on apoptosis during ALV-J infection was studied by flow cytometry and detection of apoptotic gene expression, and miR-183 was screened by a biotin-labeled RNA pull-down technique. After overexpression and inhibition of miR-183, the effect of miR-183 on apoptosis in the process of ALV-J infection was studied by flow cytometry and detection of apoptotic gene expression. (3) Results: after overexpression of circ_PIAS1, flow cytometry and apoptotic gene expression showed that circ_PIAS1 promoted apoptosis. The results of RNA pull-down showed that 173 miRNAs could bind to circ_PIAS1, and circ_PIAS1 up-regulated the expression of miR-183. On the other hand, the same results were obtained whether miR-183 was overexpressed or inhibited that miR-183 affected ALV-J infection by promoting cell apoptosis. (4) Conclusions: circ_PIAS1 up-regulated the expression of miR-183 and influenced ALV-J infection by promoting cell apoptosis.

Genetic diversity and breed identification of Chinese and Vietnamese local chicken breeds based on microsatellite analysis.

South Asia and Southeast Asia are the origins of domestic chickens and are rich in poultry genetic resources, resulting in many unique local chicken breeds. However, with the rapid intensification of poultry farming worldwide, many local chicken breeds are threatened with extinction. In response to China's "One Belt, One Road" policy, it is imperative to strengthen the conservation and breeding of local chicken breeds in China and Vietnam. This study characterized 18 microsatellite molecular genetic markers to analyze the genetic diversity of 21 local chicken populations in southern China (Yunnan and Guangxi Provinces) and Vietnam, breed identification tags for microsatellite loci were constructed. The results showed that a total of 377 alleles were detected in all breeds, and the most alleles (44) and the highest polymorphic information content (0.7820) were detected at the LEI0094 locus. The average polymorphic information content (PIC) content of the whole population was 0.65, indicating moderate polymorphism. The genetic diversity of the whole population was rich, except for two loci MCW0111 and MCW0016, that showed heterozygote excess at microsatellite loci, and the population had high genetic differentiation. The Vietnamese breeds showed low pairwise fixation coefficient (FST) and Nei's standard genetic distance (DS) between them. According to the neighbor-joining dendrogram constructed by DS and the analysis of population genetic structure using the structure program, Longshengfeng chicken, Yunlong dwarf chicken, Tengchong white chicken, Xiayan chicken, and Daweishan mini chicken are similar, and Xishuangbanna game fowl, Wuding chicken, and Lanping silky chicken are similar to Yanjin black-bone chicken. In addition, excluding Dongtao chicken, other Vietnamese breeds are clustered together, indicating that the southern chicken breeds are closely related and have experienced better breeding. Overall, the whole population is rich in genetic resources, and the chicken breeds in the three regions are genetically close because of geographical factors and human activities. Dongtao chicken in Vietnamese, Chinese Yunnan local chicken breeds (Gallus gallus spadiceus), and red jungle fowl chickens (Gallus gallus) may have the same origin. We also constructed unique microsatellite molecular markers for 20 cultivars using 15 microsatellite loci. This study provides valuable insights to facilitate breed identification, improve cultivar protection, and new germplasm construction.

China's Yunnan, Guangxi, and Vietnam are rich in biodiversity, and a wide variety of local chicken breeds exist. Due to the rapid development of intensive farming, the biodiversity of chicken breeds in these two regions has gradually decreased. To protect the diversity of local breeds, and to promote the exchange of germplasm resources and the creation of new germplasm between China and Vietnam, this study analyzed the genetic diversity of some chicken breeds in Yunnan, Guangxi, and Vietnam by using microsatellite molecular markers. Studies have shown that the entire population has rich genetic resources, and Vietnamese chickens have a strong kinship with some local chicken breeds in Yunnan Province, China, and there is also a high degree of hybridization between Vietnamese local chickens. In addition, since some chicken breeds have more similarities in appearance, this study constructed unique molecular tags for different breed-specific alleles as one of the methods to accurately distinguish different breeds for breed protection and subsequent breeding.

Proteomic and phosphoproteomic analysis reveal threonine deficiency increases hepatic lipid deposition in Pekin ducks via reducing STAT phosphorylation.

