Sichuan Shelduck, a unique Chinese indigenous duck breed, exhibits superior meat quality traits, but its genetic basis has not been systematically evaluated. This study assessed meat quality traits, including pH, color, shear force, moisture, and intramuscular fat (IMF) in 240 Sichuan Shelducks (123 males and 117 females). At 90 days, males exhibited higher IMF (2.83% ± 0.58 vs. 2.79% ± 0.63, P < 0.01) and moisture content (76.35% ± 1.04 vs. 75.68% ± 2.3, P < 0.01), but lower shear force (31.00 ± 9.11 N), compared with females (33.32 ± 10.03 N). Phenotypic correlation analysis revealed that moisture content was positively correlated with flesh color and tenderness. SNP-based heritability estimates were moderate to high for moisture (0.42), meat lightness (L*, 0.39), and IMF (0.34). Genome-wide association studies (GWAS) identified 29 significant SNPs for IMF on chromosome 21, with the peak SNP (chr21:2210804 T>C) near STK4 explaining 19.68% of the phenotypic variance. GO functional analysis results speculated that STK4 may be involved in adipocyte differentiation through the FoxO/MAPK pathway. Transcriptomic analysis of pectoral muscle with high versus low IMF highlighted enrichment of DGAT2 in Glycerolipid metabolism and PPAR signaling pathways. Regression analysis prioritized RALY for its role in cholesterol homeostasis. These candidate genes (STK4, DGAT2, RALY) and associated molecular markers provide a genetic basis for improving Sichuan Shelduck meat quality in breeding programs.

The crosstalk between the hypothalamic-pituitary-gonadal (HPG) and hypothalamic-pituitary-thyroid (HPT) axes plays an important role in gonadal development. However, the mechanism by which these 2 axes regulate early testicular development in drakes remains largely unknown. Therefore, the aim of the present study was to compare the morphology, histology, and transcriptomics between the precocious puberty (PP) and delayed puberty (DP) Longyan Shan-ma drakes (Anas platyrhynchos) to preliminarily reveal the mechanisms regulating early testicular development. The histomorphological results showed that the colloid area and integrated optical density (IOD) of thyroid in PP group were significantly lower than those in DP group (P < 0.05), and the testis weight, testis index, seminiferous tubule diameter, and number of spermatogonia in PP group were significantly higher than those in DP group (P < 0.05). The transcriptomic results showed that between PP and DP groups, a total of 232, 574, 572, and 4,129 differentially expressed genes (DEGs) were identified in the hypothalamus, pituitary, thyroid, and testis, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that DEGs in hypothalamus, pituitary, thyroid, and testis were significantly enriched in 3, 14, 16, and 27 KEGG pathways (P < 0.05), respectively, with the neuroactive ligand-receptor interaction pathway being the only one commonly enriched in all 4 tissues. Further, 11 key genes (GNRH1, AGT, AGTR1, COL1A1, ITGB6, PIK3CB, PLCB4, CALML4, ADCY1, PDE1C, and BUB1) were identified through screening based on enrichment in core reproductive pathways (including neuroactive ligand-receptor interaction and progesterone-mediated oocyte maturation) and functional links to testicular development. Their expression trends were validated by qRT-PCR (R²=0.89), confirming reliability. These genes may serve as critical nodes in HPG/HPT axis crosstalk to regulate early testicular development. This study is the first systematically comparing the transcriptomes of the HPG and HPT axes between DP and PP drakes. These results will provide novel insights into the mechanisms of crosstalk regulation of the HPG and HPT axes on early testicular development in drakes.

