The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver

Chromosome-level genome sequencing and multi-omics of the Hungarian White Goose (Anser anser domesticus) reveals novel miRNA-mRNA regulation mechanism of waterfowl feather follicle development

The Hungarian White Goose (Anser anser domesticus) is an excellent European goose breed, with high feather and meat production. Despite its importance in the poultry industry, no available genome assembly information has been published. This study aimed to present Chromosome-level and functional genome sequencing of the Hungarian White Goose. The results showed that the genome assembly has a total length of 1115.82 Mb, 39 pairs of chromosomes, 92.98% of the BUSCO index, and contig N50 and scaffold N50 were up to 2.32 Mb and 60.69 Mb, respectively. Annotation of the genome assembly revealed 19550 genes, 286 miRNAs, etc. We identified 235 expanded and 1,167 contracted gene families in this breed compared with the other 16 species. We performed a positive selection analysis between this breed and four species of Anatidae to uncover the genetic information underlying feather follicle development. Further, we detected the function of miR-199-x, miR-143-y, and miR-23-z on goose embryonic skin fibroblast. In summary, we have successfully generated a highly complete genome sequence of the Hungarian white goose, which will provide a great resource to improve our understanding of gene functions and enhance the studies on feather follicle development at the genomic level.

Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet

BACKGROUND

Goose, descendants of migratory ancestors, have undergone extensive selective breeding, resulting in their remarkable ability to accumulate fat in the liver and exhibit a high tolerance for significant energy intake. As a result, goose offers an excellent model for studying obesity, metabolic disorders, and liver diseases in mammals. Although the impact of the three-dimensional arrangement of chromatin within the cell nucleus on gene expression and transcriptional regulation is widely acknowledged, the precise functions of chromatin architecture reorganization during fat deposition in goose liver tissues still need to be fully comprehended.

RESULTS

In this study, geese exhibited more pronounced changes in the liver index and triglyceride (TG) content following the consumption of the high-fat diet (HFD) than mice without significant signs of inflammation. Additionally, we performed comprehensive analyses on 10 goose liver tissues (5 HFD, 5 normal), including generating high-resolution maps of chromatin architecture, conducting whole-genome gene expression profiling, and identifying H3K27ac peaks in the livers of geese and mice subjected to the HFD. Our results unveiled a multiscale restructuring of chromatin architecture, encompassing Compartment A/B, topologically associated domains, and interactions between promoters and enhancers. The dynamism of the three-dimensional genome architecture, prompted by the HFD, assumed a pivotal role in the transcriptional regulation of crucial genes. Furthermore, we identified genes that regulate chromatin conformation changes, contributing to the metabolic adaptation process of lipid deposition and hepatic fat changes in geese in response to excessive energy intake. Moreover, we conducted a cross-species analysis comparing geese and mice exposed to the HFD, revealing unique characteristics specific to the goose liver compared to a mouse. These chromatin conformation changes help elucidate the observed characteristics of fat deposition and hepatic fat regulation in geese under conditions of excessive energy intake.

CONCLUSIONS

We examined the dynamic modifications in three-dimensional chromatin architecture and gene expression induced by an HFD in goose liver tissues. We conducted a cross-species analysis comparing that of mice. Our results contribute significant insights into the chromatin architecture of goose liver tissues, offering a novel perspective for investigating mammal liver diseases.

Multi-omics reveals goose fatty liver formation from metabolic reprogramming

To comprehensively provide insight into goose fatty liver formation, we performed an integrative analysis of the liver transcriptome, lipidome, and amino acid metabolome, as well as peripheral adipose tissue transcriptome analysis using samples collected from the overfed geese and normally fed geese. Transcriptome analysis showed that liver metabolism pathways were mainly enriched in glucolipid metabolism, amino acid metabolism, inflammation response, and cell cycle; peripheral adipose tissue and the liver cooperatively regulated liver lipid accumulation during overfeeding. Liver lipidome patterns obviously changed after overfeeding, and 157 different lipids were yielded. In the liver amino acid metabolome, the level of Lys increased after overfeeding. In summary, this is the first study describing goose fatty liver formation from an integrative analysis of transcriptome, lipidome, and amino acid metabolome, which will provide a whole new dimension to understanding the mechanism of goose fatty liver formation.

Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis

BACKGROUND

Domestic goose breeds are descended from either the Swan goose (Anser cygnoides) or the Greylag goose (Anser anser), exhibiting variations in body size, reproductive performance, egg production, feather color, and other phenotypic traits. Constructing a pan-genome facilitates a thorough identification of genetic variations, thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic variability.

RESULTS

To comprehensively facilitate population genomic and pan-genomic analyses in geese, we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq samples. By constructing the pan-genome for geese, we generated non-reference contigs totaling 612 Mb, unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes, 1,324 softcore genes, 2,734 shell genes, and 878 cloud genes in goose genomes. Furthermore, we detected an 81.97 Mb genomic region showing signs of genome selection, encompassing the TGFBR2 gene correlated with variations in body weight among geese. Genome-wide association studies utilizing single nucleotide polymorphisms (SNPs) and presence-absence variation revealed significant genomic associations with various goose meat quality, reproductive, and body composition traits. For instance, a gene encoding the SVEP1 protein was linked to carcass oblique length, and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique length. Notably, the pan-genome analysis revealed enrichment of variable genes in the "hair follicle maturation" Gene Ontology term, potentially linked to the selection of feather-related traits in geese. A gene presence-absence variation analysis suggested a reduced frequency of genes associated with "regulation of heart contraction" in domesticated geese compared to their wild counterparts. Our study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple organs and tissues in geese and analyzing population variation.

CONCLUSION

This accomplishment originates from the discernment of a multitude of selection signals and candidate genes associated with a wide array of traits, thereby markedly enhancing our understanding of the processes underlying domestication and breeding in geese. Moreover, assembling the pan-genome for geese has yielded a comprehensive apprehension of the goose genome, establishing it as an indispensable asset poised to offer innovative viewpoints and make substantial contributions to future geese breeding initiatives.

Green cabbage supplementation influences the gene expression and fatty acid levels of adipose tissue in Chinese Wanxi White geese

OBJECTIVE

Dietary green cabbage was evaluated for its impact on fatty acid synthetic ability in different adipose tissues during fattening of Wanxi White geese.

METHODS

A total of 256 Wanxi White geese at their 70 days were randomly allocated into 4 groups with 4 replicates and fed 0%, 15%, 30%, and 45% fresh green cabbage (relative to dry matter), respectively, in each group. Adipose tissues (subcutaneous and abdominal fat), liver and blood were collected from 4 birds in each replicate at their 70, 80, 90, and 100 days for fatty acid composition, relative gene expression and serum lipid analysis. Two-way or three-way analysis of variance was used for analysis.

RESULTS

The contents of palmitic acid (C16:0), palmitoleic acid (C16:1), linoleic acid (C18:2), and alpha-linolenic acid (C18:3) were feeding time dependently increased. The C16:0 and stearic acid (C18:0) were higher in abdominal fat, while C16:1, oleic acid (C18:1), and C18:2 were higher in subcutaneous fat. Geese fed 45% green cabbage exhibited highest level of C18:3. Geese fed green cabbage for 30 d exhibited higher level of C16:0 and C18:0 in abdominal fat, while geese fed 30% to 45% green cabbage exhibited higher C18:3 in subcutaneous fat. The expression of Acsl1 (p = 0.003) and Scd1 (p<0.0001) were decreased with green cabbage addition. Interaction between feeding time and adipose tissue affected elongation of long-chain fatty acids family member 6 (Elovl6), acyl-CoA synthetase longchain family member 1 (Acsl1), and stearoly-coA desaturase 1 (Scd1) gene expression levels (p = 0.013, p = 0.003, p = 0.005). Feeding time only affected serum lipid levels of free fatty acid and chylomicron. Higher contents of C16:0, C18:1, and C18:3 were associated with greater mRNA expression of Scd1 (p<0.0001), while higher level of C18:2 was associated with less mRNA expression of Scd1 (p<0.0001).

CONCLUSION

Considering content of C18:2 and C18:3, 30% addition of green cabbage could be considered for fattening for 30 days in Wanxi White geese.

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.

