The physical properties, free amino acids, and metabolites of Beijing-You chicken (BYC) breast meat aged 90, 120, and 150 days were analyzed to investigate the flavor changes with age. The shear force and intramuscular fat increased from 90 to 120 days significantly. The contents of total free amino acids and essential amino acids decreased from 90 to 120 days significantly. No significant differences were detected between 120 and 150 days. The contents of sweet amino acids, bitter amino acids, and umami amino acids showed no significant differences between different ages. In addition, GC-MS and LC-MS were integrated for metabolite detection in breast meat. A total of 128, 142, and 88 differential metabolites were identified in the comparison groups of 120 d vs. 90 d, 150 d vs. 90 d, and 150 d vs. 120 d. Amino acids and lipids were the main differential metabolites. The pathway analysis showed that arginine biosynthesis, histidine metabolism, purine metabolism, and cysteine and methionine metabolism were the main pathways involved in flavor formation during BYC development. It was also found that the metabolites associated with flavor, such as methionine, cysteine, glucose, anserine, arachidonic acid, and glycerol 1-phosphate, were significantly affected by age.

Copy number variation (CNV) is an important genetic mechanism that drives evolution and generates new phenotypic variations. To explore the impact of CNV on chicken domestication and breed shaping, the whole-genome CNVs were detected via multiple methods. Using the whole-genome sequencing data from 51 individuals, corresponding to six domestic breeds and wild red jungle fowl (RJF), we determined 19,329 duplications and 98,736 deletions, which covered 11,123 copy number variation regions (CNVRs) and 2,636 protein-coding genes. The principal component analysis (PCA) showed that these individuals could be divided into four populations according to their domestication and selection purpose. Seventy-two highly duplicated CNVRs were detected across all individuals, revealing pivotal roles of nervous system (NRG3,NCAM2), sensory (OR), and follicle development (VTG2) in chicken genome. When contrasting the CNVs of domestic breeds to those of RJFs, 235 CNVRs harboring 255 protein-coding genes, which were predominantly involved in pathways of nervous, immunity, and reproductive system development, were discovered. In breed-specific CNVRs, some valuable genes were identified, includingHOXB7for beard trait in Beijing You chicken;EDN3,SLMO2,TUBB1, andGFPT1for melanin deposition in Silkie chicken; andSORCS2for aggressiveness in Luxi Game fowl. Moreover,CSMD1andNTRK3with high duplications found exclusively in White Leghorn chicken, andPOLR3H,MCM9,DOCK3, andAKR1B1Lfound in Recessive White Rock chicken may contribute to high egg production and fast-growing traits, respectively. The candidate genes of breed characteristics are valuable resources for further studies on phenotypic variation and the artificial breeding of chickens.

Unique metabolites contribute to the performance of meat flavor and potential function. In this study, UHPLC-Q Exactive HF-X-based metabolomics and multivariate analysis were applied to explore the characteristic metabolites in the breast meat of Beijing-You chicken (BYC) aged 150, 300, and 450 days (D150, D300, and D450). Based on the criteria of variable importance in the projection (VIP) > 1 and p < 0.05, a total of 154 and 97 differential metabolites (DMs) were screened out compared with D450 (D450 vs. D150, D450 vs. D300), respectively. In general, the relative content of carnosine, L-L-homoglutathione, demethyloleuropein, neohesperidin dihydrochalcone, 7-chloro-2-(3,4-dimethoxyphenyl)-3,5-dihydroxy-6,8-dimethoxy-4H-chromen-4-one, glycerophospholipids, exhibited the highest abundance at D450, while balenine, anserine, L-beta-aspartyl-L-leucine, glutathione, oxidized glutathione, stearoylcarnitine, ganoderic acid alpha, oleuroside, Lysoglycerophospholipid species (LGP) presented a downward trend with age. These 210 DMs were involved in 10 significantly enriched pathways related to the synthesis and metabolism of amino acids, peptides, and glycerophospholipid, such as glutathione metabolism, histidine metabolism, glycerophospholipid metabolism, arginine biosynthesis, tyrosine metabolism, and lysine degradation. In conclusion, this work could not only facilitate a better understanding of the differences of chicken flavor and benefit properties with age, but also provide potential valuable bioactive compounds for further research.

