The early growth pattern, especially the age of peak growth, of broilers affects the time to market and slaughter weight, which in turn affect the profitability of the poultry industry. However, the underlying mechanisms regulating chicken growth and development have rarely been studied. This study aimed to identify candidate genes involved in chicken growth and investigated the potential regulatory mechanisms of early growth in chicken. RNA sequencing was applied to compare the transcriptomes of chicken muscle tissues at three developmental stages during early growth. In total, 978 differentially expressed genes (DEGs) (fold change ≥ 2; false discovery rate < 0.05) were detected by pairwise comparison. Functional analysis showed that the DEGs are mainly involved in the processes of cell growth, muscle development, and cellular activities (such as junction, migration, assembly, differentiation, and proliferation). Many of the DEGs are well known to be related to chicken growth, such as MYOD1, GH, IGF2BP2, IGFBP3, SMYD1, CEBPB, FGF2, and IGFBP5. KEGG pathway analysis identified that the DEGs were significantly enriched in five pathways (P < 0.1) related to growth and development: extracellular matrix–receptor interaction, focal adhesion, tight junction, insulin signaling pathway, and regulation of the actin cytoskeleton. A total of 42 DEGs assigned to these pathways are potential candidate genes inducing the difference in growth among the three developmental stages, such as MYH10, FGF2, FGF16, FN1, CFL2, MAPK9, IRS1, PHKA1, PHKB, and PHKG1. Thus, our study identified a series of genes and several pathways that may participate in the regulation of early growth in chicken. These results should serve as an important resource revealing the molecular basis of chicken growth and development.

Objective: Inbreeding depression of reproduction is a major concern in the conservation of native chicken genetic resources. Here, based on the successful development of strongly inbred (Sinb) and weakly inbred (Winb) Langshan chickens, we aimed to evaluate inbreeding effects on reproductive traits and identify candidate genes involved in inbreeding depression of reproduction in Langshan chickens.Methods: A two-sample t-test was performed to estimate the differences in phenotypic values of reproductive traits between Sinb and Winb chicken groups. Three healthy chickens with reproductive trait values around the group mean values were selected from each of the groups. Differences in ovarian and hypothalamus transcriptomes between the two groups of chickens were analyzed by RNA sequencing (RNA-Seq).Results: The Sinb chicken group showed an obvious inbreeding depression in reproduction, especially for traits of age at the first egg and egg number at 300 days (p<0.01). Furthermore, 68 and 618 differentially expressed genes (DEGs) were obtained in the hypothalamus and ovary between the two chicken groups, respectively. In the hypothalamus, DEGs were mainly enriched in the pathways related to vitamin metabolism, signal transduction and development of the reproductive system, such as the riboflavin metabolism, Wnt signaling pathway, extracellular matrix-receptor interaction and focal adhesion pathways, including stimulated by retinoic acid 6, serpin family F member 1, secreted frizzled related protein 2, Wnt family member 6, and frizzled class receptor 4 genes. In the ovary, DEGs were significantly enriched in pathways associated with basic metabolism, including amino acid metabolism, oxidative phosphorylation, and glycosaminoglycan degradation. A series of key DEGs involved in folate biosynthesis (gamma-glutamyl hydrolase, guanosine triphosphate cyclohydrolase 1), oocyte meiosis and ovarian function (cytoplasmic polyadenylation element binding protein 1, structural maintenance of chromosomes 1B, and speedy/RINGO cell cycle regulator family member A), spermatogenesis and male fertility (prostaglandin D2 synthase 21 kDa), Mov10 RISC complex RNA helicase like 1, and deuterosome assembly protein 1) were identified, and these may play important roles in inbreeding depression in reproduction.Conclusion: The results improve our understanding of the regulatory mechanisms underlying inbreeding depression in chicken reproduction and provide a theoretical basis for the conservation of species resources.

