Body weight variation within a breed may be associated with meat flavor in chickens, but its relationship with flavor-related precursor composition across developmental stages remains unclear. Here, integrated lipidomics and metabolomics were applied to compare breast muscle from Beijing-You chickens sampled from the same cohort at 90, 110, 130, and 150 d in a stage-wise design. At each stage, higher-body-weight (HBW) and lower-body-weight (LBW) groups were independently defined from the upper and lower tails of the body weight distribution at that age. A total of 440, 259, 161, and 324 differential lipids, as well as 491, 257, 291, and 402 differential metabolites, were identified at the four stages, respectively. However, only 23 lipids and 3 metabolites were shared across all stages, indicating that metabolic differences between the HBW and LBW groups varied markedly across developmental stages. Differential lipids were mainly distributed among phosphatidylcholine, phosphatidylethanolamine, and phosphatidylserine, while glycerophospholipid metabolism was consistently identified in both lipidomic and metabolomic analyses. Notably, a key transition was observed between 110 and 130 d, during which the predominant direction of PUFA-like differential lipids shifted from HBW to LBW predominance. Representative differential metabolites included N-acetyl-L-methionine, N-methyl-L-glutamic acid, and γ-glutamyl-5-hydroxytryptophan, suggesting alterations in amino acid- and peptide-related metabolism. Overall, these findings provide insight into stage-dependent variation in flavor-related precursor composition within a breed across developmental stages. However, their direct contribution to flavor remains to be validated.

Preserving genetic diversity and maintaining population viability are critical yet challenging goals that demand rigorous evaluation of conservation strategies. Beijing-You chicken, as the sole indigenous chicken breed originating from Beijing, China, is currently maintained as four independent populations under distinct conservation programs. How different conservation regimes have shaped its genomic architecture remains largely unknown, limiting evidence-based evaluation. Here, we generated whole-genome resequencing data from 240 individuals representing four Beijing-You chicken populations to assess population structure, genetic diversity, and signatures of selection over decades of conservation. All four populations formed distinct clusters, reflecting measurable differentiation after decades of separate conservation. The differences in genetic diversity broadly consistent with the variation in effective population size estimates. Runs of homozygosity and linkage disequilibrium decay patterns further characterized each population, with extended values indicating reduced effective population size and increased inbreeding under long-term conservation. We applied the fixation index (FST) and pairwise diversity ratio (θπ) methods to identify selection signatures. A total of 171 genes were identified as candidates. These genes were enriched in pathways related to reproduction, growth regulation, and environmental adaptation. These findings highlight patterns of reduced diversity and skewed relatedness, which could arise from management-related factors such as breeding preferences or mating strategies. Still, they are also compatible with neutral processes, including drift and founder effects. Regardless of the underlying cause, integrating scientifically informed conservation strategies with routine genomic monitoring across generations is essential for sustaining genetic diversity in Beijing-You chicken and other indigenous breeds.

Methods for high resolution phase trimming of silicon Mach–Zehnder interferometers via the electrical annealing of amorphized waveguide sections are presented. A high resolution of phase change is necessary to accurately trim the performance of individual devices to correct fabrication errors and when scaling to large programmable photonic circuits. On‐chip microheaters positioned above amorphous waveguide sections are driven by short voltage pulses, causing a degree of recrystallization, controllably changing the material's refractive index. An average resolution of phase change per voltage pulse of 0.0007π is demonstrated if an adaptive method is employed, where the voltage step between successive pulses is set to be dependent on the average phase change brought about by the previous three voltage pulses.

Lutein is a dietary xanthophyll carotenoid with recognized antioxidant and immunomodulatory potential, yet the molecular basis underlying its nutritional effects in laying hens remains insufficiently understood. Here, liver transcriptomic profiling and 16S rRNA sequencing were combined to investigate the response of laying hens to dietary lutein supplementation. A total of 951 differentially expressed genes were identified in the liver, indicating marked transcriptional remodeling after lutein supplementation. Functional enrichment, gene set enrichment, and weighted gene co-expression network analyses consistently showed that these changes were mainly associated with metabolic regulation, redox/stress adaptation, and immune-related communication. In parallel, lutein supplementation changed cecal microbial community structure and shifted specific microbial biomarkers. Integrated correlation analyses further identified candidate host-microbiota association patterns, including a KLF2/FOXO3/Faecalibacterium axis and a KLF2/IL8L2/Prevotellaceae_Ga6A1_group axis. Overall, dietary lutein was associated with coordinated changes in the hepatic transcriptional profile and cecal microbial community structure, which converged on these two functional directions. These findings provide new insight into the nutritional effects of lutein in laying hens and identify candidate pathways and microbial nodes for future functional validation in poultry feeding systems.