Breast muscle yield is an economically important trait in ducks, but the contribution of population-level transposable element insertion polymorphisms (TIPs) to its genetic regulation remains poorly understood. Whole-genome resequencing data from 200 ducks representing Cherry Valley ducks, Liancheng white ducks, and five Jinling White Duck lines were used to identify population-level TIPs. After quality filtering, TIP-based genome-wide association study (TIP-GWAS) and TIP-based expression genome-wide association study (TIP-eGWAS) were performed to identify loci associated with breast muscle traits and gene expression. Candidate genes were prioritized by integrating TIP-associated expression genes, weighted gene coexpression network analysis, differential expression analysis, and gene–trait correlation analysis, followed by functional evaluation in primary duck myoblasts. A total of 3,628 TIPs were identified, and 543 high-confidence TIPs were retained for population structure and association analyses. TIP-GWAS detected 14 significant trait–locus associations, mainly involving breast muscle yield traits, which were merged into 6 nonredundant TIP loci. Targeted TIP-eGWAS followed by conservative filtering retained 1,410 priority eGenes, of which 147 were associated with at least one target trait. These genes were enriched in pathways related to the tricarboxylic acid cycle, oxidative phosphorylation, carbon metabolism, fatty acid metabolism, and fibroblast growth factor receptor signaling. Integrative analysis prioritized LOC101798742 as a candidate gene corresponding to the chr6:36133712 TIP locus. In silico annotation indicated that LOC101798742 encodes the duck ortholog of alpha-aspartyl dipeptidase (DNPEP). In primary duck myoblasts, LOC101798742 knockdown reduced proliferation-related gene expression, altered cell-cycle distribution, and enhanced myoblast fusion, whereas overexpression promoted cell-cycle progression and increased apoptosis-related changes. These findings suggest that population-level TIP variation may contribute to duck breast muscle yield through gene regulatory networks and myoblast proliferation–differentiation dynamics. This study expands the range of regulatory variants considered in duck breeding and provides candidate loci and genes for future functional validation and genetic improvement.

Production experience has shown that local meat duck breeds possess stronger immune capacities than commercial breeds. However, systematic comparisons of their immune differences remain insufficient, and the molecular basis underlying these differences is still unclear. In this study, we compared body weight, serum immune molecule levels (IgA, IgM, IgG, IFN-γ, IL-6, and IL-10), and immune organ indices during early growth stages (1, 14, and 28 days of age [D]) between Huaifu meat ducks (HF) and Cherry Valley ducks (CV). The results showed that no significant differences were observed in these parameters at 1 and 14 D. At 28 D, the body weight of CV was significantly higher than that of HF. Meanwhile, ELISA results showed significantly higher levels of serum IgA, IgM, IL-6, and IL-10 in HF. In addition, the thymus index of HF was significantly greater. Furthermore, transcriptome sequencing (RNA-seq) was performed on immune organs at 28 D. Subsequent analysis identified 443, 451, and 449 differentially expressed genes (DEGs) in the thymus, spleen, and bursa of Fabricius (BF), respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified six, five, and two immune-related pathways in the thymus, spleen, and BF. IL6, CCR9, IL10, IL12A, RIPK2, RNASEL, SPP1, TLR5, and CASR, which were enriched in these pathways, might play key regulatory roles. Then, we performed Spearman correlation analysis between them and the DEGs in their corresponding tissues and constructed gene sets based on the results. A protein–protein interaction (PPI) network was further established for the gene sets from the three tissues. Functional enrichment analysis revealed that these genes were primarily associated with metabolism. In summary, 28 D represented a critical stage for the growth and immune system development of HF and CV. The genes IL6, CCR9, IL10, IL12A, RIPK2, RNASEL, SPP1, TLR5, and CASR were identified as key candidates, which might participate in essential metabolic processes, collectively influencing immune organ development with particularly pronounced effects on the thymus. In addition, serum levels of IgA, IgM, IL-6, and IL-10 appeared to be coordinately regulated by the thymus and spleen. These findings provided the molecular basis for subsequent disease-resistant breeding.

Abstract Background The composition of fatty acids, particularly the content of unsaturated fatty acids (UFA), is closely related to meat quality and flavor in ducks. Result In this study, 38 fatty acids were detected in the breast muscle of Sansui ducks, yielding 50 distinct fatty acid composition traits. The results showed that the predominant fatty acids were C18:1n-9, C16:0, C18:2n-6, C18:0, and C20:4n-6. Moreover, the breast muscle of Sansui duck was rich in UFA, accounting for 64.01% of the total fatty acids. Genome-wide association analysis (GWAS) identified 158 single nucleotide polymorphisms (SNPs) significantly associated with fatty acid composition traits, which were annotated to 70 protein-coding genes, including LDLRAD3, ACVR1, FGF6, and CASQ2. Additionally, linkage disequilibrium (LD) analysis revealed a candidate region (10,533,318 − 10,546,189 bp) on chromosome 14, where NSG2 was identified as a key candidate gene influencing C17:1 content. Functional enrichment analysis suggested that pathways such as Adherens junctions and MAPK signaling may play significant roles in fatty acid biosynthesis. Conclusion These findings reveal the genetic structure of fatty acids composition in the breast muscle of Sansui duck, providing strong evidence for understanding the genetic regulatory mechanisms of fatty acid composition.

