Background: Duration of fertility (DF) is an important economic trait in poultry production because it has a strong effect on chick output. Various criteria or traits to assess DF on individual hens have been reported but they are affected by many nongenetic factors. Thus, a reliable definition and associated genetic parameters are needed. Because egg production is also vital in chicken breeding, knowledge of the relationship between DF and laying performance is needed for designing selection programs. Methods: We used five traits that consider both fertility and embryonic livability to delineate DF. Phenotypic and genetic analyses were completed for 2094 hens, with measurements of DF at 35 and 60 weeks of age and hatching egg production at 400 days of age (HEP400). The selection differentials for DF and HEP400 were evaluated. Results: DF is largely independent of the number of oviposited eggs in the peak laying period but both egg production and DF naturally decline with age. The heritability of the five DF traits ranged from 0.11 to 0.13 at 35 weeks of age and increased slightly in the later laying period, ranging from 0.14 to 0.17 (except for efficient duration, time between insemination and the first unhatched egg). Estimates of the genetic correlation for a given trait measured at the two ages were moderate (0.37–0.44), except for efficient duration. However, number of viable embryos depends strongly on egg production. Estimates of genetic correlations of fertility duration day (FDD) at both ages with HEP were weak. Selection for FDD improved DF but without a significant change in laying performance. Selection for increased HEP400 did not contribute to DF improvement. Conclusions: Although estimates of heritability of the five traits related to DF were low, selection to improve DF based on any one of them is possible. Among these, FDD is an effective selection criterion when the eggs are collected for approximately two weeks after insemination. The best selection procedure for DF improvement would involve multiple measurements at various ages. FDD is independent of laying performance and can be incorporated into a breeding program with egg production to improve reproductive efficiency.

Heat-stress resilience is vital for poultry in tropical/subtropical regions where high temperatures impair productivity. Ake chickens, as the only naked-neck chicken breed in China, exhibit robust resistance to heat stress, but this breed lacks clarity in its genetic origins. This study utilized the next-generation sequencing data from 22 chicken breeds to conduct phylogenetic and population analyses. Gene flow analysis revealed a gene migration event from Iranian naked-neck chickens and Indian local breeds to Ake chickens, and population separation estimates suggested that the naked-neck gene was introduced to China around 500–600 years ago. NJ-tree, PCA, and population structure analyses showed that Ake chickens cluster with Yunnan native breeds, which diverged only 100–200 years ago. A selective sweep in the candidate region on chromosome 3 (97.0–97.37 Mb) showed elevated genetic differentiation (F_ST) and reduced nucleotide diversity (π) compared to the genome-wide average, indicating rapid fixation of the trait under natural/artificial selection. Demographic reconstruction indicated that the current effective size of Ake chickens is stable at 2000–3000 individuals. These findings deepen our understanding of Ake chicken evolution and provide valuable insights for conservation and the development of heat-stress-resistant poultry breeds.

Fat deposition in laying hens involves lipid synthesis, transport, storage, and allocation across multiple tissues, yet the metabolic links between abdominal fat (AF) and egg yolk (EY) lipid deposition remain unclear. Here, we integrated whole-genome resequencing data with untargeted metabolomic profiles from the liver, duodenum, ileum, cecum, and serum of 248 purebred Rhode Island Red hens at 100 weeks of age. We estimated metabolite-explained variance (me²) for 22 fat deposition-related traits, evaluated metabolite heritability, and combined Spearman correlation analysis with bidirectional generalized summary-data-based Mendelian randomization (GSMR) to identify shared metabolites and pathways associated with AF and EY traits. The me² showed clear tissue specificity, with the liver, serum, and duodenum showing significant explanatory signals for 77.3% (17/22), 72.7% (16/22), and 68.2% (15/22) of fat-related traits. Liver-, AF-, and body weight-related traits showed stronger metabolomic explanatory signals, with significant proportions of 71.4–100.0%, 28.6–100.0%, and 100.0% across tissues, respectively, whereas EY-related traits showed more restricted and tissue-specific associations (0–33.3%). Correlation analysis identified liver-enriched AF–EY shared metabolites (e.g., NADPH, cholesteryl sulfate, N6,N6,N6-trimethyllysine), most of which showed opposite association patterns between AF- and EY-related traits. Bidirectional GSMR prioritized 20 candidate metabolites with opposite putative effects on AF and EY traits, including CDP-choline, phosphorylcholine, and allantoin. Pathway integration highlighted fructose/mannose metabolism, glycerophospholipid metabolism, ABC transporters, folate/one-carbon metabolism, amino acid metabolism, and energy metabolism as core components of the AF–EY shared network. These findings reveal tissue-specific and shared metabolic bases of fat deposition and identify candidate metabolic signatures associated with lipid partitioning between abdominal fat and egg yolk in laying hens.