Intestinal microorganisms are closely related to the health, development, and production performance of animals and can also provide basic information for us to fully understand and explore the germplasm characteristics and traits of local chicken breeds. In this experiment, we used five local Chinese chicken breeds as research materials; metagenomic sequencing technology was used to explore the differences in the composition of intestinal microorganisms in different breeds, and it was found that each local chicken breed had unique unigenes, of which Silkies had the most, with a total of 12,948. GO and KEGG analyses found that the biological processes most enriched by differential functional genes include genetic coding, macromolecular transport, protein synthesis, and molecular functions such as glycoprotein binding, protein hydrolysis, etc. Each breed is enriched with specific pathways, such as Anyi tile-like gray chickens, which are enriched with pathways related to disease resistance, while Gamecocks’ enrichment is related to amino acid metabolism. Random Forest and LEfSe analyses revealed specific species of intestinal microorganisms in the cecum of different breeds, such as Exiguobacterium, which is associated with melanin deposition in Silkies. Therefore, we infer that gut microorganisms are closely related to the formation of chicken breed characteristics, and the results of this experiment can provide a theoretical basis for the discovery of high-quality traits and the improvement of feeding conditions in the future.

Chicken embryos and stem cells require precisely regulated levels of reactive oxygen species (ROS) to maintain self-renewal and pluripotency. However, excessive ROS induces oxidative stress, leading to DNA damage, chromosomal aberrations, loss of mitochondrial membrane potential, and ultimately, abnormal differentiation or cell death. This oxidative imbalance is a significant barrier to successful embryonic development and the in vitro culture of stem cells. Innate antioxidant defense systems exist within chicken and mammalian embryos to scavenge excess ROS, a finding that has prompted the strategic addition of antioxidants to culture media. The present review has two primary foci. Firstly, it seeks to expand the understanding of the antioxidant defense mechanisms of the chicken embryo. Secondly, it explores the role of exogenous antioxidant supplementation in the culture of various stem cell types, including embryonic stem cells (ESCs), primordial germ cells (PGCs), spermatogonial stem cells (SSCs), and induced pluripotent stem cells (iPSCs). Enhancing in vitro stem cell survival and directed differentiation through antioxidant supplementation holds significant promise for advancing fields such as tissue regeneration, organ transplantation, and the development of transgenic chicken models for improved production traits, vaccine development, and recombinant protein production.

The sex-linked barring of chicken feather pattern is a fascinating trait, and it has great application value in chicken breeding by enabling autosexing. In this study, the transcriptome changes in skin follicle tissues from the back (SKs) and crown of the head (SKHs) were explored by RNA-seq in Wenshang Barred chickens during their feather pattern formation. The key genes and signaling pathways regulating sex-linked barring formation in chickens were analyzed. As a result, a total of 2291 and 4496 differentially expressed genes (DEGs) were found in SKs and SKHs, respectively, during barred feather formation. The expression pattern clusters of Profile 6 and Profile 7 were the important and mainstream expression trends of the DEGs. Melanogenesis KEGG pathway and GO terms of melanocyte differentiation, melanosome organization and melanin biosynthetic biological processes were significantly enriched in the DEGs, including the well-known TYR, TYRP1, EDNRB and PMEL genes, clustered in Profile 6 expression pattern. A series of DEGs, including CDKN2A, SFN, CDKN2B and CDK1, were significantly enriched in the cell cycle pathway and were mostly clustered in Profile 7. Protein‒protein interaction (PPI) network analysis revealed TYR, TYRP1, CDKN2A and SFN were the hub genes. It was speculated that CDKN2A may target SFN to regulate the melanocyte cycle arrest, causing the formation of white bands of sex-linked barring. TYR, TYRP1, EDNRB and PMEL genes may play important regulatory roles by melanogenesis pathway in the early growth of black feathers, as well as in the later formation of black stripes. The different expression patterns of SLC45A2, KIT, MC1R, ASIP, DCT and SOX10 in SKs and SKHs may contribute to the different formation processes of barred feather patterns on the head and the back. These results provide new insights into the regulation of sex-linked barred feather patterns in Chinese native chicken and provide a valuable theoretical foundation for future chicken breeding and related efforts.