In ducks, the sternum is the largest flat bone. Its calcification affects breast muscle development, health, and economic value. Delayed calcification can lead to sternum fractures during feeding, slaughter. Thus, we need to understand the molecular basis of sternum calcification. We compared two duck breeds with different body sizes: the fast-growing, large-bodied Cherry Valley (CV) and the smaller-bodied Huaifu (HF) ducks. Results showed a positive correlation between sternum calcification rate and both calcification length and breaking strength (r > 0.4). HF had a higher calcification rate (99%) than CV (95%), and females (HFM: 100%; CVM: 97%) had higher rates than males (HFG: 97%; CVG: 94%). Breaking strength was also higher in HF (43.29 N) than in CV (36.1 N), with females outperforming males. We performed RNA-seq and LC-MS metabolomics on sternal tissues. A clear contrast in gene expression appeared between nearly fully calcified Huaifu males (HFG) and females (HFM): genes including FGF6, BDNF, HTR4, MYLK2, MAP3K6, and CER1 were barely expressed. But these genes were significantly upregulated in CV compared to HF, in CVM compared to CVG, and in high-breaking-strength (HB) versus low-breaking-strength (DB) groups. Those genes showed low expression in fully calcified or non-calcified sterna but high expression during active calcification, suggesting they help drive calcification. Our study identifies multiple biomarkers linked to duck sternum development and offers new insights into avian sternum ossification, which may help improve poultry production and welfare.

Residual feed intake (RFI) is a key indicator of feed efficiency in poultry. Although regulatory links such as the hypothalamus-gut and gut-liver axes have been implicated, most studies remain restricted to single axes or fragmented analyses, and systematic multi-organ integration is lacking. Here, we measured feed efficiency in 1,000 Nonghua ducks and selected 12 individuals with divergent RFI for transcriptomic profiling of the hypothalamus, pituitary, liver, duodenum, jejunum, ileum, and cecum, combined with serum metabolomics. We identified 769 differentially expressed genes (DEGs), with the hypothalamus, liver, and cecum as major contributors, and 28 differential serum metabolites enriched in lipid and amino acid metabolism. Beyond tissue-specific functions, enrichment analysis highlighted several pathways that were repeatedly shared across central and peripheral tissues, including neuroactive ligand-receptor interaction, hormone signaling, steroid hormone biosynthesis, and insulin signaling, suggesting a coordinated regulation of feed efficiency between the brain, gut, and liver. To clarify their relevance, we integrated gene modules with metabolites and identified two candidate cross-organ association frameworks: the MEblack-6-Oxopiperidine-2-carboxylic acid (gut-liver) networks, enriched for liver genes CNTNAP1, SHC3, and RAB36, and cecal genes DCC and CCDC60. The MEblue-LysoPE(18:2(9Z,12Z)/0:0) (gut-brain) networks, enriched for cecal genes FABP6, KCNJ11, and the pituitary gene TRPA1, in which these genes and metabolites may contribute to RFI regulation. Together, these findings provide new insights into cross-organ molecular networks underlying feed efficiency in ducks and establish a valuable resource for future functional studies and breeding strategies.

