Genome-wide selective signatures mining the candidate genes for egg laying in goose.

BACKGROUND: Improving the egg production of goose is a crucial goal of breeding, because genetics is the key factor affecting egg production. Thus, we sequenced the genomes of 55 Chinese indigenous geese from six breeds, which were divided into the high egg-laying group (ZE, HY, and SC) and low egg-laying group (ZD, LH, and ST). Based on the results of the inter-population selection signal analysis, we mined the selected genome regions in the high egg-laying germplasm population to identify the key candidate genes affecting the egg-laying traits. RESULTS: According to the whole-genome sequencing data, the average sequencing depth reached 11.75X. The genetic relationships among those six goose breeds coincided with the breed's geographical location. The six selective signal detection results revealed that the most selected regions were located on Chr2 and Chr12. In total, 12,051 single-nucleotide polymorphism (SNP) sites were selected in all six methods. Using the enrichment results of candidate genes, we detected some pathways involved in cell differentiation, proliferation, and female gonadal development that may cause differences in egg production. Examples of these pathways were the PI3K-Akt signaling pathway (IGF2, COMP, and FGFR4), animal organ morphogenesis (IGF2 and CDX4), and female gonad development (TGFB2). CONCLUSION: On analyzing the genetic background of six local goose breeds by using re-sequencing data, we found that the kinship was consistent with their geographic location. 107 egg-laying trait-associated candidate genes were mined through six selection signal analysis. Our study provides a critical reference for analyzing the molecular mechanism underlying differences in reproductive traits and molecular breeding of geese.

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.

Identification of SNPs Associated with Goose Meat Quality Traits Using a Genome-Wide Association Study Approach.

(1) Background: Goose meat is highly valued for its economic significance and vast market potential due to its desirable qualities, including a rich nutritional profile, tender texture, relatively low-fat content, and high levels of beneficial unsaturated fatty acids. However, there is an urgent need to improve goose breeding by identifying molecular markers associated with meat quality. (2) Methods: We evaluated meat quality traits, such as meat color, shear force (SF), cooking loss rate (CLR), and crude fat content (CFC), in a population of 215 male Sichuan white geese at 70 days of age. A GWAS was performed to identify potential molecular markers associated with goose meat quality. Furthermore, the selected SNPs linked to meat quality traits were genotyped using the MALDI-TOP MS method. (3) Results: A dataset of 2601.19 Gb of WGS data was obtained from 215 individuals, with an average sequencing depth of 10.89×. The GWAS revealed the identification of 43 potentially significant SNP markers associated with meat quality traits in the Sichuan white goose population. Additionally, 28 genes were identified as important candidate genes for meat quality. The gene enrichment analysis indicated a substantial enrichment of genes within a 1Mb vicinity of SNPs in both the protein digestion and absorption pathway and the Glycerolipid metabolism pathway. (4) Conclusion: This study provides valuable insights into the genetic and molecular mechanisms underlying goose meat quality traits, offering crucial references for molecular breeding in this field.

Time-Series Clustering of lncRNA-mRNA Expression during the Adipogenic Transdifferentiation of Porcine Skeletal Muscle Satellite Cells.

Skeletal muscle satellite cells (SMSCs), which are multifunctional muscle-derived stem cells, can differentiate into adipocytes. Long-chain non-coding RNA (lncRNA) has diverse biological functions, including the regulation of gene expression, chromosome silencing, and nuclear transport. However, the regulatory roles and mechanism of lncRNA during adipogenic transdifferentiation in muscle cells have not been thoroughly investigated. Here, porcine SMSCs were isolated, cultured, and induced for adipogenic differentiation. The expressions of lncRNA and mRNA at different time points during transdifferentiation were analysed using RNA-seq analysis. In total, 1005 lncRNAs and 7671 mRNAs showed significant changes in expression at differential differentiation stages. Time-series expression analysis showed that the differentially expressed (DE) lncRNAs and mRNAs were clustered into 5 and 11 different profiles with different changes, respectively. GO, KEGG, and REACTOME enrichment analyses revealed that DE mRNAs with increased expressions during the trans-differentiation were mainly enriched in the pathways for lipid metabolism and fat cell differentiation. The genes with decreased expressions were mainly enriched in the regulation of cell cycle and genetic information processing. In addition, 1883 DE mRNAs were regulated by 193 DE lncRNAs, and these genes were related to the controlling in cell cycle mainly. Notably, three genes in the fatty acid binding protein (FABP) family significantly and continuously increased during trans-differentiation, and 15, 13, and 11 lncRNAs may target FABP3, FABP4, and FABP5 genes by cis- or trans-regulation, respectively. In conclusion, these studies identify a set of new potential regulator for adipogenesis and cell fate and help us in better understanding the molecular mechanisms of trans-differentiation.