Developmental Changes of Duckling Liver and Isolation of Primary Hepatocytes

The liver is the main site of fat synthesis and plays an important role in the study of fat deposition in poultry. In this study, we investigated the developmental changes of duckling livers and isolated primary duck hepatocytes. Firstly, we observed morphological changes in duckling livers from the embryonic period to the first week after hatching. Liver weight increased with age. Hematoxylin-eosin and Oil Red O staining analyses showed that hepatic lipids increased gradually during the embryonic period and declined post-hatching. Liver samples were collected from 21-day-old duck embryos for hepatocyte isolation. The hepatocytes showed limited self-renewal and proliferative ability and were maintained in culture for up to 7 days. Typical parenchymal morphology, with a characteristic polygonal shape, appeared after two days of culture. Periodic acid-Schiff (PAS) staining analysis confirmed the characteristics of duck embryo hepatocytes. PCR analysis showed that these cells from duck embryos expressed the liver cell markers ALB and CD36. Immunohistochemical staining and immunofluorescence analysis also confirmed ALB and CK18 expression. Our findings provide a novel insight regarding in vitro cell culture and the characteristics of hepatocytes from avian species, which could enable further studies concerning specific research on duck lipid metabolism.

Comparative Transcriptome Analyses of Leg Muscle during Early Growth between Geese (Anser cygnoides) Breeds Differing in Body Size Characteristics

Goose is an important poultry commonly raised for meat. The early growth performance of geese significantly influences their market weight and slaughter weight, affecting the poultry industry's economic benefits. To identify the growth surge between the Shitou goose and the Wuzong goose, we collected the early growth body traits from 0 to 12 weeks. In addition, we investigated the transcriptomic changes in leg muscles at the high growth speed period to reveal the difference between the two geese breeds. We also estimated the growth curve parameters under three models, including the logistic, von Bertalanffy, and Gompertz models. The results showed that except for body length and keel length, the best-fitting model between the body weight and body size of the Shitou and Wuzong was the logistic model. The growth turning points of Shitou and Wuzong were 5.954 and 4.944 weeks, respectively, and the turning point of their body weight was 1459.01 g and 478.54 g, respectively. Growth surge occurred at 2-9 weeks in Shitou goose and at 1-7 weeks in Wuzong goose. The body size traits of the Shitou goose and Wuzong goose showed a trend of rapid growth in the early stage and slow growth in the later stage, and the Shitou goose growth was higher than the Wuzong goose. For transcriptome sequencing, a total of 87 differentially expressed genes (DEGs) were identified with a fold change ≥ 2 and a false discovery rate < 0.05. Many DEGs have a potential function for growth, such as CXCL12, SSTR4, FABP5, SLC2A1, MYLK4, and EIF4E3. KEGG pathway analysis identified that some DEGs were significantly enriched in the calcium signaling pathway, which may promote muscle growth. The gene-gene interaction network of DEGs was mainly related to the transmission of cell signals and substances, hematological system development, and functions. This study can provide theoretical guidance for the production and breeding management of the Shitou goose and Wuzong goose and help reveal the genetic mechanisms underlying diverse body sizes between two goose breeds.

Population Structure and Selection Signatures of Domestication in Geese

The goose is an economically important poultry species and was one of the first to be domesticated. However, studies on population genetic structures and domestication in goose are very limited. Here, we performed whole genome resequencing of geese from two wild ancestral populations, five Chinese domestic breeds, and four European domestic breeds. We found that Chinese domestic geese except Yili geese originated from a common ancestor and exhibited strong geographical distribution patterns and trait differentiation patterns, while the origin of European domestic geese was more complex, with two modern breeds having Chinese admixture. In both Chinese and European domestic geese, the identified selection signatures during domestication primarily involved the nervous system, immunity, and metabolism. Interestingly, genes related to vision, skeleton, and blood-O2 transport were also found to be under selection, indicating genetic adaptation to the captive environment. A forehead knob characterized by thickened skin and protruding bone is a unique trait of Chinese domestic geese. Interestingly, our population differentiation analysis followed by an extended genotype analysis in an additional population suggested that two intronic SNPs in EXT1, an osteochondroma-related gene, may plausibly be sites responsible for knob. Moreover, CSMD1 and LHCGR genes were found to be significantly associated with broodiness in Chinese domestic geese and European domestic geese, respectively. Our results have important implications for understanding the population structure and domestication of geese, and the selection signatures and variants identified in this study might be useful in genetic breeding for forehead knob and reproduction traits.

Bacterial lipopolysaccharide with different administration routes affects intestinal mucosal morphological, immunological, and microbial barrier functions in goslings

The current study was conducted to evaluate the effects of different administration routes of bacterial lipopolysaccharide (LPS) on intestinal mucosal morphological, immunological, and microbial barrier functions in goslings. First, we compared intestinal villi morphology of goslings under intraperitoneal or oral LPS treatment through hematoxylin and eosin staining. Then, we determined the signatures of the microbiome in the ileum mucosa of goslings subjected to oral LPS treatment at 0, 2, 4, and 8 mg/kg BW by 16S sequencing, and analyzed the changes in intestinal barrier functions and permeability, levels of LPS in the ileum mucosa, plasma, and liver tissue, and the induced inflammatory response of Toll-like receptor 4 (TLR4). As a result, intraperitoneal LPS injection resulted in a thicker intestinal wall in the ileum within a short time, whereas villus height was less affected; in contrast, oral LPS treatment exerted a stronger influence on villus height but not on intestinal wall thickness. We also found that oral LPS treatment affected the structure of the intestinal microbiome, reflected by changes in the clustering of intestinal microbiota. The average abundance of Muribaculaceae showed an increasing trend with increasing LPS levels, and that of the genus Bacteroides decreased, compared with the control group. In addition, oral LPS treatment with 8 mg/kg BW affected the intestinal epithelial morphology, damage the mucosal immune barrier, downregulated the expression of tight junction proteins, increased circulating D-lactate levels, and stimulated the secretion of various inflammatory mediators and activation of the TLR4/MyD88/NFκB pathway. This study presented the injuries of intestinal mucosal barrier function induced by LPS challenges in goslings and provided a scientific model for searching the novel strategies to attenuate the immunological stress and gut injury caused by LPS.

Egg Yolk Fat Deposition Is Regulated by Diacylglycerol and Ceramide Enriched by Adipocytokine Signaling Pathway in Laying Hens

The mechanism which regulates differential fat deposition in egg yolk from the indigenous breeds and commercial laying hens is still unclear. In this research, Chinese indigenous Huainan Partridge chickens and Nongda III commercial laying hens were used for egg collection and liver sampling. The weight of eggs and yolk were recorded. Yolk fatty acids were determined by gas chromatography-mass spectrometry. Lipid metabolites in the liver were detected by liquid chromatography-mass spectrometry. Yolk weight, yolk ratio and yolk fat ratio exhibited higher in the Huainan Partridge chicken than that of the Nongda III. Compared to the Nongda III, the content of total saturated fatty acid was lower, while the unsaturated fatty acid was higher in the yolk of the Huainan Partridge chicken. Metabolites of phosphatidylinositol and phosphatidylserine from glycerolphospholipids, and metabolites of diacylglycerol from glycerolipids showed higher enrichment in the Huainan Partridge chicken than that of the Nongda III, which promoted the activation of the adipocytokine signaling pathway. However, metabolites of phosphatidic acid, phosphatidylcholine, phosphatidylethanolamine and lysophosphatidylcholine from glycerol phospholipids, and metabolites of triacylglycerol from glycerolipids showed lower enrichment in the Huainan Partridge chicken than that of the Nongda III. The high level of yolk fat deposition in the Huainan Partridge chicken is regulated by the activation of the adipocytokine signaling pathway which can promote the accumulation of diacylglycerol and ceramide in the liver.

Integrative analysis of transcriptome and lipidome reveals fructose pro-steatosis mechanism in goose fatty liver

To further explore the fructose pro-steatosis mechanism, we performed an integrative analysis of liver transcriptome and lipidome as well as peripheral adipose tissues transcriptome analysis using samples collected from geese overfed with maize flour (control group) and geese overfed with maize flour supplemented with 10% fructose (treatment group). Overfeeding period of the treatment group was significantly shorter than that of the control group (p < 0.05). Dietary supplementation with 10% fructose induced more severe steatosis in goose liver. Compared with the control group, the treatment group had lower in ceramide levels (p < 0.05). The key differentially expressed genes (DEGs) (control group vs. treatment group) involved in liver fatty acid biosynthesis and steroid biosynthesis were downregulated. The conjoint analysis between DEGs and different lipids showed that fatty acid biosynthesis and steroid biosynthesis were the highest impact score pathways. In conclusion, fructose expedites goose liver lipid accumulation maximization during overfeeding.