As an important economic trait in ducks, residual feed intake (RFI) may be influenced by the intestinal microbiota. However, the mechanisms underlying microbiota-host crosstalk remain unclear. We analyzed the total egg number (TEN), total egg weight (TEW), total feed intake (TFI), feed conversion ratio (FCR), and RFI of 1,370 ducks over a 32-day period. Within the high-TEW ducks, 60 low RFI ducks and 60 high RFI ducks were selected to form the LH group (LH) and HH group (HH), respectively. The TFI, FCR, and RFI were significantly lower in the LH than in the HH (P < 0.001). Based on 16S rRNA sequencing, the duodenal microbiota in the LH showed a significantly higher evenness index compared to the HH (P < 0.05). Using linear discriminant analysis effect size (LEfSe), differential bacterial genera were identified in the duodenum and jejunum between groups (LDA > 3.5, P < 0.05). Functional prediction results indicated that, compared to the HH, the duodenal microbiota of the LH appeared to be more active in metabolism. Further analysis revealed four genera (Paenibacillus, Kocuria, Corynebacterium, and Bacillus) that showed significant differences in both the duodenum and jejunum (LDA > 3.5, P < 0.05). Their abundances in the LH were significantly higher than those in the HH (P < 0.05). Subsequently, 419 and 384 differentially expressed genes (DEGs) were identified in the duodenum and jejunum using DESeq2, respectively (|Log2FC)|≥ 1, P < 0.05). Functional enrichment analysis showed that 22 and 16 pathways were significantly enriched in the duodenum and jejunum (P < 0.05). Among them, five metabolism-related pathways, such as steroid biosynthesis, were co-enriched in both intestinal segments. We constructed a protein–protein interaction (PPI) network of DEGs from the five pathways and utilized the MCODE plugin to extract the top-ranking subnetwork. The expression levels of genes in this subnetwork (HMGCS1, MSMO1, ACAT2, LSS, FDFT1, SQLE, IDI1, CYP51A1) were significantly correlated with the abundance of key genera. Paenibacillus, Kocuria, Corynebacterium, and Bacillus were identified as key microbiota influencing feed efficiency in ducks. Their abundances were closely associated with the expression of HMGCS1, MSMO1, ACAT2, LSS, FDFT1, SQLE, IDI1, and CYP51A1. The specific mechanisms require further validation in future studies. These findings provide a preliminary investigation into the intestinal microbiota-host crosstalk affecting feed efficiency and offer novel perspectives for reducing RFI in egg-type ducks.

Avian eggshell coloration provides a useful model for connecting evolutionary ecology with poultry genetics, but studies have yet to integrate molecular regulation and phenotypic evolution into a unified framework. This review identifies the conserved heme pathway involving 5’-Aminolevulinate Synthase 1, Ferrochelatase, and Heme Oxygenase 1 as the metabolic basis for protoporphyrin IX and biliverdin deposition and the resulting continuum of shell colors. Eggshell coloration is therefore treated as a multilevel trait governed by genomic architecture, the shell-gland microenvironment, epigenetic regulation, nutrition, and physiological stress. Blue-green coloration is largely stabilized by major-effect genes, whereas brown and speckled phenotypes show stronger polygenic control and genotype-by-environment interactions. These regulatory differences may explain why blue shells are more evolutionarily conserved while brown phenotypes remain more responsive to environmental conditions, with each mode carrying distinct constraints and physiological costs. Key research priorities include single-cell and spatial transcriptomics, interactions between epigenetic regulation and the microbiota, comparative genomics of convergent phenotypes, and the use of artificial intelligence in multi-omics breeding.

The Sansui duck is a valuable Chinese genetic resource. However, incomplete exploration of its genetic resources has limited the full utilization of its genetic potential. This study systematically evaluated the growth and carcass performance in 305 Sansui ducks and explored their genetic basis through genome-wide association studies (GWAS). Body weight (recorded biweekly from 0 to 20 weeks), body measurement traits, and carcass yield traits (measured at 20 weeks) were collected. Growth curve analysis revealed a relatively slow growth rate, with early growth occurring from 0 to 14 weeks and a critical period for weight gain observed at 8-10 weeks. Sansui ducks exhibited small body size with favorable meat production traits: half-eviscerated yield percentage (HEYP) and eviscerated yield percentage (EYP) both above 70%, while breast muscle percentage (BMP) and leg muscle percentage (LMP) reached 11.99% and 11.01%, respectively. SNP-based heritability estimates indicated moderate to high heritability for growth and slaughter traits. GWAS identified 222 SNPs associated with growth and slaughter traits, which were annotated to 53 candidate genes, including EFEMP1, SKAP1, and MYO19. Linkage disequilibrium (LD) analysis further pinpointed two key genomic regions on chromosome 28 (1-200 kb and 250-320 kb) influencing multiple traits. These regions harbor critical candidate genes, including the HOXB family and IGF2BP1, which play important roles in regulating skeletal development, energy allocation, and growth rhythm in poultry. These findings enrich the genetic resource database of the Sansui duck and provide an important theoretical basis for further elucidating the genetic foundation of its growth and carcass performance.