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.

Genome-Wide Gene Expression Profiles Reveal Distinct Molecular Characteristics of the Goose Granulosa Cells.

Granulosa cells (GCs) are decisive players in follicular development. In this study, the follicle tissues and GCs were isolated from the goose during the peak-laying period to perform hematoxylin-eosin staining and RNA-seq, respectively. Moreover, the dynamic mRNA and lncRNA expression profiles and mRNA-lncRNA network analysis were integrated to identify the important genes and lncRNAs. The morphological analysis showed that the size of the GCs did not significantly change, but the thickness of the granulosa layer cells differed significantly across the developmental stages. Subsequently, 14,286 mRNAs, 3,956 lncRNAs, and 1,329 TUCPs (transcripts with unknown coding potential) were detected in the GCs. We identified 37 common DEGs in the pre-hierarchical and hierarchical follicle stages, respectively, which might be critical for follicle development. Moreover, 3,089 significant time-course DEGs (Differentially expressed genes) and 13 core genes in 4 clusters were screened during goose GCs development. Finally, the network lncRNA G8399 with CADH5 and KLF2, and lncRNA G8399 with LARP6 and EOMES were found to be important for follicular development in GCs. Thus, the results would provide a rich resource for elucidating the reproductive biology of geese and accelerate the improvement of the egg-laying performance 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.

Dynamic Cluster Formation Game for Attributed Graph Clustering.

Besides the topological structure, there are additional information, i.e., node attributes, on top of the plain graphs. Usually, these systems can be well modeled by attributed graphs, where nodes represent component actors, a set of attributes describe users' portraits and edges indicate their connections. An elusive question associated with attributed graphs is to study how clusters with common internal properties form and evolve in real-world networked systems with great individual diversity, which leads to the so-called problem of attributed graph clustering (AGC). In this paper, we comprehended AGC naturally as a dynamic cluster formation game (DCFG), where each node's feasible action set can be constrained by every cluster in a discrete-time dynamical system. Specifically, we carried out a deep research on a special case of finite dynamic games, named dynamic social game (DSG), the convergence of the finite Nash equilibrium sequence in a DSG was also proved strictly. By carefully defining the feasible action set and the utility function associated with each node, the proposed DCFG can be well related to a DSG; and we showed that a balanced solution of AGC could be found by solving a finite set of coupled static Nash equilibrium problems in the related DCFG. We, finally, proposed a self-learning algorithm, which can start from any arbitrary initial cluster configuration, and, finally, find the corresponding balanced solution of AGC, where all nodes and clusters are satisfied with the final cluster configuration. Extensive experiments were applied on real-world social networks to demonstrate both effectiveness and scalability of the proposed approach by comparing with the state-of-the-art graph clustering methods in the literature.

Genome-Wide Chromatin Structure Changes During Adipogenesis and Myogenesis.