Nonlinear model fitting analysis of feather growth and development curves in the embryonic stages of Jilin white geese (Anser cygnoides)

Poultry is subject to varying degrees of feather loss and feather pecking during production, which seriously affects the live appearance and carcass appearance of their commercial traits and greatly reduces the production profitability of the farming enterprise. It also has an impact on down production and quality in the case of geese. In this study, mathematical models (Logistic, Gompertz, and Von Bertalanffy) were used to assess feather growth and development during the embryonic period in Jilin white geese (Anser cygnoides) predicting the weight and length of feathers from the back, chest, and belly tracts at different embryonic ages, to determine which growth model more accurately described feather growth patterns. The result first showed that the primary feather follicles of the Jilin white goose developed at E14 and secondary feather follicles at E18; primary feather follicle density increased and then decreased, whereas secondary feather follicle density increased continuously and the primary and secondary feather follicles developed independently. Secondly, the embryonic feather growth followed a slow-fast-slow pattern, with feathers growing slowly from E12 to E18, quickly from E18 to E24, and then decreasing after E24 until just before emergence (E30). In addition, before E14, feathers were concentrated in the back tracts, and no feathers were found on the head, neck, chest, abdomen, or wings. By E22, the whole body of the embryo was covered with feathers, and the back feathers were the earliest and fastest to develop. Compared to the Gompertz and von Bertalanffy models, the logistic model fit (R2 = 0.997) was the highest, while the sum of residual squares (RSS = 25661.67), Akaike's information criterion (AIC = 77.600), Bayesian information criterion (BIC = 78.191), and mean square error (MSE = 2851.296) were the lowest. Therefore, the logistic model was more suitable for describing the changes in whole-body feather growth during the embryonic period in Jilin white geese. In conclusion, using the growth curve model to explain the relationship between feather growth and embryonic age in geese will potentially speed up the process of genetic improvement in Jilin white geese (A. cygnoides) and thus provide scientific support for molecular genetic breeding.

Chromosome-level genome assembly of goose provides insight into the adaptation and growth of local goose breeds

BACKGROUND

Anatidae contains numerous waterfowl species with great economic value, but the genetic diversity basis remains insufficiently investigated. Here, we report a chromosome-level genome assembly of Lion-head goose (Anser cygnoides), a native breed in South China, through the combination of PacBio, Bionano, and Hi-C technologies.

FINDINGS

The assembly had a total genome size of 1.19 Gb, consisting of 1,859 contigs with an N50 length of 20.59 Mb, generating 40 pseudochromosomes, representing 97.27% of the assembled genome, and identifying 21,208 protein-coding genes. Comparative genomic analysis revealed that geese and ducks diverged approximately 28.42 million years ago, and geese have undergone massive gene family expansion and contraction. To identify genetic markers associated with body weight in different geese breeds, including Wuzong goose, Huangzong goose, Magang goose, and Lion-head goose, a genome-wide association study was performed, yielding an average of 1,520.6 Mb of raw data that detected 44,858 single-mucleotide polymorphisms (SNPs). Genome-wide association study showed that 6 SNPs were significantly associated with body weight and 25 were potentially associated. The significantly associated SNPs were annotated as LDLRAD4, GPR180, and OR, enriching in growth factor receptor regulation pathways.

CONCLUSIONS

We present the first chromosome-level assembly of the Lion-head goose genome, which will expand the genomic resources of the Anatidae family, providing a basis for adaptation and evolution. Candidate genes significantly associated with different goose breeds may serve to understand the underlying mechanisms of weight differences.

Single-cell RNA sequencing revealed the liver heterogeneity between egg-laying duck and ceased-laying duck

BACKGROUND

In the late phase of production, ducks untimely cease laying, leading to a lower feed conversion. Liver plays a vital role in the synthesis and transport of yolk materials during egg formation in birds. However, the molecular mechanism of liver in ceased-laying duck is far from clear, higher resolution and deeper analysis is needed. Sing-cell RNA-sequencing of 10 × Genomics platform can help to map the liver single cell gene expression atlas of Shaoxing duck and provide new insights into the liver between egg-laying and ceased-laying ducks.

RESULTS

About 20,000 single cells were profiled and 22 clusters were identified. All the clusters were identified as 6 cell types. The dominant cell type is hepatocyte, accounted for about 60% of all the cells. Of note, the heterogeneity of cells between egg-laying duck and ceased-laying duck mainly occurred in hepatocytes. Cells of cluster 3 and 12 were the unique hepatocyte states of egg-laying ducks, while cells of cluster 0 and 15 were the unique hepatocyte states of ceased-laying ducks. The expression mode of yolk precursor transporters, lipid metabolizing enzymes and fibrinogens were different in hepatocytes between egg-laying duck and ceased-laying duck. APOV1, VTG2, VTG1, APOB, RBP, VTDB and SCD might be activated in egg-laying ducks, while APOA1, APOA4, APOC3, FGB and FGG might be activated in ceased-laying ducks.

CONCLUSIONS

Our study further proofs that APOV1 and APOB play key roles in egg production, rather than APOA1 and APOA4. It is also the first to detect a correlation between the higher expression of APOC3, FGB, FGG and ceased-laying in duck.

Effects of a high-fat diet on the growth performance, lipid metabolism, and the fatty acids composition of liver and skin fat in Pekin ducks aged from 10 to 40 days

This study aimed to investigate the effect of a high-fat diet on the growth performance, serum, liver, and skin lipid metabolism as well as the fatty acids composition of liver and skin fat in Pekin ducks from 10 to 40 d of age based on a pair-fed group. Two hundred forty healthy male ducks (10 d old, 470.53 ± 0.57 g) were randomly divided into 3 groups (8 replicates per cage of 10 ducks): a normal diet (ND, 3% fat), a high-fat diet (HFD, 9% fat), and a pair-fed diet (PFD, given the ND in an amount equal to that consumed of the HFD to eliminate the effects of feed intake). The results were as follows: compared to ND feeding, HFD feeding significantly decreased (P < 0.05) the feed intake and feed:gain ratio (F:G), along with serum triglyceride and nonesterified fatty acid contents. When compared with the ND and PFD, the HFD significantly decreased (P < 0.05) the liver weight and inhibited hepatic de novo lipogenesis (glucose-6-phosphate dehydrogenase and malate dehydrogenase activities), β-oxidation (carnitine palmitoyltransferase-1 content), and decreased saturated fatty acids and monounsaturated fatty acids deposition. Moreover, the HFD significantly increased (P < 0.05) the total fat content, lipid droplet area, and polyunsaturated fatty acids (PUFAs) content in the liver, as well as the abdominal fat weight, subcutaneous fat weight, the total fat and PUFAs content in skin fat. These results suggested that the HFD improved feed efficiency, which was related to HFD feeding inhibiting hepatic de novo lipogenesis and β-oxidation and promoting the deposition of fat in skin as well as altering the fatty acids composition of the liver and skin fat in Pekin ducks.

Lipidomics analysis reveals new insights into the goose fatty liver formation

Our previous study described the mechanism of goose fatty liver formation from cell culture and transcriptome. However, how lipidome of goose liver response to overfeeding is unclear. In this study, we used the same batch of geese (control group and corn flour overfeeding group) to explore the lipidome changes and underlying metabolic mechanisms of goose fatty liver formation. Liquid chromatography-mass spectrometry (LC-MS) was provided to lipidome detection. Liver lipidomics profiles analysis was performed by principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA) and orthogonal partial least squares-discriminant analysis (OPLS-DA), different lipids were identified and annotated, and the enriched metabolic pathways were showed. The results of PCA, PLS-DA, and OPLS-DA displayed a clear separation and discrimination between control group and corn flour overfeeding group. Two hundred and fifty-one different lipids were yielded, which were involved in triglyceride (TG), diglyceride (DG), phosphatidic acids (PA), phosphatidylinositols (PI), phosphatidylethanolamines (PE), phosphatidylcholines (PC), lyso-phosphatidylcholines (LPC), monogalactosylmonoacylglycerol (MGMG), sphingolipids (SM), ceramides (Cer), and hexaglycosylceramides (Hex1Cer). Different lipids were enriched in glycerophospholipid metabolism, glycerolipid metabolism, phosphatidylinositol signaling system, inositol phosphate metabolism, glycosylphosphatidylinositol (GPI)-anchor biosynthesis and sphingolipid metabolism. In conclusion, this is the first report describing the goose fatty liver formation from lipidomics, this study might provide some insights into the underlying glucolipid metabolism disorders in the process of fatty liver formation.

