The study was conducted to investigate the transcriptomic differences of the hypothalamic-pituitary-gonadal axis between Xinjiang Yili geese with high and low egg production and to find candidate genes regulating the egg production of Xinjiang Yili geese. The 8 selected Xinjiang Yili Geese with high or low egg production (4 for each group) were 3 years old, with good health, and under the same feeding condition. High-throughput sequencing technology was used to sequence cDNA libraries of the hypothalami, pituitary glands, and ovaries. The sequencing data were compared and analyzed, and the transcripts with significant differences were identified and analyzed with bioinformatics. The study showed that the transcriptome sequencing data of the 24 samples contained a total of 1,176,496,146 valid reads and 176.47 gigabase data. Differential expression analyses identified 135, 56, and 331 genes in the hypothalami, pituitary glands, and ovaries of Xinjiang Yili geese with high and low egg production. Further annotation of these differentially expressed genes in the non-redundant protein sequence database (Nr) revealed that 98, 52, and 309 genes were annotated, respectively. Through the annotations of GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases, 30 candidate genes related to the egg production of Xinjiang Yili geese were preliminarily selected. The gap junction, focal adhesion, and ECM-receptor interaction signaling pathways were enriched with the hypothalamic, pituitary, and ovarian differentially expressed genes, and the calcium signaling pathway was enriched with the pituitary and ovarian differentially expressed genes. Thus, these pathways in the hypothalamic-pituitary-gonadal axis may play an important role in regulating egg production of Xinjiang Yili geese. The results provided the transcriptomic information of the hypothalamic-pituitary-gonadal axis of Xinjiang Yili geese and laid the theoretical basis for revealing the molecular mechanisms regulating the egg-laying traits of Xinjiang Yili geese.

Avian eggshell color is an interesting genetic trait. Here, we report that the blue eggshell color of the domestic duck is caused by two cis-regulatory G to A transitions upstream of ABCG2, which encodes an efflux transporter. The juxtaposed blue eggshell allele A-A exhibited higher promoter activity and stronger nuclear protein binding capacity than the white eggshell allele G-G. Transcription factor analysis suggested differential binding capability of CTCF between blue eggshell and white eggshell alleles. Knockdown of CTCF expression significantly decreased the promoter activity of the blue eggshell but not the white eggshell allele. DNA methylation analysis revealed similar high methylation of the region upstream of the CTCF binding sites in both blue-eggshelled and white-eggshelled ducks. However, DNA methylation levels downstream of the binding sites were decreased and 35% lower in blue-eggshelled ducks than in white-eggshelled ducks. Consistent with the in vitro regulatory pattern of causative sites, ABCG2 exhibited higher expression in uteruses of blue-eggshelled ducks and also showed polarized distribution in their endometrial epithelial cells, distributing at the apical surface of endometrial epithelial cells and with orientation toward the uterine cavity, where the eggshell is pigmented. In conclusion, our results suggest that two cis-regulatory SNPs upstream of ABCG2 are the causative mutations for blue eggshells in ducks. The blue eggshell variant up-regulated ABCG2 expression through recruiting CTCF binding, which may function as a barrier element to shield the downstream region from high methylation levels present upstream. ABCG2 was identified as the only candidate causative gene for blue eggshells; it may function as an efflux transporter of biliverdin to the uterine cavity.

This study investigated the impact of Bacillus coagulans (BC) and tributyrin (TB) supplementation on the growth performance, serum antioxidant capacity, intestinal morphology, and cecal microbiota of yellow-feathered broilers. Using a 2 × 2 factorial design, 480 broilers were randomly assigned to four experimental diets, comprising two levels of BC (0 and 1 g/kg) and two levels of TB (0 and 1 g/kg), over a 36-day period. A significant interaction was observed between BC and TB, impacting the average daily feed intake (ADFI) of broilers aged between 26 and 40 days (p < 0.01). BC and TB also displayed a significant interaction in relation to serum malondialdehyde levels and total antioxidant capacity (p < 0.05). Additionally, there was a significant interaction between BC and TB concerning the duodenal villus-to-crypt ratio, crypt depth, and jejunal villus-to-crypt ratio (p < 0.05). The addition of BC and TB significantly enhanced the richness and diversity of cecal microbiota, with a notable interactive effect observed for the abundance of Faecalibacterium, Ruminococcus_torques_group, and Phascolarctobacterium. In conclusion, supplementation with BC and TB can effectively improve the growth performance, serum antioxidant capacity, intestinal morphology, and cecal microbiota composition of yellow-feathered broilers, indicating the presence of an interactive effect.

Objective: Tibetan chickens, which have unique adaptations to extreme high-altitude environments, exhibit phenotypic and physiological characteristics that are distinct from those of lowland chickens. However, the mechanisms underlying hypoxic adaptation in the liver of chickens remain unknown.Methods: RNA-sequencing (RNA-Seq) technology was used to assess the differentially expressed genes (DEGs) involved in hypoxia adaptation in highland chickens (native Tibetan chicken [HT]) and lowland chickens (Langshan chicken [LS], Beijing You chicken [BJ], Qingyuan Partridge chicken [QY], and Chahua chicken [CH]).Results: A total of 352 co-DEGs were specifically screened between HT and four native lowland chicken breeds. Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analyses indicated that these co-DEGs were widely involved in lipid metabolism processes, such as the peroxisome proliferator-activated receptors (PPAR) signaling pathway, fatty acid degradation, fatty acid metabolism and fatty acid biosynthesis. To further determine the relationship from the 352 co-DEGs, protein-protein interaction network was carried out and identified eight genes (ACSL1, CPT1A, ACOX1, PPARC1A, SCD, ACSBG2, ACACA, and FASN) as the potential regulating genes that are responsible for the altitude difference between the HT and other four lowland chicken breeds.Conclusion: This study provides novel insights into the molecular mechanisms regulating hypoxia adaptation via lipid metabolism in Tibetan chickens and other highland animals.

H5N1, a highly pathogenic avian influenza virus that is prevalent in Asia, seriously harms the poultry industry and global public health. However, its pathogenesis is still not well understood. Circular RNAs (circRNAs), a newly identified type of RNA, reportedly play crucial roles in various pathogenic processes. In this study, RNA sequencing was performed to analyze the expression profile of circRNAs in H5N1-infected chicken embryo fibroblast (DF1) cells. A total of 14,586 circRNAs were identified. The expression profiles of infected cells changed more significantly, relative to uninfected cells, as the infection period was extended; namely, 261, 626, and 1103 circRNAs exhibited differential expression in cells infected for 6 h, 12 h, and 20 h, respectively. GO and KEGG enrichment analysis revealed significant enrichment of the parental genes of the differentially expressed circRNAs for viral replication and immune response-related pathways, such as positive regulation of transcription from the RNA polymerase II promoter, positive regulation of I-kappaB kinase/NF-kappaB signaling, innate immune response, and ubiquitin protein ligase activity. In conclusion, we identified the expression profile of circRNAs in H5N1-infected chicken DF1 cells. Bioinformatic analyses of the dysregulated circRNAs suggest that circRNAs might play important roles in the pathogenesis of H5N1 infection, offering new insights into the mechanisms underlying H5N1–host interaction.

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.