Background Semen collection is a crucial step in artificial insemination of geese, directly affecting semen quality and fertilization success. To investigate the effects and regulatory mechanisms of sustained semen collection on semen quality in ganders, 36-week-old healthy ganders that pre-trained for semen collection were randomly allocated to either a sustained semen collection (SC) group (semen collection every three days) or a non-semen collection (NSC) group. At 66 weeks, we compared semen quality, semen microbiota, and metabolites between the SC and NSC groups. Results Compared with the NSC group, the SC group exhibited significantly higher ejaculate volume, sperm density, viability, motility, and semen quality factor ( SQF ) ( P <0.01), along with higher sperm acrosomal integrity ( P <0.05), and a lower sperm deformity rate ( P <0.05). 16S rRNA sequencing showed that Proteobacteria was the most abundant phylum in gander semen, with Acinetobacter and Oceanivirga being the predominant genera in the SC and NSC groups, respectively. The differential microbial taxa in the SC group were Bacillales, Corynebacteriaceae, Corynebacterium1 , Megamonas , Pasteurellaceae bacterium20215_4. Whereas those in NSC group were Burkholderiaceae, Ralstonia , Hydrogenophaga , Sphingomonadales, Sphingomonadaceae, Sphingomonas , Arthrobacter , and Escherichia_Shigella . Metabolome analysis revealed that the metabolites in gander semen were mainly lipids and lipid-like molecules. Furthermore, 38 differential expressed metabolites ( DEM ) were identified between the SC and NSC groups, especially the five metabolites, including PG (16:0/20:4 (5Z,8Z,11Z,14Z)), PI 40:6, 3-hydroxyoctanoyl carnitine, crotonic acid, and isobutyrylglycine, being the most significant. The online Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the DEM were significantly enriched in 20 metabolic pathways. Among these, lipoarabinomannan ( LAM ) biosynthesis and glycerophospholipid metabolism were associated with immunity and sperm motility, respectively. Integrated analysis further showed that the differential microbial taxa in the SC group ( Bacillales and Megamonas ) were significantly positively correlated with several lipids and amino acid derivatives. In the NSC group, the differential microbial taxa ( Escherichia_Shigella , Burkholderiaceae , and Hydrogenophaga ) were significantly negatively correlated with CAR8:0 Conclusions In conclusion, sustained semen collection contributes to a stable seminal milieu, alleviates oxidative stress, facilitates sperm metabolism, and consequently improves semen quality. In contrast, extended periods without semen collection may compromise spermatogenesis and sperm maturation.

Geese, descendants of migratory birds, have preserved the distinct reproductive and lipid metabolism traits of their wild ancestors. Therefore, compared to other poultry, geese have lower egg production ability and greater susceptibility to fatty liver. Recent research underscores the impact of lipid metabolism disorders on female reproductive health. In this context, we observed reproductive disorders (RD) and lipid metabolism anomalies in certain geese populations. This study systematically elucidated the differences between RD and normal geese at various levels, including genomics, transcriptomics, bile acid metabolomics, and microbiomics, revealing the crucial role of microorganisms. Our study provides a thorough examination of the ovarian anatomical, histological, and transcriptomic profiles between normal and RD geese. Genomic analyses pinpoint mutations in genes associated with bile acid metabolism, highlighting their potential role in RD pathogenesis. The genomic discoveries are substantiated by precise bile acid assays and ileum transcriptome analyses, which expose a significant disruption in bile acid absorption, activation of FXR, and an increase in serum chenodeoxycholic acid (CDCA) concentrations within RD geese. Notably, 16S rRNA sequencing uncovers significantly greater beta diversity in the ileum microbiota of RD geese than in the normal group. Both Wilcoxon rank sum test and LEfSe analyses highlighted a marked increase in Romboutsia abundance in RD geese. Experimental cultivation of microbiota with CDCA supplementation confirms the impact of CDCA on Romboutsia lituseburensis proliferation. Gavage experiments with R. lituseburensis elucidate its involvement in primary follicle reduction via immune-mediated pathways. Collectively, our multifaceted analysis unravels the intricate involvement of Romboutsia in goose RD, offering insights from genetic, physiological, and microbial dimensions. Our findings not only deepen understanding of the etiology of RD in geese but also suggest potential avenues for therapeutic interventions targeting bile acid metabolism and modulation of specific microbiota components.