This study utilized high-throughput lipidomics to investigate the effects of age (90-150 days, 20-day intervals: D90, D110, D130, D150; 40 birds per age group) on intramuscular fat (IMF) deposition and lipid transformation in the breast muscle of Beijing-You chicken (BYC). A total of 1725 lipid molecules, predominantly categorized as glycerophospholipids (GP), glycerolipids (GL), and sphingolipids (SP), along with 53 lipid subclasses, were identified. Age-dependent IMF increase was mainly associated with triglyceride (TG), cardiolipin (CL) and phosphatidylglycerol (PG) accumulation. Additionally, based on the cutoff criteria of variable importance in projection (VIP) > 1, fold change (FC) > 1.1 or FC < 0.91, and p-value < 0.05, fifty-two lipids were further identified as differentially expressed lipid molecules (DELMs) between the three age pairwise-comparable groups (D110 vs D90, D130 vs D110, and D150 vs D130). Great variation in side fatty-acyl chains characteristics of DELMs, including saturation degree, average number of carbon atoms and double bonds, were observed within GL and GP due to age. TG(18:3/20:4/22:6), TG(22:5/18:2/22:6), and TG(16:0/22:6/22:6) were identified by Pearson correlation analysis as significantly positive correlates with IMF deposition, suggesting their potential as crucial biomarkers. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway topology analysis based on all 1725 detected lipid molecules indicated that lipid transformations were primarily involved in sphingolipid and glycerophospholipid metabolic pathways. In conclusion, this study used lipidomic analysis to clarify dynamic lipid changes, key lipid molecules (including three specific TG metabolites) and enriched metabolic pathways during BYC growth, providing insights into IMF-related lipid regulation and theoretical support for improving chicken meat quality.

Methods to achieve a high-resolution phase trimming within silicon waveguides incorporating Ge implanted sections are investigated. The trimming is performed electrically using on-chip microheaters. The average resolution of phase change per voltage pulse achieved by this work was approximately 0.0007 pi radians.

Lutein- and astaxanthin-fortified eggs can greatly improve both nutritional and economic values of eggs. High doses of lutein and astaxanthin are often supplemented in hen diets to rapidly accumulate lutein and astaxanthin in eggs. In this study, an additional 100, 200, and 400 mg/kg lutein and astaxanthin were added in hen diets to explore the effects of high-dose lutein and astaxanthin on egg quality, egg production, and carotenoid deposition in eggs, which remains unclear. The results showed that high-dose lutein and astaxanthin supplementation had no significant impact on laying rates and egg quality, except for markedly improving yolk color. Additionally, a quantitative profile of carotenoids in egg yolk was performed through liquid chromatography–mass spectrometry. A total of 26 carotenoids were detected including 14 whose concentrations exceed 0.1 µg/g. Notably, the zeaxanthin content in yolk decreased with the increase in levels of lutein supplementation. Conversely, the content of lutein, zeaxanthin, 5,6 epoxy-lutein-caprate-palmitate in yolk decreased as astaxanthin supplementation increased. These findings suggest that high doses of lutein and astaxanthin supplementation may competitively inhibit the deposition of other carotenoids in egg yolk. Overall, this study suggests that during the production of functional eggs enriched with lutein and astaxanthin, it is important to consider the interaction effects among different carotenoids.

Due to the effects of pigment deposition and microstructure, the color of eggshells may influence the quality traits and hatchability of eggs. These traits are critical for breeding efficiency and economic outcomes in poultry production. Herein, Beijing-You chicken eggs were used as a model to investigate the effects of eggshell color due to their color-related polymorphism. A total of 4422 eggs were analyzed for their hatchability, categorized by storage duration and eggshell color. Results revealed that white-shelled eggs exhibit significantly lower hatchability and higher early embryo mortality compared to other colors, particularly after long-term storage. Purple-shelled eggs demonstrated superior eggshell quality, including higher strength, thickness, and weight, as well as better internal egg quality indicators such as thick albumen height, Haugh units, and yolk color. Eggshell translucency showed a positive correlation with storage time and egg weight loss at all shell color types, with higher translucency levels associated with greater weight loss over time. This study examines associations between eggshell color, hatchability, translucency, and quality traits.

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.

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.

Thigh meat from Cobb 500 broiler (Cobb) and Beijing-You chicken (BYC) at marketable age were compared to explore the impact of growth rate on meat quality. BYC had a higher water capacity, as well as lower shear forces and IMF content than Cobb, indicating that the growth rate has a significant influence on meat quality. Additionally, 144 upregulated and 44 downregulated differential metabolites were identified using gas chromatography mass spectroscopy (GC-MS) and liquid chromatography mass spectrometer (LC-MS). Moreover, we found a significant difference between the dominant expression of metabolites in the two genotypes. The highly expressed metabolites in Cobb were amino acids and their derivatives, including l-citrulline, dimethylglycine, 1,4-butanediamine, alanine, and creatine. In contrast, BYC deposited more bioactive compounds, such as, α-linolenic acid, linoleic acid, eicosapentaenoic acid, anserine, and taurine. These results indicate that meat quality and metabolite profiles differ greatly between fast- and slow-growing chickens.

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.