Dietary threonine (Thr) deficiency enhances triglyceride (TG) deposition in the liver of Pekin ducks, which injures hepatic function and impairs growth performance. However, the underlying molecular mechanisms remain unclear. In the present study, we investigated the effects of dietary Thr deficiency on the expressions of proteins and phosphoproteins in liver of Pekin ducks, to identify the underlying molecular changes. A total of 300 one-day-old ducklings were divided into 3 groups with 10 replicates of 10 birds. All ducks were fed corn-wheat-peanut meal diets containing 0.46%, 0.71%, and 0.96% Thr, respectively, from 1 to 21 days of age. Growth performance, serum parameters, hepatic TG content, and expression of genes involved in lipid metabolism of Pekin ducks were determined. A Thr deficiency group (Thr-D, 0.46% Thr) and a Thr sufficiency group (Thr-S, 0.71% Thr) were selected for subsequent proteomic and phosphoproteomic analysis. The results showed that Thr-D reduced the growth performance (P < 0.001), and increased the plasma concentrations of cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and hepatic TG (P < 0.05). Thr-D increased gene expression related to fatty acid and TG synthesis (P < 0.05). A total of 176 proteins and 259 phosphosites (containing 198 phosphoproteins) were observed to be differentially expressed as a result of Thr-D. The upregulated proteins were enriched in the pathway related to amino acid metabolism, peroxisome. The downregulated proteins were enriched in linolenic and arachidonic acid metabolism, and the Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway. The upregulated phosphoproteins were enriched in the pathways related to fatty acid biosynthesis, fructose and mannose metabolism, and glycolysis/gluconeogenesis. Thr-D reduced the phosphorylation of STAT1 at S729 and STAT3 at S728, and expression of STAT5B. In contrast, Thr-D increased non-receptor tyrosine-protein kinase (TYK2) expression and STAT1 phosphorylation at S649. Taken together, dietary Thr-D increased hepatic TG accumulation by upregulating the expression of genes and proteins, and phosphoproteins related to fatty acid and triglyceride synthesis. Furthermore, these processes might be regulated by the JAK-STAT signaling pathway, especially the phosphorylation of STAT1 and STAT3.

Identification, biogenesis, and function prediction of a novel circRNA_3238 of chicken.

With the development of high-throughput sequencing, circular RNA has come into people's vision and attracted more and more attention. Many studies have found that circular RNA plays an important role in a variety of biological processes and the occurrence and development of diseases. According to the previous sequencing results, circRNA_3238 was differentially expressed in ALV-J infected group and the non-infected group was selected for subsequent verification and analysis. We found that circRNA_3238 is a stable, circular transcript, which mainly exists in the cytoplasm. And it is widely expressed in various tissues of chickens, and highly expressed in lung, lymph, and bursa of fabricius. Bioinformatics results show that circRNA_3238 and the predicted target genes enriched MAPK signaling pathway, Notch signaling pathway, and other pathways related to disease or immune, revealing circRNA_3238 may indirectly regulate the process of ALV-J infection by regulating target genes.

Metabolomics and Proteomics Characterizing Hepatic Reactions to Dietary Linseed Oil in Duck.

The imbalance in polyunsaturated fatty acid (PUFA) composition in human food is ubiquitous and closely related to obesity and cardiovascular diseases. The development of n-3 PUFA-enriched poultry products is of great significance for optimizing fatty acid composition. This study aimed to improve our understanding of the effects of dietary linseed oil on hepatic metabolism using untargeted metabolomics and 4D label-free proteome analysis. A total of 91 metabolites and 63 proteins showed differences in abundance in duck livers between the high linseed oil and control groups. Pathway analysis revealed that the biosynthesis of unsaturated fatty acids, linoleic acid, glycerophospholipid, and pyrimidine metabolisms were significantly enriched in ducks fed with linseed oil. Meanwhile, dietary linseed oil changed liver fatty acid composition, which was reflected in the increase in the abundance of downstream metabolites, such as α-linolenic acid (ALA; 18:3n-3) as a substrate, including n-3 PUFA and its related glycerophospholipids, and a decrease in downstream n-6 PUFA synthesis using linoleic acid (LA; 18:2n-6) as a substrate. Moreover, the anabolism of PUFA in duck livers showed substrate-dependent effects, and the expression of related proteins in the process of fatty acid anabolism, such as FADS2, LPIN2, and PLA2G4A, were significantly regulated by linseed oil. Collectively, our work highlights the ALA substrate dependence during n-3 PUFA synthesis in duck livers. The present study expands our knowledge of the process products of PUFA metabolism and provides some potential biomarkers for liver health.

MYOZ1 Gene Promotes Muscle Growth and Development in Meat Ducks.