The recently developed high-throughput chromatin conformation capture (Hi-C) technology enables us to explore the spatial architecture of genomes, which is increasingly considered an important regulator of gene expression. To investigate the changes in three-dimensional (3D) chromatin structure and its mediated gene expression during adipogenesis and myogenesis, we comprehensively mapped 3D chromatin organization for four cell types (3T3-L1 pre-adipocytes, 3T3-L1-D adipocytes, C2C12 myoblasts, and C2C12-D myotubes). We demonstrate that the dynamic spatial genome architecture affected gene expression during cell differentiation. A considerable proportion (~22%) of the mouse genome underwent compartment A/B rearrangement during adipogenic and myogenic differentiation, and most (~80%) upregulated marker genes exhibited an active chromatin state with B to A switch or stable A compartment. More than half (65.4%-73.2%) of the topologically associating domains (TADs) are dynamic. The newly formed TAD and intensified local interactions in the Fabp gene cluster indicated more precise structural regulation of the expression of pro-differentiation genes during adipogenesis. About half (32.39%-59.04%) of the differential chromatin interactions (DCIs) during differentiation are promoter interactions, although these DCIs only account for a small proportion of genome-wide interactions (~9.67% in adipogenesis and ~4.24% in myogenesis). These differential promoter interactions were enriched with promoter-enhancer interactions (PEIs), which were mediated by typical adipogenic and myogenic transcription factors. Differential promoter interactions also included more differentially expressed genes than nonpromoter interactions. Our results provide a global view of dynamic chromatin interactions during adipogenesis and myogenesis and are a resource for studying long-range chromatin interactions mediating the expression of pro-differentiation genes.

Nutritive Value of Sorghum Dried Distillers Grains with Solubles and its Effect on Performance in Geese.

The study was conducted to determine the chemical composition and nutritive value of sorghum dried distillers grains with solubles (sDDGS) and its effect as a feed supplement on the performance of geese. Experiment 1 showed that the gross energy, crude protein, ether extract, crude fiber, calcium, phosphorus, and amino acid content values of sDDGS were 17.87 MJ/kg and 15.48, 4.26, 31.46, 0.17, 0.25, and 0.06-3.18% [dry matter basis (DM)], respectively. Experiment 2 used fasting-force feeding to measure the true metabolizable energy of sDDGS (11.38 MJ/kg DM) and true total tract digestibility of amino acids (43.16-80.92% DM) in geese. Experiment 3 examined the effectiveness of sDDGS as a feed supplement for geese. Three hundred and fifteen 35-day-old male Sichuan white geese with an initial average bodyweight of 1,732 g were randomly allocated to five treatments. Geese in each treatment group were fed one of five experimental diets (control diet alone, or supplemented with 4, 8, 12, or 16% sDDGS) until 70 days of age. Inclusion of sDDGS in the diet did not affect daily average weight gain (P>0.05). Birds fed diets containing up to 8% sDDGS had higher average feed intake (P<0.05) than geese fed the control diet, and the feed/gain ratio in geese fed diets containing 16% sDDGS was higher (P<0.05) than in the control and the 4% sDDGS group. The yields of breast meat, leg meat, subcutaneous fat and skin, and abdominal fat were not affected (P>0.05) bydietary sDDGS levels. Generally, sDDGS is a potentially valuable feedstuff for geese, but it should be supplemented with a high-energy or protein-rich ingredient. To improve growth performance and carcass yield, up to 12% sDDGS can be included in diets from 35 to 70 days of age.

Goose FMO3 gene cloning, tissue expression profiling, polymorphism detection and association analysis with trimethylamine level in the egg yolk.

Flavin-containing monooxygenase 3 (FMO3) plays a critical role in catalyzing the conversion of trimethylamine (TMA) to trimethylamine-N-oxide (TMAO) in vivo. Despite the well-documented association between FMO3 mutations and a 'fishy' off-flavor eggs in chicken and quail, little information is available regarding the molecular characteristic of goose (Anser cygnoides) FMO3 and its relationship with the yolk TMA content. To fill these gaps, we cloned the full-length cDNA sequence of goose FMO3, which comprised 1851bp encoding 531 amino acids. FMO3 mRNA was dramatically expressed in liver than in other tissues in the geese. Eight single nucleotide polymorphisms (SNPs) were detected in the entire coding region. The CC genotype at the T669C site, GG at the A723G site, and AA at the G734A site of FMO3 were highly significantly associated with elevated TMA content in goose egg yolk (P<0.001). Carriers of the A allele of G734A or C allele of T885C had yolk TMA content that had a high probability of being elevated after feeding with additional choline chloride (P=0.0429, OR=4.1300, 95%CI=1.0390-16.4270, and P=0.0251, OR=4.6060, 95%CI=1.1620-18.2620, respectively). This work lays a foundation for studying the function of FMO3 and yolk TMA content in goose. However, studies using larger sample sizes and more goose breeds are required to determine whether the fishy off-flavor trait exists in goose.

Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose.

The goose is an economically important waterfowl that exhibits unique characteristics and abilities, such as liver fat deposition and fibre digestion. Here, we report de novo whole-genome assemblies for the goose and swan goose and describe the evolutionary relationships among 7 bird species, including domestic and wild geese, which diverged approximately 3.4~6.3 million years ago (Mya). In contrast to chickens as a proximal species, the expanded and rapidly evolving genes found in the goose genome are mainly involved in metabolism, including energy, amino acid and carbohydrate metabolism. Further integrated analysis of the host genome and gut metagenome indicated that the most widely shared functional enrichment of genes occurs for functions such as glycolysis/gluconeogenesis, starch and sucrose metabolism, propanoate metabolism and the citrate cycle. We speculate that the unique physiological abilities of geese benefit from the adaptive evolution of the host genome and symbiotic interactions with gut microbes.

MicroRNA-199a Targets the Fatty Acid Transport Protein 1 Gene and Inhibits the Adipogenic Trans-Differentiation of C2C12 Myoblasts.

BACKGROUND/AIMS: Muscle cells are able to trans-differentiate into adipocytes with adipogenesis induction. MicroRNAs (miRNAs), a class of small non-coding RNAs, widely participate in the regulation of growth and development of cells. However, the expression and regulatory role of miRNAs in the trans-differentiation of muscle cell are largely unknown. METHODS: C2C12 myoblasts were inducted to adipogenesis trans-differentiation and microarrays were used to assay the changes of expression profile of miRNAs. MiR-199a, a miRNA showed significant change in the trans-differentiation, was selected for the subsequent function study via over- expression and knock down. RESULTS: Dozens of miRNAs showed different changes followed the adipogenesis trans-differentiation of C2C12 cells. In which, miR-199a was decreased in the adipogenic cells and miR-199a over-expression inhibited the trans-differentiation and decreased lipid accumulation in the cells. Moreover, Fatty acid transport protein 1 (Fatp1), a major regulator of trans-membrane transportation and the oxidative metabolism of free fatty acids, was showed to be a target of miR-199a by computational and luciferase reporter assays. Additionally, Fatp1 knock-down by small interfering RNA had similar inhibitory effects on the trans-differentiation in C2C12 cells. CONCLUSION: Our study reveals an important role for miR-199a in the regulation of adipogenic trans-differentiation in muscle cells via suppression of Fatp1 gene.

Transcriptome profiling of the hypothalamus during prelaying and laying periods in Sichuan white geese (Anser cygnoides).

The Sichuan White goose is a Chinese breed well known for the quality of its meat. However, reproductive performance in this goose is not ideal, and little information is available regarding the abundance of transcripts. To better understand the molecular mechanism(s) underpinning prelaying and laying periods in the Sichuan white goose, high-throughput RNA sequencing was performed to analyze the transcriptome in the hypothalamus. After sequencing and annotation, 26,921 unigenes were obtained, with 48 transcripts up-regulated in the prelaying period and 180 transcripts up-regulated during the laying period. These transcripts were primarily related to diseases, cancers, signaling molecules and interactions, the nervous system and the immune system. Eight transcripts were selected for further analyses with quantitative reverse-transcription polymerase chain reaction (qRT-PCR). The qRT-PCR results were mostly consistent with those from the high-throughput RNA sequencing. Among these transcripts, serine/threonine-protein kinase (AMPK), heat shock protein 70 (HSP70) and NADH dehydrogenase 1 (ND1) were differentially expressed during the prelaying and laying periods. The results of this study provide a useful resource for future studies examining the hypothalamus in geese.