Residual feed intake (RFI) is a key indicator for assessing feed efficiency in animals. Although olfactory cues are known to influence feeding behavior, their underlying molecular mechanisms in RFI regulation remain unclear. This study characterized the expression profiles of long non-coding RNAs (lncRNAs) and mRNAs in the olfactory tissue of Tianfu Nonghua ducks with divergent RFI phenotypes. RNA sequencing was conducted on olfactory tissue samples from low-RFI (n = 6) and high-RFI (n = 6) individuals. A total of 40 differentially expressed lncRNAs and 157 differentially expressed mRNAs were identified. Target gene prediction revealed 88 putative lncRNA target genes, primarily regulated through trans-acting mechanisms. Functional enrichment analysis highlighted significant involvement in neuroactive ligand-receptor interactions, neurotransmitter transport, and metabolic pathways. Notably, differentially expressed G protein-coupled receptors (GPCRs) were enriched in neuroactive ligand-receptor interaction pathways, suggesting their potential role in modulating olfactory signal transduction. Co-expression network analysis identified 155 lncRNA-mRNA regulatory pairs, with key interactions involving lncRNAs ENSAPLG00000024078.1 and ENSAPLG00000030384.1 and their associated target mRNAs: IQCM, LAG3, GBX2, SLC6A6, and RP1L1. These findings provide novel insights into lncRNA-mRNA regulatory networks within duck olfactory tissue and suggest a potential mechanism by which olfactory signaling may influence feed efficiency.

Duck meat is highly appreciated for its unique flavor and rich nutritional value, and metabolites have become important phenotypic indicators of meat quality. The Sansui duck, a celebrated local breed from Guizhou, is known for its tender, savory meat, yet its metabolomic composition and underlying genetic basis remain unexplored. In our study, non-targeted LC-MS/MS metabolomics of 305 Sansui duck breast muscles detected 4,729 metabolic features (459 annotated) and identified 136 sex-differential metabolites enriched in fatty acid and amino acid metabolism pathways. Metabolite-based genome-wide association studies (mGWAS) further identified 355 significant LD-independent SNPs and 267 potential candidate genes associated with 103 metabolites. The signal peaks for amino acid metabolites were mainly concentrated on chromosomes 1, 5, and 20. A QTL on chromosome 2 (63.90-64.10 Mb), containing candidate genes ZNF407, CNDP1, and CNDP2, was identified for three methylglyoxal derivatives, with the lead SNP (chr2: 63928783) accounting for about 18.3% of their variance. Additional QTLs on chromosomes 5, 20, 1, and 24 were associated with Carnosine, N-Acetylhistidine, Acetylcholine, N-Acetyl-L-aspartic acid, 11b-PGF2a, and 12(S)-HpETE. These intervals harbor BBOX1 and ACACA, two key rate-limiting enzymes in fatty acid metabolism. Our results revealed the genetic basis of breast muscle metabolites in Sansui ducks and identified associated genetic loci and candidate genes. These findings deepen our understanding of muscle metabolism and provide valuable insights for improving meat quality and nutritional breeding.

Feeding behavior is a key factor influencing growth performance and feed efficiency in poultry, yet its complex phenotypes remain difficult to quantify accurately, limiting the application of large-scale behavioral data in genetic and molecular analyses. In this study, feeding behavior and feed efficiency-related phenotypes were recorded in 829 Tianfu Nonghua ducks using an automated feeding monitoring system integrated with radio frequency identification (RFID) technology. Genetic parameter estimation indicated that the heritability of feeding behavior traits ranged from 0.25 to 0.39. Individuals were classified into high-frequency feeding (HFF) and low-frequency feeding (LFF) groups. Phenotypic analysis showed that ducks in the HFF group had significantly higher residual feed intake (RFI) and feed conversion ratio (FCR) than those in the LFF group. Based on this grouping, transcriptome sequencing was performed on the hypothalamus, pituitary, and liver tissues. A total of 266, 181, and 94 differentially expressed genes (DEGs) were identified in the three tissues, respectively. Enrichment analysis highlighted tissue-specific pathways, including neuroactive ligand-receptor interaction and calcium signaling in the hypothalamus, the Apelin signaling pathway in the pituitary, and steroid hormone biosynthesis in the liver. Appetite-related genes in the hypothalamus (PMCH, HCRT, and CCKAR) and endocrine and metabolic genes in the pituitary and liver (TRH and NEGR1) showed differential expression between feeding strategies. Weighted gene co-expression network analysis further identified hub genes (ITPKB, BAMBI, and BCKDHB) associated with total feeding bouts (TFB). These findings provide new insights into the genetic architecture of feeding behavior traits and the molecular differences associated with divergent feeding patterns in ducks.