Effects of Dietary Zinc Deficiency on Skin Breaking Strength and Fatty Acid Composition in Broiler Chickens and Pekin Ducks

This study is aimed at investigating the effect of dietary zinc deficiency (ZnD) on skin breaking strength and skin chemical and fatty acid composition in broiler chickens and Pekin ducks. A total of 200 1-day-old male broiler chickens and 200 1-day-old male ducklings were used in a 2 × 2 factorial design and randomly allocated to 4 treatments with 10 replicated cages of 10 birds per cage. Diets containing zinc at 84.77 mg/kg and 20.42 mg/kg were regarded as the control diet and zinc-deficient diet, respectively. The results showed the following: (1) dietary ZnD decreased (P < 0.05) the breast skin weight (day 21), breast skin index (day 21), skin fat content (day 7), and skin Zn content (days 7, 14, and 21) of ducks, but only increased (P < 0.05) the skin fat content of broiler chickens at 7 days of age; ducks had a higher (P < 0.05) breast skin weight, breast skin index, and skin breaking strength as well as a lower skin fat content (days 7 and 14) than those in broiler chickens. (2) Dietary ZnD decreased the content of myristic acid (day 21) and increased the content of oleic acid (day 7) content in the skin of ducks and increased the palmitic acid (day 7) content in the skin of broiler chickens (P < 0.05) and increased the MUFA (day 7) content in the skin and the atherogenic index (day 21) in ducks. The contents of myristic acid (day 21), stearic acid (day 21), and oleic acid (days 7, 14, and 21) in the skin of broiler chickens were lower (P < 0.05) than those in ducks of the same age. In conclusion, using skin weight, skin index and skin MUFA content as criteria, the results indicated that meat ducks were more sensitive to dietary ZnD than broiler chickens. Using skin fat content as criterion, the results indicated that broiler chickens were more sensitive to dietary ZnD than meat ducks.

Regulation of the cecal microbiota community and the fatty liver deposition by the addition of brewers’ spent grain to feed of Landes geese

The effects of brewers’ spent grain (BSG) diets on the fatty liver deposition and the cecal microbial community were investigated in a total of 320 healthy 5-day-old Landes geese. These geese were randomly and evenly divided into 4 groups each containing 8 replicates and 10 geese per replicate. These four groups of geese were fed from the rearing stage (days 5–60) to the overfeeding stage (days 61–90). The Landes geese in group C (control) were fed with basal diet (days 5–90); group B fed first with basal diet in the rearing stage and then basal diet + 4% BSG in the overfeeding stage; group F first with basal diet + 4% BSG during the rearing stage and then basal diet in the overfeeding stage; and group W with basal diet + 4% BSG (days 5–90). The results showed that during the rearing stage, the body weight (BW) and the average daily gain (ADG) of Landes geese were significantly increased in groups F and W, while during the overfeeding stage, the liver weights of groups W and B were significantly higher than that of group C. The taxonomic structure of the intestinal microbiota revealed that during the overfeeding period, the relative abundance of Bacteroides in group W was increased compared to group C, while the relative abundances of Escherichia–Shigella and prevotellaceae_Ga6A1_group were decreased. Results of the transcriptomics analysis showed that addition of BSG to Landes geese diets altered the expression of genes involved in PI3K-Akt signaling pathway and sphingolipid metabolism in the liver. Our study provided novel experimental evidence based on the cecal microbiota to support the application of BSG in the regulation of fatty liver deposition by modulating the gut microbiota in Landes geese.

Using comparative genomics to detect mutations regulating plumage variations in graylag (A. anser) and swan geese (A. cygnoides)

Although graylag geese (A. anser) showed similar plumages of white, grey, and white with grey patches compared to those in swan geese (A. cygnoides), it was believed the substantial molecular mechanism for plumage variations were different. To date, studies on genes responsible for diverse plumages among graylag geese were limited and causal mutations remain unknown. In this study, genomes from 57 individuals belonging to six breeds showing different plumages were sequenced at ∼10X depth. Firstly, the allele frequency differences (AFD) of variants on the scaffold394 (NW_013185915.1) between grey and white goose breeds (A. anser) was calculated and a genomic region between 768,290-779,889 bp was detected to carry candidate variants associated with plumages, including one SNP (g. 775,151G > T, ∼18.6 kb upstream of EDNRB2) found to be fixed in white geese. This region was overlapped with the one detected by the haplotype-based sweep analysis, in which significant signals defined a candidate region of 736,610-820,622 bp on the same scaffold. Results from the transcriptomic data showed that expression levels of EDNRB2 and many other melanogenesis-related genes were significantly decreased among white geese compared to that in grey geese, especially at late embryonic stages (>E15). Modifications at transcriptional levels might result in abnormal melanocyte developments and thus the white plumages when they grow up. In addition, a frameshift mutation (C > -) in exon4 of MLANA gene on scaffold176 (NW_013185876.1) was suggested as the causal mutation for sex-linked dilution phenotype in graylag geese although this requires more demonstration experiments. Together with observed white plumages caused by EDNRB2 mutations in coding regions among swan geese and chicken, our study provided new examples to study the parallel evolution.

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

Simple Summary

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

Abstract

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

Betaine Promotes Fat Accumulation and Reduces Injury in Landes Goose Hepatocytes by Regulating Multiple Lipid Metabolism Pathways

Betaine is a well-established supplement used in livestock feeding. In our previous study, betaine was shown to result in the redistribution of body fat, a healthier steatosis phenotype, and an increased liver weight and triglyceride storage of the Landes goose liver, which is used for foie-gras production. However, these effects are not found in other species and strains, and the underlying mechanism is unclear. Here, we studied the underpinning molecular mechanisms by developing an in vitro fatty liver cell model using primary Landes goose hepatocytes and a high-glucose culture medium. Oil red-O staining, a mitochondrial membrane potential assay, and a qRT-PCR were used to quantify lipid droplet characteristics, mitochondrial β-oxidation, and fatty acid metabolism-related gene expression, respectively. Our in vitro model successfully simulated steatosis caused by overfeeding. Betaine supplementation resulted in small, well-distributed lipid droplets, consistent with previous experiments in vivo. In addition, mitochondrial membrane potential was restored, and gene expression of fatty acid synthesis genes (e.g., sterol regulatory-element binding protein, diacylglycerol acyltransferase 1 and 2) was lower after betaine supplementation. By contrast, the expression of lipid hydrolysis transfer genes (mitochondrial transfer protein and lipoprotein lipase) was higher. Overall, the results provide a scientific basis and theoretical support for the use of betaine in animal production.

In Ovo Injection of CHIR-99021 Promotes Feather Follicle Development via Modulating the Wnt Signaling Pathway and Transcriptome in Goose Embryos (Anser cygnoides)

Feather performs important physiological functions in birds, and it is also one of the economic productions in goose farming. Understanding and modulating feather follicle development during embryogenesis are essential for bird biology and the poultry industry. CHIR-99021 is a potent Wnt/β-catenin signaling pathway activator associated with feather follicle development. In this study, goose embryos (Anser cygnoides) received an in ovo injection of CHIR-9902, which was conducted at the beginning of feather follicle development (E9). The results showed that feather growth and feather follicle development were promoted. The Wnt signaling pathway was activated by the inhibition of GSK-3β. Transcriptomic analyses showed that the transcription changes were related to translation, metabolism, energy transport, and stress in dorsal tissue of embryos that received CHIR-99021, which might be to adapt and coordinate the promoting effects of CHIR-99021 on feather follicle development. This study suggests that in ovo injection of CHIR-99021 is a potential strategy to improve feather follicle development and feather-related traits for goose farming and provides profiling of the Wnt signaling pathway and transcriptome in dorsal tissue of goose embryos for further understanding of feather follicle development.

Metabolic Profiling Analysis of Liver in Landes Geese During the Formation of Fatty Liver via GC-TOF/MS

Fatty liver production results from the process of overfeeding geese, inducing a dramatic increase in de novo liver lipogenesis. To investigate the alteration of liver metabolites by overfeeding, especially lipid metabolites, and the potential pathways causing these changes, 60 Landes geese at 65 days old were raised in three groups with 20 geese per group, namely, the D0 group (free from gavage), D7 group (overfeeding for 7 days), and D25 group (overfeeding for 25 days). At 90 days old, segments of liver tissue were collected from 10 geese of each group for gas chromatography time-of-flight/mass spectrometry (GC-TOF/MS) analysis. A large number of endogenous molecules in the livers of geese were altered dramatically by overfeeding. In the livers of overfed geese, the level of oleic acid was observed to continuously increase, while the levels of phenylalanine, methyl phosphate, sulfuric acid, and 3-hydroxybenzaldehyde were decreased. The most significantly different metabolites were enriched in amino acid, lipid, and nucleotide metabolism pathways. The present study further supports the idea that Landes geese efficiently produce fatty liver, and potential biomarkers and disturbed metabolic pathways during the process of forming fatty liver were identified. In conclusion, this study might provide some insights into the underlying mechanisms of fatty liver formation.