The T329S mutation in flavin-containing monooxygenase 3 (FMO3) impairs the trimethylamine (TMA) metabolism in laying hens. The TMA metabolic pathway is closely linked to lipid metabolic diseases, such as atherosclerosis and fatty liver disease. We aimed to evaluate the effects of the T329S mutation in FMO3 on lipid metabolism in chickens during the late laying period. We selected 18 FMO3 genotyped individuals (consisting of six AA, six AT, and six TT hens) with similar body weight and production performance. The lipid metabolism and deposition characteristics of the laying hens with different genotypes were compared. The T329S mutation moderated the serum-lipid parameters in TT hens compared to those in AA and AT hens from 49 to 62 weeks. Furthermore, it reduced the serum trimethylamine N-oxide concentrations and increased the serum total bile acid (p < 0.05) and related lipid transporter levels in TT hens. Moreover, it significantly (p < 0.01) decreased atherosclerotic lesions and hepatic steatosis in TT hens compared to those in the AA and AT hens. Our findings may help improve the health status in laying hens during the late laying period.

Germanium (Ge) ion implantation into silicon waveguides will induce lattice defects in the silicon, which can eventually change the crystal silicon into amorphous silicon and increase the refractive index from 3.48 to 3.96. A subsequent annealing process, either by using an external laser or integrated thermal heaters can partially or completely remove those lattice defects and gradually change the amorphous silicon back into the crystalline form and, therefore, reduce the material’s refractive index. Utilising this change in optical properties, we successfully demonstrated various erasable photonic devices. Those devices can be used to implement a flexible and commercially viable wafer-scale testing method for a silicon photonics fabrication line, which is a key technology to reduce the cost and increase the yield in production. In addition, Ge ion implantation and annealing are also demonstrated to enable post-fabrication trimming of ring resonators and Mach–Zehnder interferometers and to implement nonvolatile programmable photonic circuits.

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, including HOXB7 for beard trait in Beijing You chicken; EDN3, SLMO2, TUBB1, and GFPT1 for melanin deposition in Silkie chicken; and SORCS2 for aggressiveness in Luxi Game fowl. Moreover, CSMD1 and NTRK3 with high duplications found exclusively in White Leghorn chicken, and POLR3H, MCM9, DOCK3, and AKR1B1L found 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.

Studies on trimethylamine (TMA) in egg yolk have focused on how it impacts the flavor of eggs, but there has been little focus on its other functions. We designed an in vitro antibacterial test of TMA according to TMA concentrations that covered the TMA contents typically found in egg yolk. The change in TMA content in yolk was analyzed at different storage temperatures and for different storage durations. The known antibacterial components of eggs, including the cuticle quality of the eggshell and the lysozyme activity and content in egg white, were also assessed. The total bacterial count (TBC) of different parts of eggs were detected. The results showed that the inhibitory effect of TMA on Escherichia coli (E. coli) growth increased with increasing TMA concentration, and the yolk TMA content significantly increased with storage duration (p < 0.05). The cuticle quality and lysozyme content and activity significantly decreased with storage time and increasing temperature, accompanied by a significant increase in the TBC on the eggshell surface and in the egg white (p < 0.05). This work reveals a new role for trace TMA in yolks because it reduces the risk of bacterial colonization, especially when the antibacterial function of eggs is gradually weakened during storage.

We present a silicon photonic beam steering device based upon an 8 x 8 grating coupler focal plane array fed by a MZI switching tree. Transmission of the light from the grating couplers is made through the back side of the chip using topside mirrors.

The cuticle formed in the uterus is the outermost layer as the first defense line of eggshell against microbial invasions in most avian species, and analyzing its genetic regulation and influencing factors are of great importance to egg biosecurity in poultry production worldwide. The current study compared the uterine transcriptome and proteome of laying hens producing eggs with good and poor cuticle quality (GC and PC, the top and tail of the cuticle quality distribution), and identified several genes involved with eggshell cuticle quality (ESCQ). Overall, transcriptomic analysis identified 53 differentially expressed genes (DEGs) between PC versus GC group hens, among which 25 were up-regulated and 28 were down-regulated. No differences were found in the uterine proteome. Several DEGs, including PTGDS , PLCG2 , ADM and PRLR related to uterine functions and reproductive hormones, were validated by qPCR analysis. Egg quality measurements between GC and PC hens showed GC hens had longer laying interval between two consecutive ovipositions (25.64 ± 1.23 vs 24.94 ± 1.12 h) and thicker eggshell thickness (352.01 ± 23.04 vs 316.20 ± 30.58 μm) ( P < 0.05). Apart from eggshell traits, other egg quality traits didn’t differ. The result demonstrated eggshell and cuticle deposition duration in the uterus is one of the major factors affecting ESCQ in laying hens. PTGDS , PLCG2 , ADM and PRLR genes were discovered and might play crucial roles in cuticle deposition by regulating the uterine muscular activities and secretion function. The findings in the present study provide new insights into the genetic regulation of cuticle deposition in laying hens and establish a foundation for further investigations.