The complex and diverse ecological environment of southwestern China has exerted significant influences on the domestication and genetic adaptation of local duck breeds. Although ducks exhibit extensive genetic variation in heterogeneous environments, the genomic mechanisms underlying their adaptation to the complex topography and high-altitude conditions of southwestern China remain unclear. To elucidate the evolutionary processes of genetic differentiation and environmental adaptation in regional duck populations, this study analyzed the genetic diversity, population structure, and selection characteristics based on the whole-genome resequencing data from a total of 500 individuals, encompassing 7 local duck breeds from the southwest region, 2 wild duck breeds, and 6 duck breeds from other regional. Analysis of nucleotide diversity (π) revealed that 2 wild duck breeds exhibited the highest genetic diversity (π = 0.0047-0.0052), Jianchang duck (JC) has the lowest (π = 0.0026). Among domestic breeds, those from plains areas-Sichuan Shelduck (SC), Hanzhong duck (HZ), Kaijiang duck (KJ), and Jianshui yellow-brown duck (JS) (π = 0.00360-0.00377)-showed significantly higher genetic diversity than those from topographically complex regions-Yunnan Sheldrake (YN), Sansui duck (SS), and Jianchang duck (π = 0.00259-0.00311). Populations from complex terrain (JC, YN, and SS) also displayed a high abundance of long runs of homozygosity (ROH). Analysis of the fixation index (Fst) demonstrated low genetic differentiation among YN, SS, and JC, as well as among SC, HZ, and KJ. Genomic scans comparing zFst and the log2(π ratio) identified regions in the top 5% as candidate regions, revealing 20 domestication-related genes, which are functionally associated with nervous system remodeling, angiogenesis, cell adhesion, mitochondrial metabolism, growth and reproduction; 15 regional adaptation-related genes, primarily involved in cell signal transduction, protein synthesis, hormone production, gene expression and DNA damage repair; and 15 candidate genes related to adaptation to the complex high-altitude terrain, participating in nervous system development, immune adaptation, synaptic transmission, sensory systems, cytoskeletal remodeling, and endocrine functions. Collectively, these findings enhance our understanding of evolutionary processes in southwestern Chinese ducks and provide actionable insights for their conservation and breeding programs.

Olfaction is crucial for ducks, influencing essential behaviors such as foraging and mating. However, the molecular basis of sex-associated variation in duck olfactory tissues remains poorly understood. Here, we performed bulk RNA-seq on turbinate tissue from male and female Tianfu Nonghua Mottled Ducks (Anas platyrhynchos domesticus Linnaeus, 1758; Anatidae) to characterize sex-biased transcriptional programs. Our results suggest strong global transcriptomic separation between males and females, with 1906 differentially expressed genes (DEGs) identified. These DEGs were enriched in pathways related to neuronal signaling, cell adhesion, and extracellular matrix organization, suggesting coordinated sex-associated differences in signaling and tissue-organization programs. While olfactory receptor (OR) and trace amine-associated receptor (TAAR) genes showed limited sex-biased expression in bulk tissue, two neuromodulatory GPCRs, TACR2 and DRD4, were prioritized as hub genes within sex-biased co-expression networks. Notably, both genes also showed relatively high expression in turbinate tissue and neuroendocrine centers in an integrated multi-tissue transcriptomic dataset, nominating them as candidate targets for future functional and cell-type-resolved investigations. Overall, our study provides a descriptive molecular profile of sex-biased transcription in duck turbinate tissue, laying a foundation for follow-up studies and potential applications in poultry breeding and management.