Genome-Wide Association Study Based on Random Regression Model Reveals Candidate Genes Associated with Longitudinal Data in Chinese Simmental Beef Cattle

Simple Summary

Genome-wide association study (GWAS) has become the main approach for detecting functional genes that affects complex traits. For growth traits, the conventional GWAS method can only deal with the single-record traits observed at specific time points, rather than the longitudinal traits measured at multiple time points. Previous studies have reported the random regression model (RRM) for longitudinal data could overcome the limitation of the traditional GWAS model. Here, we present an association analysis based on RRM (GWAS-RRM) for 808 Chinese Simmental beef cattle at four stages of age. Ultimately, 37 significant single-nucleotide polymorphisms (SNPs) and several important candidate genes were screened to be associated with the body weight. Enrichment analysis showed these genes were significantly enriched in the signaling transduction pathway and lipid metabolism. This study not only offers a further understanding of the genetic basis for growth traits in beef cattle, but also provides a robust analytics tool for longitudinal traits in various species.

Abstract

Body weight (BW) is an important longitudinal trait that directly described the growth gain of bovine in production. However, previous genome-wide association study (GWAS) mainly focused on the single-record traits, with less attention paid to longitudinal traits. Compared with traditional GWAS models, the association studies based on the random regression model (GWAS-RRM) have better performance in the control of the false positive rate through considering time-stage effects. In this study, the BW trait data were collected from 808 Chinese Simmental beef cattle aged 0, 6, 12, and 18 months, then we performed a GWAS-RRM to fit the time-varied SNP effect. The results showed a total of 37 significant SNPs were associated with BW. Gene functional annotation and enrichment analysis indicated FGF4, ANGPT4, PLA2G4A, and ITGA5 were promising candidate genes for BW. Moreover, these genes were significantly enriched in the signaling transduction pathway and lipid metabolism. These findings will provide prior molecular information for bovine gene-based selection, as well as facilitate the extensive application of GWAS-RRM in domestic animals.

Integrated mRNA and miRNA transcriptome analysis provides novel insights into the molecular mechanisms underlying goose pituitary development during the embryo-to-hatchling transition

It is well established that the endocrine system plays a pivotal role in preparing the avian embryos for the abrupt switch from chorioallantoic to pulmonary respiration during the critical embryo-to-hatchling transition. However, as the master gland of the endocrine system, there has been little research focusing on the molecular mechanisms controlling the development and function of the pituitary gland during the peri-hatch period in birds. In the present study, we aimed to determine the genome-wide mRNA and miRNA transcriptome profiles of the pituitary during the embryo-to-hatchling transition period from embryonic day 22 (E22) to post-hatching day 6 (P6) in the goose (Anser cygnoides). Of note, expression of Anser_cygnoides_newGene_32456 and LOC106031011 were significantly different among these 4 stages (i.e., E22, E26, P2, and P6). Meanwhile, the neuroactive ligand-receptor interaction pathway was significantly enriched by the DEGs commonly identified among three pairwise comparisons. At the miRNA transcriptome level, there were not commonly identified DE miRNAs among these 4 stages, while the 418 of their predicted target genes were mutually shared. Both the target genes of DE miRNAs in each comparison and these 418 shared target genes were significantly enriched in the ECM-receptor interaction and focal adhesion pathways. In the predicted miRNA-mRNA interaction networks of these 2 pathways, novel_miRNA_467, novel_miRNA_154, and novel_miRNA_340 were the hub miRNAs. In addition, multiple DE miRNAs also showed predicted target relationships with the DEGs associated with extracellular matrix (ECM) components. Among them, expression of novel_miR_120, tgu-miR-92-3p, and novel_miR_398 was significantly negatively correlated with that of LAMC3 (laminin subunit gamma3), suggesting that these miRNAs may regulate pituitary tissue remodeling and functional changes through targeting LAMC3 during development. These identified DE mRNAs and miRNAs as well as their predicted interaction networks involved in regulation of tissue remodeling and cellular functions were most likely to play critical roles in facilitating the embryo-to-hatchling transition. These results provide novel insights into the early developmental process of avian pituitary gland and will help better understand the underlying molecular mechanisms.

Integrative analysis of histomorphology, transcriptome and whole genome resequencing identified DIO2 gene as a crucial gene for the protuberant knob located on forehead in geese

Background

During domestication, remarkable changes in behavior, morphology, physiology and production performance have taken place in farm animals. As one of the most economically important poultry, goose owns a unique appearance characteristic called knob, which is located at the base of the upper bill. However, neither the histomorphology nor the genetic mechanism of the knob phenotype has been revealed in geese.

Results

In the present study, integrated radiographic, histological, transcriptomic and genomic analyses revealed the histomorphological characteristics and genetic mechanism of goose knob. The knob skin was developed, and radiographic results demonstrated that the knob bone was obviously protuberant and pneumatized. Histologically, there were major differences in structures in both the knob skin and bone between geese owing knob (namely knob-geese) and those devoid of knob (namely non-knob geese). Through transcriptome analysis, 592 and 952 genes differentially expressed in knob skin and bone, and significantly enriched in PPAR and Calcium pathways in knob skin and bone, respectively, which revealed the molecular mechanisms of histomorphological differences of the knob between knob- and non-knob geese. Furthermore, integrated transcriptomic and genomic analysis contributed to the identification of 17 and 21 candidate genes associated with the knob formation in the skin and bone, respectively. Of them, DIO2 gene could play a pivotal role in determining the knob phenotype in geese. Because a non-synonymous mutation (c.642,923 G > A, P265L) changed DIO2 protein secondary structure in knob geese, and Sanger sequencing further showed that the AA genotype was identified in the population of knob geese, and was prevalent in a crossing population which was artificially selected for 10 generations.

Conclusions

This study was the first to uncover the knob histomorphological characteristics and genetic mechanism in geese, and DIO2 was identified as the crucial gene associated with the knob phenotype. These data not only expand and enrich our knowledge on the molecular mechanisms underlying the formation of head appendages in both mammalian and avian species, but also have important theoretical and practical significance for goose breeding.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07822-9.

Pooled Sequencing Analysis of Geese (Anser cygnoides) Reveals Genomic Variations Associated With Feather Color

During the domestication of the goose a change in its feather color took place, however, the molecular mechanisms responsible for this change are not completely understood. Here, we performed whole-genome resequencing on three pooled samples of geese (feral and domestic geese), with two distinct feather colors, to identify genes that might regulate feather color. We identified around 8 million SNPs within each of the three pools and validated allele frequencies for a subset of these SNPs using PCR and Sanger sequencing. Several genomic regions with signatures of differential selection were found when we compared the gray and white feather color populations using the F_ST and Hp approaches. When we combined previous functional studies with our genomic analyses we identified 26 genes (KITLG, MITF, TYRO3, KIT, AP3B1, SMARCA2, ROR2, CSNK1G3, CCDC112, VAMP7, SLC16A2, LOC106047519, RLIM, KIAA2022, ST8SIA4, LOC106044163, TRPM6, TICAM2, LOC106038556, LOC106038575, LOC106038574, LOC106038594, LOC106038573, LOC106038604, LOC106047489, and LOC106047492) that potentially regulate feather color in geese. These results substantially expand the catalog of potential feather color regulators in geese and provide a basis for further studies on domestication and avian feather coloration.

Molecular changes associated with migratory departure from wintering areas in obligate songbird migrants

Day length regulates the development of spring migratory and subsequent reproductive phenotypes in avian migrants. This study used molecular approaches, and compared mRNA and proteome-wide expression in captive redheaded buntings that were photostimulated under long-day (LD) conditions for 4 days (early stimulated, LD-eS) or for ∼3 weeks until each bird had shown 4 successive nights of Zugunruhe (stimulated, LD-S); controls were maintained under short days. After ∼3 weeks of LD, photostimulated indices of the migratory preparedness (fattening, weight gain and Zugunruhe) were paralleled with upregulated expression of acc, dgat2 and apoa1 genes in the liver, and of cd36, fabp3 and cpt1 genes in the flight muscle, suggesting enhanced fatty acid (FA) synthesis and transport in the LD-S state. Concurrently, elevated expression of genes involved in the calcium ion signalling and transport (camk1 and atp2a2; camk2a in LD-eS), cellular stress (hspa8 and sod1, not nos2) and metabolic pathways (apoa1 and sirt1), but not of genes associated with migratory behaviour (adcyap1 and vps13a), were found in the mediobasal hypothalamus (MBH). Further, MBH-specific quantitative proteomics revealed that out of 503 annotated proteins, 28 were differentially expressed (LD-eS versus LD-S: 21 up-regulated and 7 down-regulated) and they enriched five physiological pathways that are associated with FA transport and metabolism. These first comprehensive results on gene and protein expression suggest that changes in molecular correlates of FA transport and metabolism may aid the decision for migratory departure from wintering areas in obligate songbird migrants.