To explore the effect of MYOZ1 in the muscle growth and development of meat ducks, MYOZ1 single-nucleotide polymorphism loci were screened at the DNA level in the meat duck population with highest and lowest feed conversion rates. The expression of MYOZ1 was detected using reverse-transcription quantitative polymerase chain reaction. The protein expression of MYOZ1 was detected using Western blotting at the protein level. The results showed that there was a base mutation site at 30 bp and 158 bp in the fourth exon of MYOZ1, which was mutated from C to T (exon4 C30T) and from G to A (exon4 G158A), respectively. The allele frequency of the locus was significantly different between the high and low feed conversion rate groups (p < 0.01). The relative expression of MYOZ1 mRNA in breast muscle tissue of HF ducks was significantly higher than that of LF ducks (p < 0.01). The MYOZ1 protein expression of HF ducks was significantly higher than that of LF ducks (p < 0.01). In general, MYOZ1 has a positive regulatory effect on the muscle growth and development of meat ducks. The results of this study lay a certain theoretical basis for the muscle growth and development of meat ducks.

Genome-Wide Association Study for Screening and Identifying Potential Shin Color Loci in Ducks.

Shin color diversity is a widespread phenomenon in birds. In this study, ducks were assessed to identify candidate genes for yellow, black, and spotted tibiae. For this purpose, we performed whole-genome resequencing of an F2 population consisting of 275 ducks crossed between Runzhou crested-white ducks and Cherry Valley ducks. We obtained 12.6 Mb of single nucleotide polymorphism (SNP) data, and the three shin colors were subsequently genotyped. Genome-wide association studies (GWASs) were performed to identify candidate and potential SNPs for the three shin colors. According to the results, 2947 and 3451 significant SNPs were associated with black and yellow shins, respectively, and six potential SNPs were associated with spotted shins. Based on the SNP annotations, the MITF, EDNRB2, POU family members, and the SLC superfamily were the candidate genes regulating pigmentation. In addition, the isoforms of EDNRB2, TYR, TYRP1, and MITF-M were significantly different between the black and yellow tibiae. MITF and EDNRB2 may have synergistic roles in the regulation of melanin synthesis, and their mutations may lead to phenotypic differences in the melanin deposition between individuals. This study provides new insights into the genetic factors that may influence tibia color diversity in birds.

Genome-Wide Analysis Identifies Candidate Genes Encoding Feather Color in Ducks.

Comparative population genomics and genome-wide association studies (GWAS) offer opportunities to discover human-driven detectable signatures within the genome. From the point of view of evolutionary biology, the identification of genes associated with the domestication of traits is of interest for the elucidation of the selection of these traits. To this end, an F2 population of ducks, consisting of 275 ducks, was genotyped using a whole genome re-sequence containing 12.6 Mb single nucleotide polymorphisms (SNPs) and four plumage colors. GWAS was used to identify the candidate and potential SNPs of four plumage colors in ducks (white, spot, grey, and black plumage). In addition, FST and genetic diversity (π ratio) were used to screen signals of the selective sweep, which relate to the four plumage colors. Major genomic regions associated with white, spotted, and black feathers overlapped with their candidate selection regions, whereas no such overlap was observed with grey plumage. In addition, MITF and EDNRB2 are functional candidate genes that contribute to white and black plumage due to their indirect involvement in the melanogenesis pathway. This study provides new insights into the genetic factors that may influence the diversity of plumage color.

Genome-Wide Analysis Identifies Candidate Genes Encoding Beak Color of Duck.

Beak color diversity is a broadly occurring phenomenon in birds. Here, we used ducks to identify candidate genes for yellow, black, and spotted beaks. For this, an F2 population consisting of 275 ducks was genotyped using whole genome resequencing containing 12.6 M single-nucleotide polymorphisms (SNPs) and three beak colors. Genome-wide association studies (GWAS) was used to identify the candidate and potential SNPs for three beak colors in ducks (yellow, spotted, and black). The results showed that 2753 significant SNPs were associated with black beaks, 7462 with yellow, and 17 potential SNPs with spotted beaks. Based on SNP annotation, MITF, EDNRB2, members of the POU family, and the SLC superfamily were the candidate genes regulating pigmentation. Meanwhile, isoforms MITF-M and EDNRB2 were significantly different between black and yellow beaks. MITF and EDNRB2 likely play a synergistic role in the regulation of melanin synthesis, and their mutations contribute to phenotypic differences in beak melanin deposition among individuals. This study provides new insights into genetic factors that may influence the diversity of beak color.