The differences fatty acids and amino acids composition may be key factors influencing flavor variation among duck breeds. This study systematically analyzed the fatty acids and amino acids compositions in the pectoral muscle of 49 days old Cherry valley ducks (CV), Jinling white ducks (JL), and Liancheng white ducks (LC). Fatty acid analysis identified 27 fatty acids that exhibited significant differences across breeds (P < 0.05). The CV group had the highest total saturated fatty acid (SFAs) content, while total monounsaturated fatty acid (MUFAs) content ranked in the order of LC > JL > CV (P < 0.05). The total polyunsaturated fatty acids (PUFAs) content was significantly higher in both the JL and LC groups than in the CV group (P < 0.05), while the LC group showed a higher content than the JL group, though the difference was not significant. Amino acid analysis identified 20 amino acids that showed significant differences among breeds (P < 0.05). Furthermore, the total essential amino acids (EAAs) and non-essential amino acids (NEAAs) content ranked in the order of LC > JL > CV (P < 0.05). Whole-genome resequencing identified 2734 selected genes. The joint pathway analysis revealed co-enrichment of 9 fatty acids and 110 selected genes across 25 KEGG pathways, as well as 20 amino acids and 266 selected genes co-enriched in 78 KEGG pathways. RNA sequencing revealed 2539 differentially expressed genes (DEGs) between JL and CV, 6574 DEGs between JL and LC, and 7072 DEGs between LC and CV. Venn analysis showed that 9 and 24 of these DEGs overlapped with selected genes associated with fatty acid and amino acid variation, respectively. Further analysis revealed that the DEGs MGLL, NDUFV1, NDUFS4, and GNG10 may cooperatively regulate retrograde endocannabinoid signaling, thereby jointly influencing the deposition levels of arachidonic acid, γ-Aminobutyric-Acid, and L-glutamate in duck pectoral muscle. These findings provide a theoretical basis for the genetic improvement of meat quality traits.

Feather-related traits in poultry give rise to a vibrant array of visually striking characteristics. Among these, the Yanying chickens, an indigenous breed, displays a variably expressed feathered-leg phenotype. However, the underlying genetic mechanisms remain largely unexplored, making this breed a valuable model for investigation. In present study, we performed Genome-wide association studies (GWAS) based on whole-genome resequencing data (average depth: 10 ×) of 123 chickens, and found a locus on chromosome 13 (chr13: 14.97-15.05 Mb) that is significantly associated with leg feather trait. By gene annotation, we found a coding gene for H2A-histone-family, member-Y (H2AFY), which encodes a histone variant crucial for chromatin architecture and the regulation of developmental genes, was located in this region. We then identified an approximately 18-kb deletion up-stream of H2AFY. Through PCR validation, we confirmed that this structural variation is significantly associated with the feathered-leg trait. The segregation pattern suggests it is a major genetic determinant, though with incomplete penetrance. This study not only deepens our understanding of the genetic mechanisms underlying feather-related traits but also provides a reliable genetic marker, offering a potential target for molecular-assisted selection of external characteristics in chickens.

Duck meat and broth are widely consumed for their distinctive flavors, which are significantly influenced by breed—a critical determinant of consumer preference. Using untargeted metabolomics, this study identified key molecular compounds underlying flavor differences in cooked meat and broth across duck breeds: Cherry Valley Duck (CV), Jinling White Duck (JL), and Liancheng White Duck (LD). The results revealed that JL exhibited intermediate levels of flavor-related metabolites—including cysteine, 4‑butyl‑5-propylthiazole, furaneol A, and several dipeptides—compared to CV and LD, which may contribute to its more balanced and appealing flavor profile. Water boiling induced significant biochemical transformations in the meat, ultimately shaping the characteristic flavor profiles of both the cooked meat and the resulting broth. KEGG pathway enrichment analysis revealed that amino acid metabolism, nucleotide catabolism, fatty acid metabolism, and carbohydrate catabolism were the primary metabolic pathways underlying breed-related flavor differences and flavor evolution during cooking. This study demonstrates that untargeted metabolomics is an effective tool for elucidating the molecular basis of meat flavor formation and transformation, offering valuable insights for future research on poultry flavor profiling and the impact of thermal processing on meat quality.