Molecular characterization, developmental expression, and modulation of occludin by early intervention with Clostridium butyricum in Muscovy ducks

Occludin is an important component of tight junction proteins and has been extensively studied in animals such as mice, chickens, geese, and pigs. As one of the most important waterfowl species in China, Muscovy duck (Cairina moschata) is an important economic animal for meat. However, research on the occludin gene in Muscovy duck is lacking. In the present study, Muscovy duck occludin cDNA was cloned for the first time. The length of the cDNA was 1,699 bp, and it showed a high sequence similarity with the Anser cygnoides domesticus and Gallus gallus occludin genes. The occludin gene was differentially expressed in the tissues of healthy ducks. The highest and lowest expressions of occludin were observed in the crop and the spleen, respectively. After the oral administration of Clostridium butyricum (CB), the occludin expression in the ileum of 7-day-old Muscovy ducks was significantly upregulated and subsequently showed a decreasing trend in 14-day-old Muscovy ducks. Under the early intervention of CB, no significant difference was observed in the occludin expression of cecum between the control and CB group. Collectively, these results suggest that CB plays an important role in regulating the expression of the occludin gene in Muscovy ducks, and adding CB in feed may maintain the intestinal barrier of ducks by regulating the expression of occludin.

Genomic Analyses of Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa

Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long- and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.

Difference in developmental dynamics between subcutaneous and abdominal adipose tissues in goose (Anser Cygnoides)

Goose (Anas cygnoides), as a typical species domesticated from a migratory bird, has maintained the capability of depositing excess lipid and preferentially accumulating fat within the abdomen and subcutaneous, which not only leads to decrease in yield of meat product, but also affects the feed conversion rate. Here, an experiment was conducted to examine the difference in developmental dynamics between subcutaneous (SAT) and abdominal adipose tissues (AAT) in goose. The results showed that SAT could be clearly observed at embryonic days (E) 15, whereas AAT were clearer until E20. Although the weights of SAT and AAT showed a significant rising with advancing age (P < 0.05), their gains were not completely uniform, and more adipose deposited preferentially toward AAT after birth (P < 0.05). Additionally, a clear expansion in adipocyte size was observed in AAT and SAT during embryonic stages (P < 0.05). The average adipocyte area in AAT continued to increase after birth (P < 0.05), while the cell areas in SAT were relatively invariable (P > 0.05). Furthermore, the expression levels of FABP4/aP2, ACSL1 and PPARγ were much higher in SAT than in AAT, whereas relative higher expression level of IL-6 was observed in the AAT during embryonic stages. After birth, the more expression of LPL and PPARα were detected in AAT than did in SAT (P < 0.05), whereas greater ATGL expression was in SAT (P < 0.05). Taken together, these findings suggest that AAT may display greater fat storage capacity than SAT accompanied by changes in cell area and lipogenic capacity. Considering that there is disparity in the individual adipose tissues, we suggested that careful consideration for the precise interventions used to control SAT or AAT deposition in meat-producing animals to improve feed efficiency.

Genome-Wide Association Study-Based Identification of SNPs and Haplotypes Associated With Goose Reproductive Performance and Egg Quality

Geese are one of the most economically important waterfowl. However, the low reproductive performance and egg quality of geese hinder the development of the goose industry. The identification and application of genetic markers may improve the accuracy of beneficial trait selection. To identify the genetic markers associated with goose reproductive performance and egg quality traits, we performed a genome-wide association study (GWAS) for body weight at birth (BBW), the number of eggs at 48 weeks of age (EN48), the number of eggs at 60 weeks of age (EN60) and egg yolk color (EYC). The GWAS acquired 2.896 Tb of raw sequencing data with an average depth of 12.44× and identified 9,279,339 SNPs. The results of GWAS showed that 26 SNPs were significantly associated with BBW, EN48, EN60, and EYC. Moreover, five of these SNPs significantly associated with EN48 and EN60 were in a haplotype block on chromosome 35 from 4,512,855 to 4,541,709 bp, oriented to TMEM161A and another five SNPs significantly correlated to EYC were constructed in haplotype block on chromosome 5 from 21,069,009 to 21,363,580, which annotated by TMEM161A, CALCR, TFPI2, and GLP1R. Those genes were enriched in epidermal growth factor-activated receptor activity, regulation of epidermal growth factor receptor signaling pathway. The SNPs, haplotype markers, and candidate genes identified in this study can be used to improve the accuracy of marker-assisted selection for the reproductive performance and egg quality traits of geese. In addition, the candidate genes significantly associated with these traits may provide a foundation for better understanding the mechanisms underlying reproduction and egg quality in geese.

A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals

BACKGROUND

Ducks have a typical avian karyotype that consists of macro- and microchromosomes, but a pair of much less differentiated ZW sex chromosomes compared to chickens. To elucidate the evolution of chromosome architectures between ducks and chickens, and between birds and mammals, we produced a nearly complete chromosomal assembly of a female Pekin duck by combining long-read sequencing and multiplatform scaffolding techniques.

RESULTS

A major improvement of genome assembly and annotation quality resulted from the successful resolution of lineage-specific propagated repeats that fragmented the previous Illumina-based assembly. We found that the duck topologically associated domains (TAD) are demarcated by putative binding sites of the insulator protein CTCF, housekeeping genes, or transitions of active/inactive chromatin compartments, indicating conserved mechanisms of spatial chromosome folding with mammals. There are extensive overlaps of TAD boundaries between duck and chicken, and also between the TAD boundaries and chromosome inversion breakpoints. This suggests strong natural selection pressure on maintaining regulatory domain integrity, or vulnerability of TAD boundaries to DNA double-strand breaks. The duck W chromosome retains 2.5-fold more genes relative to chicken. Similar to the independently evolved human Y chromosome, the duck W evolved massive dispersed palindromic structures, and a pattern of sequence divergence with the Z chromosome that reflects stepwise suppression of homologous recombination.

CONCLUSIONS

Our results provide novel insights into the conserved and convergently evolved chromosome features of birds and mammals, and also importantly add to the genomic resources for poultry studies.

A Serum Metabolic Profiling Analysis During the Formation of Fatty Liver in Landes Geese via GC-TOF/MS

During the process of fatty liver production by overfeeding, the levels of endogenous metabolites in the serum of geese would change dramatically. This study investigated the effects of overfeeding on serum metabolism of Landes geese and the underlying mechanisms using a metabolomics approach. Sixty Landes geese of the same age were randomly divided into the following three groups with 20 replicates in each group: D0 group (free from gavage); D7 group (overfeeding for 7 days); D25 group (overfeeding for 25 days). At the end of the experiment, 10 geese of similar weight from each group were selected for slaughter and sampling. The results showed that overfeeding significantly increased the body weight and the liver weight of geese. Serum enzymatic activities and serum lipid levels were significantly enhanced following overfeeding. Gas chromatography time-of-flight/mass spectrometry (GC-TOF/MS) was employed to explore the serum metabolic patterns, and to identify potential contributors to the formation of fatty liver and the correlated metabolic pathways. Relative to overfeeding for 7 days, a large number of endogenous molecules in serum of geese overfed for 25 days were altered. Continuous elevated levels of pyruvic acid, alanine, proline and beta-glycerophosphoric acid and reduced lactic acid level were observed in the serum of overfed geese. Pathway exploration found that the most of significantly different metabolites were involved in amino acids, carbohydrate and lipid metabolism. The present study exhibited the efficient capability of Landes geese to produce fatty liver, identified potential biomarkers and disturbed metabolic pathways in liver steatosis. These findings might reveal the underlying mechanisms of fatty liver formation and provide some theoretical basis for the diagnosis and treatment of liver diseases.

Seasonal differences in the transcriptome profile of the Zhedong white goose (Anser cygnoides) pituitary gland

In animals, the adaptation to breed at the time of greatest survival of the young is known as seasonal reproduction. This is mainly controlled by the photoperiod, which stimulates the hypothalamic-pituitary-gonadal axis and starts the breeding season. Herein, we have determined the seasonal changes in gene expression patterns of Zhedong white geese pituitary glands under a natural photoperiodism, conducted at autumn equinox (AE), winter solstice (WS), spring equinox (SE), and summer solstice (SS). Pairwise comparisons of WS vs. AE, SE vs. WS, SS vs. SE, and AE vs. SS resulted in 1,139, 33, 704, and 3,503 differently expressed genes, respectively. When compared with SS, AE showed downregulation of genes, such as vasoactive intestinal peptide receptor, prolactin receptor, and thyroid hormone receptor beta, whereas gonadotropin-releasing hormone II receptor was upregulated, indicating that these genes may be responsible for the transition from cessation to egg laying. In addition, the expression levels of 5 transcription factors (POU1F1, Pitx2, NR5A1, NR4A2, and SREBF2) and 6 circadian clock-associated genes (Clock, Per2, ARNTL2, Eya3, Dio2, and NPAS2) also changed seasonally. Gene Ontology term and Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that “response to oxidative stress” and steroid biosynthesis pathway also participate in regulating the reproduction seasonality of geese. Overall, these results contribute to the identification of genes involved in seasonal reproduction, enabling a better understanding of the molecular mechanism underlying seasonal reproduction of geese.

