The detection and functional characterization of genomic structural variations are important for understanding the landscape of genetic variation in the chicken. A recently recognized aspect of genomic structural variation, called copy number variation (CNV), is gaining interest in chicken genomic studies. The aim of the present study was to investigate the pattern and functional characterization of CNVs in five characteristic chicken breeds, which will be important for future studies associating phenotype with chicken genome architecture. Using a commercial 385 K array-based comparative genomic hybridization (aCGH) genome array, we performed CNV discovery using 10 chicken samples from four local Chinese breeds and the French breed Houdan chicken. The female Anka broiler was used as a reference. A total of 281 copy number variation regions (CNVR) were identified, covering 12.8 Mb of polymorphic sequences or 1.07% of the entire chicken genome. The functional annotation of CNVRs indicated that these regions completely or partially overlapped with 231 genes and 1032 quantitative traits loci, suggesting these CNVs have important functions and might be promising resources for exploring differences among various breeds. In addition, we employed quantitative PCR (qPCR) to further validate several copy number variable genes, such as prolactin receptor, endothelin 3 (EDN3), suppressor of cytokine signaling 2, CD8a molecule, with important functions, and the results suggested that EDN3 might be a molecular marker for the selection of dark skin color in poultry production. Moreover, we also identified a new CNVR (chr24: 3484617–3512275), encoding the sortilin-related receptor gene, with copy number changes in only black-bone chicken. Here, we report a genome-wide analysis of the CNVs in five chicken breeds using aCGH. The association between EDN3 and melanoblast proliferation was further confirmed using qPCR. These results provide additional information for understanding genomic variation and related phenotypic characteristics.

Introduction: The long egg-laying interval of pigeons leads to low egg production, and the hypothalamus-pituitary-ovary (HPO) axis plays a crucial role in regulating the egg-laying process of poultry. European meat pigeons have a shorter egg-laying interval than Shiqi pigeons, but the molecular mechanism underlying this difference remains unclear.Methods: Reproductive phenotypic data of 300 pairs of pigeons from each breed were collected for 6 months. Five 2-2.5-year-old female pigeons from each breed were selected, and their hypothalamus, pituitary, and ovary tissues were collected for transcriptome sequencing. Differentially Expressed Genes (DEGs) were identified, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed.Results: The egg-laying interval of European meat pigeons (32.76 ± 3.25 days) was significantly shorter than that of Shiqi pigeons (33.11 ± 3.86 days, P=0.024). A total of 39, 101, and 199 DEGs were identified in the comparisons of SH vs EH, SP vs EP, and SO vs EO, respectively. DEGs in the hypothalamus and pituitary were enriched in pathways such as thyroid hormone transport and calcium-mediated signaling; DEGs in the ovary were enriched in pathways such as embryonic development and steroid biosynthesis. The thyroid hormone signaling pathway (in the hypothalamus and pituitary) and the steroid hormone biosynthesis pathway (in the ovary) were significantly enriched, and key genes such as StAR, EYA1, HAND2, HOXB8, and NRN1 were identified.Discussion: The hypothalamus-pituitary-ovary axis regulates the egg-laying interval of pigeons through tissue-specific pathways. Among them, the thyroid hormone signaling pathway controls upstream hormone secretion, and the steroid biosynthesis pathway affects follicle maturation. The identified key genes may serve as targets for shortening the egg-laying interval.

The duodenum is a key site of nutrient digestion and absorption in meat pigeons, and its microbial community may be associated with host body weight and breast muscle development. In this study, the duodenal microbiota of European meat pigeons and Shiqi pigeons at 14 and 28 days of age were analyzed using 16S rRNA gene sequencing. At 14 days of age, Firmicutes abundance was significantly higher in Shiqi pigeons than in European meat pigeons, whereas Proteobacteria showed the opposite pattern. Lactobacillus constituted the most abundant microbial group in both breeds. Spearman correlation analysis showed that Firmicutes and Lactobacillus were positively correlated with body weight and pectoral muscle percentage at 14 days of age, whereas Proteobacteria were negatively correlated with these traits. At 28 days of age, fewer between-breed differences in microbial community composition were detected; nevertheless, Firmicutes and Lactobacillus remained significantly positively correlated with body weight and pectoral muscle percentage in both breeds. These cross-sectional associations provide a preliminary reference for future studies of the duodenal microbiota and growth traits in meat pigeons.