Genome-Wide Association Study of Potential Meat Quality Trait Loci in Ducks.

With continuously increasing living standards and health requirements of consumers, meat quality is becoming an important consideration while buying meat products. To date, no genome-wide association study (GWAS) for copy number variants (CNVs) and single nucleotide polymorphisms (SNPs) has been conducted to reveal the genetic effects on meat quality in ducks. This study analyzed the phenotypic correlation and heritability of fat, water, collagen, and protein content of duck breast muscle. To identify the candidate variants for meat quality, we performed a GWAS using 273 ducks from an F2 population. The results of the SNP GWAS showed that the BARHL2, COPS7B, and CCDC50 genes were associated with fat content; BLM, WDR76, and EOMES with water content; CAMTA1, FGD5, GRM7, and RAPGEF5 with collagen production; and RIMS2, HNRNPU, and SPTBN1 with protein content. Additionally, 3, 7, 1, and 3 CNVs were associated with fat, water, collagen, and protein content, respectively, in duck breast muscle. The genes identified in this study can serve as markers for meat quality. Furthermore, our findings may help devise effective breeding plans and selection strategies to improve meat quality.

Genome-Wide Association Study of Feed Efficiency Related Traits in Ducks.

Feed efficiency (FE) is the most important economic trait in the poultry and livestock industry. Thus, genetic improvement of FE may result in a considerable reduction of the cost and energy burdens. As genome-wide association studies (GWASs) can help identify candidate variants influencing FE, the present study aimed to analyze the phenotypic correlation and identify candidate variants of the seven FE traits in ducks. All traits were found to have significant positive correlations with varying degrees. In particular, residual feed intake presented correlation coefficients of 0.61, 0.54, and 0.13 with feed conversion ratio, and feed intake, respectively. Furthermore, data from seven FE-related GWAS revealed 4 (FCR), 3 (FI), 36 (RFI), 6 (BWG), 8 (BW21), and 10 (BW42) SNPs were significantly associated with body weight gain, feed intake, residual feed intake, feed conversion ratio, and weight at 21 and 42 days, respectively. Candidate SNPs of seven FE trait-related genes were involved in galactose metabolism, starch, propanoate metabolism, sucrose metabolism and etc. Taken together, these findings provide insight into the genetic mechanisms and genes involved in FE-related traits in ducks. However, further investigations are warranted to further validate these findings.

Transcriptome Sequencing to Identify Important Genes and lncRNAs Regulating Abdominal Fat Deposition in Ducks.

Abdominal fat deposition is an important trait in meat-producing ducks. F2 generations of 304 Cherry Valley and Runzhou Crested White ducks were studied to identify genes and lncRNAs affecting abdominal fat deposition. RNA sequencing was used to study abdominal fat tissue of four ducks each with high or low abdominal fat rates. In all, 336 upregulated and 297 downregulated mRNAs, and 95 upregulated and 119 downregulated lncRNAs were identified. Target gene prediction of differentially expressed lncRNAs identified 602 genes that were further subjected to Gene Ontology and KEGG pathway analysis. The target genes were enriched in pathways associated with fat synthesis and metabolism and participated in biological processes, including Linoleic acid metabolism, lipid storage, and fat cell differentiation, indicating that these lncRNAs play an important role in abdominal fat deposition. PPAPA, FOXO3, FASN, PNPLA2, FKBP5, TCF7L2, BMP2, FGF2, LIFR, ZBTB16, SIRT, GYG2, NCOR1, and NR3C1 were involved in the regulation of abdominal fat deposition. PNPLA2, TCF7L2, FGF2, LIFR, BMP2, FKBP5, GYG2, and ZBTB16 were regulated by the lncRNAs TCONS_00038080, TCONS_0033547, TCONS_00066773, XR_001190174.3, XR_003492471.1, XR_003493494.1, XR_001192142.3, XR_002405656.2, XR_002401822.2, XR_003497063.1, and so on. This study lays foundations for exploring molecular mechanisms underlying the regulation of abdominal fat deposition in ducks and provides a theoretical basis for breeding high-quality meat-producing ducks.

Effect of stocking density on performance, meat quality and cecal bacterial communities of yellow feather broilers.