Pacific Biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genome

BACKGROUND

The domestic goose is an economically important and scientifically valuable waterfowl; however, a lack of high-quality genomic data has hindered research concerning its genome, genetics, and breeding. As domestic geese breeds derive from both the swan goose (Anser cygnoides) and the graylag goose (Anser anser), we selected a female Tianfu goose for genome sequencing. We generated a chromosome-level goose genome assembly by adopting a hybrid de novo assembly approach that combined Pacific Biosciences single-molecule real-time sequencing, high-throughput chromatin conformation capture mapping, and Illumina short-read sequencing.

FINDINGS

We generated a 1.11-Gb goose genome with contig and scaffold N50 values of 1.85 and 33.12 Mb, respectively. The assembly contains 39 pseudo-chromosomes (2n = 78) accounting for ∼88.36% of the goose genome. Compared with previous goose assemblies, our assembly has more continuity, completeness, and accuracy; the annotation of core eukaryotic genes and universal single-copy orthologs has also been improved. We have identified 17,568 protein-coding genes and a repeat content of 8.67% (96.57 Mb) in this genome assembly. We also explored the spatial organization of chromatin and gene expression in the goose liver tissues, in terms of inter-pseudo-chromosomal interaction patterns, compartments, topologically associating domains, and promoter-enhancer interactions.

CONCLUSIONS

We present the first chromosome-level assembly of the goose genome. This will be a valuable resource for future genetic and genomic studies on geese.

Role of stearyl-coenzyme A desaturase 1 in mediating the effects of palmitic acid on endoplasmic reticulum stress, inflammation, and apoptosis in goose primary hepatocytes

Objective

Unlike mammals, goose fatty liver shows a strong tolerance to fatty acids without obvious injury. Stearyl-coenzyme A desaturase 1 (SCD1) serves crucial role in desaturation of saturated fatty acids (SAFs), but its role in the SAFs tolerance of goose hepatocytes has not been reported. This study was conducted to explore the role of SCD1 in regulating palmitic acid (PA) tolerance of goose primary hepatocytes.

Methods

3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide was examined to reflect the effect of PA on hepatocytes viability, and quantitative polymerase chain reaction was used to detect the mRNA levels of several genes related to endoplasmic reticulum (ER) stress, inflammation, and apoptosis, and the role of SCD1 in PA tolerance of goose hepatocytes was explored using RNA interfere.

Results

Our results indicated that goose hepatocytes exhibited a higher tolerant capacity to PA than human hepatic cell line (LO2 cells). In goose primary hepatocytes, the mRNA levels of fatty acid desaturation-related genes (SCD1 and fatty acid desaturase 2) and fatty acid elongate enzyme-related gene (elongase of very long chain fatty acids 6) were significantly upregulated with 0.6 mM PA treatment. However, in LO2 cells, expression of ER stress-related genes (x box-binding protein, binding immunoglobulin protein, and activating transcription factor 6), inflammatory response-related genes (interleukin-6 [IL-6], interleukin-1β [IL-1β], and interferon-γ) and apoptosis-related genes (bcl-2-associated X protein, b-cell lymphoma 2, Caspase-3, and Caspase-9) was significantly enhanced with 0.6 mM PA treatment. Additionally, small interfering RNA (siRNA) mediated downregulation of SCD1 significantly reduced the PA tolerance of goose primary hepatocytes under the treatment of 0.6 mM PA; meanwhile, the mRNA levels of inflammatory-related genes (IL-6 and IL-1β) and several key genes involved in the phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT), forkhead box O1 (FoxO1), mammalian target of rapamycin and AMPK pathways (AKT1, AKT2, FoxO1, and sirtuin 1), as well as the protein expression of cytochrome C and the apoptosis rate were upregulated.

Conclusion

In conclusion, our data suggested that SCD1 was involved in enhancing the PA tolerance of goose primary hepatocytes by regulating inflammation- and apoptosis-related genes expression.

Long-Term Reciprocal Gene Flow in Wild and Domestic Geese Reveals Complex Domestication History

Hybridization has frequently been observed between wild and domestic species and can substantially impact genetic diversity of both counterparts. Geese show some of the highest levels of interspecific hybridization across all bird orders, and two of the goose species in the genus Anser have been domesticated providing an excellent opportunity for a joint study of domestication and hybridization. Until now, knowledge of the details of the goose domestication process has come from archaeological findings and historical writings supplemented with a few studies based on mitochondrial DNA. Here, we used genome-wide markers to make the first genome-based inference of the timing of European goose domestication. We also analyzed the impact of hybridization on the genome-wide genetic variation in current populations of the European domestic goose and its wild progenitor: the graylag goose (Anser anser). Our dataset consisted of 58 wild graylags sampled around Eurasia and 75 domestic geese representing 14 breeds genotyped for 33,527 single nucleotide polymorphisms. Demographic reconstruction and clustering analysis suggested that divergence between wild and domestic geese around 5,300 generations ago was followed by long-term genetic exchange, and that graylag populations have 3.2–58.0% admixture proportions with domestic geese, with distinct geographic patterns. Surprisingly, many modern European breeds share considerable (> 10%) ancestry with the Chinese domestic geese that is derived from the swan goose Anser cygnoid. We show that the domestication process can progress despite continued and pervasive gene flow from the wild form.

Exploring the genetic basis of fatty liver development in geese

Although geese possess an adaptive physiological capacity for lipid storage, few candidate genes contributing to this ability are characterised. By comparing the genomes of individuals with extremely high and low fatty liver weights (FLW), candidate genes were identified, including ARAP2, GABRE, and IL6. Single-nucleotide polymorphisms in or near these genes were significantly (p < 0.05) associated with carcass traits (FLW) and biochemical indexes (very-low-density lipoprotein and N-terminal procollagen III), suggesting contribution to trait variation. A common variant at the 5'-end of LCORL explained ~ 18% and ~ 26% of the phenotypic variance in body weight with/without overfeeding and had significant effects on FLW (p < 0.01). ZFF36L1, ARHGEF1 and IQCJ, involved in bile acid metabolism, blood pressure, and lipid concentration modulation, were also identified. The presence of highly divergent haplotypes within these genes suggested involvement in protection against negative effects from excessive lipids in the liver or circulatory system. Based on this and transcriptomic data, we concluded that geese hepatosteatosis results from severe imbalance between lipid accumulation and secretion, comparable to human non-alcohol fatty liver disease but involving other genes. Our results provided valuable insights into the genesis of geese fatty liver and detected potential target genes for treatment of lipid-related diseases.

Transcriptome analysis of pituitary gland revealed candidate genes and gene networks regulating the growth and development in goose

Goose is important meat poultry and its growth and development has always been the focus of attention, but the regulation mechanisms of genes and gene network underlying growth and development of goose are still unclear. Three males of large-size Shitou goose and three males of small size Wuzong goose at 5 weeks of age were used for transcriptome analysis with deep sequencing. After slaughter, their pituitary gland was taken for RNA-seq. A total of 290 DEGs were identified by fold change ≥2 and false discovery rate (FDR) <0.05, where there were 148 upregulated genes and 142 downregulated genes in Shitou goose compared to Wuzong goose. Results also showed that the DEGs related to insulin signaling pathway could increase protein synthesis and fat production, and the interaction network of DEGs was mainly related to development, endocrine system, inflammatory diseases, tissue damage and abnormality. The DEGs involved in the growth and function of the pituitary organs may regulate the growth and development of the body by affecting the synthesis and secretion of pituitary hormones. The results of this study will help to understand the regulatory mechanism of goose growth and development.

