Search

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., (© The Author(s) 2020. Published by Oxford University Press GigaScience.)

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.

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., (© 2015 Japanese Society of Animal Science.)

High-throughput RNA sequencing was performed for comprehensively analyzing the transcriptome of geese. A total of 28,803,759 bp of raw sequence data was generated by 454 GS Flx+. After removal of adaptor sequences, 28,730,361 bp remained and 117,279 reads were obtained, with an average length of 244 bases. Simultaneously, complementary DNA samples from two different reproductive stages of goose ovarian, hypothalamus and pituitary tissue were sequenced separately using Illumina MiSeq platform. A total of 12 688 673 148 bp of raw sequence data were generated by Illumina MiSeq. After removal of adaptor sequences, 8 198 126 562 bp remained and 60 382 786 clean reads were obtained, with an average length of 135 bases. Assembly of all the reads from both 454 Flx+ and Illumina platforms formed 56,839 contigs. The sequence size ranges from 38 to 28,206 bp in size, with an average size of 2584 bp and an N50 of 4624. The assembly produced a substantial number of large contigs: 35,545 (62.5%) were longer than 1 kb, of which 8850 (15.6%) were longer than 5 kb. The sequencing depth was 85 X on average. We performed comprehensive function annotations on unigenes including protein sequence similarity, gene ontology (GO) term classification, and Kyoto Encylcopedia of Genes and Genomes (KEGG) pathway enrichment. GO analysis showed that approximately 63% of the contigs had annotation information, among the 35,953 annotated isotigs in Nr database, 24,783 (68.9%) sequences were assigned with one or more GO terms. There were 14,634 (40.7%) isotigs for biological processes, 10,557(29.3%) isotigs for cellular component, 22,607 (62.9%) isotigs for molecular function. The result of KEGG pathway mapping 8926 sequences had the pathway annotation, and took part in 477 pathways. Additionally, 10,685 simple sequence repeat (SSR) markers were identified from the assembled sequences. The most frequent repeat motifs were trinucleotides, which accounted for 53.03% of all SSRs, followed by dinucleotides (39.9%), tetranucleotides (5.08%), pentanucleotides (1.68%) and hexanucleotides (0.32%). Transcriptome sequencing on mixture issue of the geese yielded substantial transcriptional sequences and potentially useful SSR markers which provide an important data source for geese research., (© 2014 Japanese Society of Animal Science.)

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. [ABSTRACT FROM AUTHOR]

Simple Summary: Goose meat is an ideal nutrition source with high protein, low fat, and low cholesterol, and dietary acidifiers supplementation are considered an efficient nutritional regulation approach to promote poultry industry development. Hence, this study was conducted to evaluate the benefits of citric acid supplementation in growing geese. The specific results found that citric acid supplementation showed a significant growth-promoting function, and benefited the antioxidant capacity and cecum microbiota of the geese. An inclusion level of 3.2% CA in growing geese diets is recommended based on this study. To investigate the efficiency and optimum inclusion level of CA in growing geese diets on performance, plasma constituents, and intestinal health, 240 healthy female geese at the age of 28d were randomly allotted six treatment diets incorporated with 0, 0.8, 1.6, 2.4, 3.2, and 4% CA. Each treatment group consisted of five replicates and eight birds per replicate. The findings demonstrated that 3.2% CA supplementation resulted in improved growth performance (ADG, ADFI, and FBW) (p = 0.001), and geese who received CA also showed lower body fat contents (p < 0.05) than the control group. Moreover, geese from the 2.4% and 3.2% CA group had the highest plasma glutathione peroxidase and insulin-like growth factor 1 levels compared to the other groups (p < 0.05). A microbial diversity analysis of the cecum conducted by 16S rDNA sequencing revealed that 3.2% CA supplementation showed a significantly higher abundance of beneficial bacteria (Muribaculaceae, CHKCI001, Erysipelotricha-ceae_UCG_003, and UCG_009) (p < 0.05) and a lower abundance of harmful bacteria (Atopobiaceae, Streptococcus, Acinetobacter, Pseudomonas, and Alistipes) (p < 0.10). Collectively, our results revealed that dietary supplementation with 3.2% CA had several benefits on the performance and physiological health of growing geese by promoting nutrients metabolism, improving antioxidant capacity, and modulating cecum microbiota. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Simple Summary: To screen and identify single nucleotide polymorphisms (SNPs) associated with geese meat quality traits, we performed genome-wide association study (GWAS) in a population of male Sichuan white geese (a Chinese local breed) at 70 days old to screen the SNPs in the goose genome. Additionally, genotypes of the selected SNPs associated with goose meat were detected using the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOP MS) method. The results revealed 43 SNPs that showed potentially significant associations with these traits. Additionally, we detected 28 annotated genes as potential candidate genes for the five meat quality traits. The enrichment analysis of genes within a 1Mb vicinity of SNPs showed potentially significant enrichment in the protein digestion and absorption pathway, as well as the Glycolipid metabolism pathway. The findings of this study offer novel genetic markers and candidate genes that can be used for marker-assisted selection of geese, laying the groundwork for understanding the genetic basis of goose meat quality traits and establishing a foundation for comprehending their genetic basis. (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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]