Totally, 315 42-day-old male Xueshan chickens were allocated into 3 caging densities, 14, 21 and 28 birds/m2. Each treatment was represented by 5 replicates. The body weight (BW), slaughter performance, meat quality, behavioral assessment, and the cecal microorganisms were detected at the market age. The results showed that the BW of broilers in the low- and medium-density groups was significantly higher (p < 0.05) than that of the high-density group from the age of 10 weeks. Only the feather quality of the broilers in the low-density group improved significantly (p < 0.05) compared with those of the other two groups. And, the abdominal fat percentage and the fat content of thigh muscle of broilers in the low- and medium-density groups were higher (p < 0.05) than those in the high-density group. No significant difference (p > 0.05) was noted in the other traits. The abundance of some microbial like Akkermansiaceae, Lactobacillaceae and Faecalibacterium may be correlated with the BW and fat content of broilers. The findings of this study suggest that increasing the stocking density decreased the final BW, fat content and the feather quality, whereas no evidence was found that stocking density caused changes in other parameters.

Metagenomic insights into the relationship between gut microbiota and residual feed intake of small-sized meat ducks.

Introduction: The objective of this study was to determine the regulatory effects of gut microbiota on the feed efficiency (FE) of small-sized meat ducks by evaluating correlations between gut microbiota and residual feed intake (RFI). Methods: A total of 500 21-day-old healthy male ducks with similar initial body weights (645 ± 15.0 g) were raised contemporaneously in the same experimental facility until slaughter at 56 days of age. In total, nine low-RFI (LR) and nine high-RFI (HR) birds were selected for further gut microbiota composition and functional analyses based on the production performance, and the RFI was calculated from 22 to 56 days of age. Results: Growth performance results indicated a significantly lower RFI, feed conversion ratio, feed intake, and average daily feed intake in the LR ducks (P < 0.05). Taxonomy results of gut microbiota showed the identification of 19 kinds of phyla and more than 250 kinds of genera in all samples. No significant discrepancies in cecal bacterial α-diversity were discovered between the LR and HR groups, which indicated that the microbial modulatory effects on RFI may be attributed to the bacterial composition, rather than the species diversity. Differential analysis of bacterial communities between the LR and HR groups showed a significant increment of Firmicutes and a significant decline of Bacteroidetes in the LR group (P < 0.05). Specifically, genera of Erysipelatoclostridium, Parasutterella, Fournierella, and Lactococcus significantly proliferated, while Bacteroides significantly decreased in the LR group (P < 0.05). Furthermore, correlation analysis showed that the RFI was significantly correlated with carbohydrate metabolism-related bacteria including Bacteroides, Alistipes, Bifidobacterium, Ruminiclostridium_9, Sellimonas, Oscillibacter, Escherichia-Shigella, Lactococcus, and Streptococcus. Conclusion: In conclusion, the communities related to carbohydrate metabolism had positive regulatory effects on the FE of small-sized meat ducks, promoting it by improving the relative abundance and utilization of these communities. The present study provides valuable insight into the dynamics of gut microbiota underlying the variations in the FE of small-sized meat ducks.

Expression analysis of genes related to lipid metabolism in peripheral blood lymphocytes of chickens challenged with reticuloendotheliosis virus.

The underlying molecular mechanism of lipid metabolism in peripheral blood lymphocytes from chicken infected with reticuloendotheliosis virus (REV) remains poorly understood. Therefore, this scientific question was explored in vitro and in vivo. The results indicated that triglyceride content was significantly reduced, but the free fatty acid content and carnitine palmitoyltransferase-1 activity were significantly increased in blood lymphocytes after REV infection. By RNA sequencing, 97 known differentially expressed genes (DEG) related to lipid metabolism or glycometabolism were screened via Gene Ontology term analysis. On the basis of these 97 DEG, enriched pathways, including the peroxisome proliferators-activated receptor (PPAR) signaling pathway, were identified. Among these 97 DEG, some representative genes were related to lipolysis and fatty acid utilization (PPARG, LPL, PLIN2, ACOX1, ACSL1, FABP3, and FABP4). However, other genes related to lipid biosynthesis (ACSL3, ACSL6, DGAT2, LPIN1, and LPIN2) were downregulated. The quantitative polymerase chain reaction results confirmed the accuracy of the RNA sequencing data, and the in vivo outcome supports theses in vitro results. Our findings revealed that REV regulates fatty acid and lipid metabolism in peripheral blood lymphocytes from chicken. After the lymphocytes were infected with REV, the exogenous fatty acids were preferentially used; genes involved in fatty acid utilization were upregulated via the PPAR pathway, whereas genes involved in lipid and fatty acid biosynthesis were downregulated.