The Hepatoprotective Effects of Zinc Glycine on Liver Injury in Meat Duck Through Alleviating Hepatic Lipid Deposition and Inflammation

Dietary zinc status was recently approved to exert a powerful influence on liver health, and zinc deficiency results in hepatic injury caused by fat deposition, inflammation, and oxidant stress, but the effect of zinc on hepatic lipid metabolism and liver injury in meat duck has not been well defined. To determine the hepatoprotective effects of graded zinc glycine in meat ducks. A total of 384 1-day-old male meat ducks were subjected to 5 weeks feeding program with three experimental diets: (1) low-zinc diet, (2) adequate-zinc diet, and (3) high-zinc diet. Blood and liver samples were collected for biochemical analysis, gene expression analysis, and histopathological study. Diet with low zinc increased hepatic lipid content and triglyceride concentration. Meat ducks fed low-zinc diet exhibited considerably increased serum alanine aminotransferase (ALT) activity than birds fed other diets among all groups (P < 0.05). Low zinc administration also notably induced hepatocyte apoptosis and stimulated hepatic inflammatory gene expression. Adequate or high zinc supplementation increased hepatic zinc level, reduced hepatic lipid deposition and hepatosomatic indices through suppressing the expression of lipogenic genes including fatty acid synthase (FAS) and acetyl-CoA carboxylase (ACC) (P < 0.05), and upregulated the mRNA expression of both fatty acid secretion and β-oxidation, including carnitine palmitoyltransferase 1a (Cpt1a), peroxisome proliferator-activated receptor (PPAR)α, and apolipoprotein B (ApoB) (P < 0.05). Dietary zinc addition also declined hepatic mRNA expression of interleukin (IL)-1β and IL-6 (P < 0.05). Furthermore, diets with adequate or high zinc significantly decreased serum ALT activity and hepatocyte apoptosis. These data revealed that supplementing adequate- or high-zinc glycine efficiently protects liver injury by attenuating lipid deposition and hepatic inflammation.

Molecular characterization, mRNA gene expression, and antimicrobial activity of 2 new cathelicidin genes in goose

Cathelicidins represent a major group of host defense peptides (HDPs) that share a highly conserved cathelin-like domain. In birds, this gene family has been identified in many species. However, no information was available in the goose until now. In this study, we present the molecular characterization of 2 goose cathelicidin genes, namely goose CATH2 and goose CATH3, for the first time. The complete cDNA of goose CATH2 and goose CATH3 were 571 bp and 573 bp in length, respectively, and the deduced amino acid sequences exhibited high similarity with other avian cathelicidins. Furthermore, evolutionary analyses indicated that all known cathelicidins form 3 distinct clusters from reptiles, while the oldest cathelicidin member, which is known as CATHB1, is very likely absent in the goose genome. Meanwhile, highly expressed goose CATH2 and goose CATH3 were also observed in primary and secondary lymphoid tissues, same as the observations in other avian species. In addition, chemically synthesized mature peptides of the 2 cathelicidins exerted optimal antimicrobial abilities to a range of gram-negative and gram-positive bacteria. The discovery and characterization of goose cathelicidins complete the knowledge for goose HDPs and might contribute to understanding the evolution of avian cathelicidins as well as for the development of antibacterial agents.

First de novo whole genome sequencing and assembly of the bar-headed goose

Background

The bar-headed goose (Anser indicus) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, biochemical and behavioral adaptations of bar-headed geese to high-altitude living and flying have raised much interest. However, to date, there is still no genome assembly information publicly available for bar-headed geese.

Methods

In this study, we present the first de novo whole genome sequencing and assembly of the bar-headed goose, along with gene prediction and annotation.

Results

10X Genomics sequencing produced a total of 124 Gb sequencing data, which can cover the estimated genome size of bar-headed goose for 103 times (average coverage). The genome assembly comprised 10,528 scaffolds, with a total length of 1.143 Gb and a scaffold N50 of 10.09 Mb. Annotation of the bar-headed goose genome assembly identified a total of 102 Mb (8.9%) of repetitive sequences, 16,428 protein-coding genes, and 282 tRNAs. In total, we determined that there were 63 expanded and 20 contracted gene families in the bar-headed goose compared with the other 15 vertebrates. We also performed a positive selection analysis between the bar-headed goose and the closely related low-altitude goose, swan goose (Anser cygnoides), to uncover its genetic adaptations to the Qinghai-Tibetan Plateau.

Conclusion

We reported the currently most complete genome sequence of the bar-headed goose. Our assembly will provide a valuable resource to enhance further studies of the gene functions of bar-headed goose. The data will also be valuable for facilitating studies of the evolution, population genetics and high-altitude adaptations of the bar-headed geese at the genomic level.

Mycoplasma anserisalpingitidis sp. nov., isolated from European domestic geese (Anser anser domesticus) with reproductive pathology

In 1983, Mycoplasma sp. strain 1220 was isolated in Hungary from the phallus lymph of a gander with phallus inflammation. Between 1983 and 2017, Mycoplasma sp. 1220 was also identified and isolated from the respiratory tract, liver, ovary, testis, peritoneum and cloaca of diseased geese in several countries. Seventeen studied strains produced acid from glucose and fructose but did not hydrolyse arginine or urea, and all grew under aerobic, microaerophilic and anaerobic conditions at 35 to 37 ˚C in either SP4 or pleuropneumonia-like organism medium supplemented with glucose and serum. Colonies on agar showed a typical fried-egg appearance and transmission electron microscopy revealed a typical mycoplasma cellular morphology. Molecular characterization included analysis of the following genetic loci: 16S rRNA, 23S rRNA, 16S-23S rRNA ITS, rpoB, rpoC, rpoD, uvrA, parC, topA, dnaE, fusA and pyk. The genome was sequenced for type strain 1220^T. The 16S rRNA gene sequences of studied strains of Mycoplasma sp. 1220 shared 99.02-99.19 % nucleotide similarity with M. anatis strains but demonstrated ≤95.00-96.70 % nucleotide similarity to the 16S rRNA genes of other species of the genus Mycoplasma. Phylogenetic, average nucleotide and amino acid identity analyses revealed that the novel species was most closely related to Mycoplasma anatis. Based on the genetic data, we propose a novel species of the genus Mycoplasma, for which the name Mycoplasma anserisalpingitidis sp. nov. is proposed with the type strain 1220^T (=ATCC BAA-2147^T=NCTC 13513^T=DSM 23982^T). The G+C content is 26.70 mol%, genome size is 959110 bp.

Characterization of Embryonic Skin Transcriptome in Anser cygnoides at Three Feather Follicles Developmental Stages

In order to enrich the Anser cygnoides genome and identify the gene expression profiles of primary and secondary feather follicles development, de novo transcriptome assembly of skin tissues was established by analyzing three developmental stages at embryonic day 14, 18, and 28 (E14, E18, E28). Sequencing output generated 436,730,608 clean reads from nine libraries and de novo assembled into 56,301 unigenes. There were 2,298, 9,423 and 12,559 unigenes showing differential expression in three stages respectively. Furthermore, differentially expressed genes (DEGs) were functionally classified according to genes ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and series-cluster analysis. Relevant specific GO terms such as epithelium development, regulation of keratinocyte proliferation, morphogenesis of an epithelium were identified. In all, 15,144 DEGs were clustered into eight profiles with distinct expression patterns and 2,424 DEGs were assigned to 198 KEGG pathways. Skin development related pathways (mitogen-activated protein kinase signaling pathway, extra-cellular matrix -receptor interaction, Wingless-type signaling pathway) and genes (delta like canonical Notch ligand 1, fibroblast growth factor 2, Snail family transcriptional repressor 2, bone morphogenetic protein 6, polo like kinase 1) were identified, and eight DEGs were selected to verify the reliability of transcriptome results by real-time quantitative PCR. The findings of this study will provide the key insights into the complicated molecular mechanism and breeding techniques underlying the developmental characteristics of skin and feather follicles in Anser cygnoides.

Genome-Wide Association Analysis Reveals Key Genes Responsible for Egg Production of Lion Head Goose

The lion head goose is one of the most important agricultural resources in China; however, its breeding process is relatively slow. In the present study, a genome-wide association study was performed for the genetic selection of egg production characters in lion head geese. We detected 30 single-nucleotide polymorphisms located in or near 30 genes that might be associated with egg production character, and quantitative real-time polymerase chain reaction was used to verify their expression level in lion head geese. The results showed that the expression levels of CRTC1 (encoding CREB-regulated transcription coactivator 1), FAAH2 (encoding fatty acid amide hydrolase 2), GPC3 (encoding glypican 3), and SERPINC1 (encoding serpin family C member 1) in high egg production population were significantly lower than those in the low egg production populations (*P < 0.05). The expression levels of CLPB (encoding caseinolytic peptidase B protein homolog), GNA12 (encoding guanine nucleotide-binding protein subunit alpha-12), and ZMAT5 (encoding zinc finger, matrin type 5) in the high egg production population were significantly higher than those in the low egg production populations (*P < 0.05). The expression of BMP4 (encoding bone morphogenetic protein 4), FRMPD3 (encoding FERM and PDZ domain containing 3), LIF (encoding leukemia inhibitory factor), and NFYC (encoding nuclear transcription factor Y subunit gamma) in the high egg production population were very significantly lower than those in the low egg production population (**P < 0.01). Our findings provide an insight into the economic traits of lion head goose. These candidate genes might be valuable for future breeding improvement.