Lipopolysaccharide (LPS) is ubiquitous in the environment and is released after the death of gram-negative bacteria, which may be related to inflammation and immunosuppression. However, its impact on the reproduction of animals and their offspring, especially the underlying mechanism need further elucidation. Here, we used laying hens as a model organism to investigate the effects of maternal exposure to LPS (LPS maternal stimulation) on animal and their offspring's immunity and reproductive performance, as well as the regulatory role of the transcriptome. We found that the LPS maternal stimulation could reduce the egg-laying rate of hens and their offspring, especially during the early and late laying stages. The transcriptome study of the spleen in F0, F1 and F2 generations showed that the maternal stimulation of the LPS affects the patterns of gene expression in laying hens, and this change has a long-lasting effect. Further analysis of DEGs and their enrichment pathways found that the LPS maternal stimulation mainly affects the reproduction and immunity of laying hens and their offspring. The DEGs such as AVD, HPS5, CATHL2, S100A12, EXFABP, RSFR, LY86, PKD4, XCL1, FOS, TREM2 and MST1 may play an essential role in the regulation of the immunity and egg-laying rate of hens. Furthermore, the MMR1L3, C3, F13A1, LY86 and GDPD2 genes with heritable effects are highly correlated with the egg-laying rate, may have an important reference value for further research. Our study reveals the profound implications of LPS exposure on immunity and reproduction of offspring, elaborating the impact of immune alteration on the egg-laying rate, emphasizing the regulatory role of intergenerational transmission of the transcriptome, implying that the environment parents being exposed to has an important impact on offspring.

Chicken age contributes to the meat characteristics; however, knowledge regarding the pathways and proteins associated with meat quality and muscle development are still scarce, especially in chicken thigh meat. Hence, the objective of this study was to elucidate the intricate relationship between these traits by liquid chromatography mass spectrometry at three different ages. A total of 341 differential expressed proteins (DEPs) were screened out (fold change ≥ 1.50 or ≤0.67 and p < 0.05) among 45 thigh meat samples (15 samples per age) of Beijing-You chicken (BYC), collected at the age of 150, 300, or 450 days (D150, D300, and D450), respectively. Subsequently, based on the protein interaction network and Markov cluster algorithm (MCL) analyses, 91 DEPs were divided into 26 MCL clusters, which were associated with pathways of lipid transporter activity, nutrient reservoir activity, signaling pathways of PPAR and MAPK, focal adhesion, ECM-receptor interaction, the cell cycle, oocyte meiosis, ribosomes, taurine and hypotaurine metabolism, glutathione metabolism, muscle contraction, calcium signaling, nucleic acid binding, and spliceosomes. Overall, our data suggest that the thigh meat of BYC at D450 presents the most desirable nutritional value in the term of free amino acids (FAAs) and intramuscular fat (IMF), and a series of proteins and pathways associated with meat quality and development were identified. These findings also provide comprehensive insight regarding these traits across a wide age spectrum.

A systematic dissection of the functional impacts of non-coding variations across diverse tissues and cell types is essential for deciphering the molecular architecture underlying complex traits. Given the significance of chickens as both a key livestock species and a fundamental model organism, the development of an integrative genomics resource is imperative. Leveraging SNP-to-gene-to-trait linking strategies—including molecular quantitative trait loci (molQTL), regulatory elements, and context- or environment-dependent regulatory heterogeneity—we developed the ChickenGTEx portal (http://chicken.farmgtex.org), which provides a comprehensive catalogue of regulatory effects on transcriptomic and phenotypic diversity across tissues, cell types, and sexes. Key features of the resource include a genotype imputation panel of 2869 chickens from 123 breeds worldwide, five types of molecular phenotypes across 28 tissues, ∼2.2 million molQTL, 806 229 fine-mapped molQTL, 1956 context-dependent molQTL, 257 genome-wide profiles of 7 epigenetic marks (representing 15 chromatin states) from 23 tissues, 185 376 single-cell expression profiles across 191 cell clusters from 9 tissues, and 96 386 gene-trait associations covering 108 economically important traits. In summary, the ChickenGTEx portal will serve as an invaluable resource for advancing research in fundamental and evolutionary biology, chicken precision breeding, and eventually human biomedicine.