Embryonic Development Research Articles

Graduate Student Literature Review: Implications of transition cow health for reproductive function and targeted reproductive management.

Negative associations of health disorders with reproductive performance, often measured with pregnancy risk per artificial insemination (AI) or the risk of pregnancy loss, have been demonstrated extensively. Most studies investigated common clinical diseases but did not include subclinical disorders comprehensively. They often evaluated cows subjected to hormonal synchronization protocols for timed AI, limiting the ability to understand how disease may affect spontaneous reproductive function, which is essential for targeted management programs with selective hormonal intervention. It is plausible that metabolic and inflammatory disorders have short- and long-term detrimental effects on different features of reproductive function that result in or contribute to reduced fertility. These may include: 1) reestablishment of endocrine function to promote follicular growth and first ovulation postpartum, 2) corpus luteum (CL) function, 3) estrus expression, and 4) uterine environment, fertilization, and embryonic development. In this narrative literature review, we discuss insights and knowledge gaps linking health disorders with these processes of reproductive function. A growing set of observational studies with adequate internal validity suggest that these outcomes may be affected by metabolic and inflammatory disorders that are common in the early postpartum period. A better characterization of these risk factors in multi-site studies with greater external validity is warranted to develop decision-support tools to identify subgroups of cows that are more or less likely to be successful in targeted reproductive management programs.

Transient chromatin decompaction at the start of D. melanogaster male embryonic germline development.

Embryonic germ cells develop rapidly to establish the foundation for future developmental trajectories, and in this process, they make critical lineage choices including the configuration of their unique identity and a decision on sex. Here, we use single-cell genomics patterns for the entire embryonic germline in Drosophila melanogaster along with the somatic gonadal precursors after embryonic gonad coalescence to investigate molecular mechanisms involved in the setting up and regulation of the germline program. Profiling of the early germline chromatin landscape revealed sex- and stage-specific features. In the male germline immediately after zygotic activation, the chromatin structure underwent a brief remodeling phase during which nucleosome density was lower and deconcentrated from promoter regions. These findings echoed enrichment analysis results of our genomics data in which top candidates were factors with the ability to mediate large-scale chromatin reorganization. Together, they point to the importance of chromatin regulation in the early germline and raise the possibility of a conserved epigenetic reprogramming-like process required for proper initiation of germline development.

A spotlight on the role of copper in the epithelial to mesenchymal transition.

The complex process known as epithelial to mesenchymal transition (EMT) plays a fundamental role in several biological settings, encompassing embryonic development, wound healing, and pathological conditions such as cancer and fibrosis. In recent years, a bulk of research has brought to light the key role of copper, a trace element with essential functions in cellular metabolism, cancer initiation and progression. Indeed, copper, besides functioning as cofactor of enzymes required for essential cellular processes, such as energy production and oxidation reactions, has emerged as an allosteric regulator of kinases whose activity is required to fulfill cancer dissemination through the EMT. In this comprehensive review, we try to describe the intricate relationship between the transition metal copper and EMT, spanning from the earliest foundational studies to the latest advancements. Our aim is to shed light on the multifaceted roles undertaken by copper in EMT in cancer and to unveil the diverse mechanisms by which copper homeostasis exerts its influence over EMT regulators, signaling pathways, cell metabolic reprogramming and transcription factors ultimately contributing to the spread of cancer. Therefore, this review not only may contribute to a deeper comprehension of copper-mediated mechanisms in EMT but also supports the hypothesis that targeting copper may contribute to counteract the progression of EMT-associated pathologies.

Antimony exposure affects oocyte quality and early embryo development via excessive mitochondrial oxidation and dysfunction

Antimony (Sb) is a metalloid, widely presents in the environment and associates with human health. In this study, we aimed to decipher whether Sb exposure is harmful to female reproduction and explore the underlying mechanisms. The ICR mice were exposed to 0, 5, 10, and 20mg/kg acetate potassium Sb tartrate trihydrate by intraperitoneal injection for 10 days, then mouse oocytes were collected for further analysis. We first found a significant decrease in the proportion of MII-stage oocytes obtained from supernumerary ovulation in the fallopian tubes and early embryo development under Sb treatment. Then a series of tests showed Sb affects oocyte maturation by damaging the cytoskeleton of microtubule and actin. Moreover, the abnormal distribution of cortical granules and their component Ovastacin in oocytes, combined with reduced expression levels of Juno, affected sperm-oocyte binding and led to fertilization failure. Based on the sequencing results and experimental validation, it was demonstrated that Sb exposure impairs mitochondrial distribution and membrane potential, elevated levels of mitochondrial superoxide, finally caused energy supply deficits. Mitochondrial damage in oocytes after Sb exposure results in the excessive oxidative stress and early apoptosis. Taken together, these data suggest that Sb exposure decreases oocyte quality and female fertilization ability by impairing mitochondrial function and redox perturbation.

Reproductive Structures of Female Phytoseiulus persimilis (Acari: Phytoseiidae) and the Development of Egg and Embryo in the Body

Reproductive Structures of Female Phytoseiulus persimilis (Acari: Phytoseiidae) and the Development of Egg and Embryo in the Body

Embryonic development grand challenge: crosslinking advances

Research on embryonic development is entering into a new era. As a traditionally descriptive discipline within anatomy, embryologists have formed international consortia and digitized important histological collections for preservation and open access. Embryonic development has recently received a wider attention in context with temporo-spatial transcriptomics at single cell level. These can be expected to fuel the realization of the transdisciplinary significance of efforts to decipher embryonic development. Addressing its complexities encompasses a wealth of challenges that intersect across the domains of science, society, and politics underlining its outstanding importance as well as its inherently interdisciplinary nature. The challenges of this field are by no means confined to understanding the intricate biological mechanisms but also have humanitarian implications. To fully appreciate the mechanisms underlying human development, principles of embryogenesis have predominantly been analyzed employing animal models which allow us to broaden our view on developmental processes. As a result of recent pioneering work and technical progress centered around stem cell-based 3D approaches, we are entering into a historical new phase of learning about mammalian embryonic development. In vertebrates, a growing concern now focuses the reduction of animal experimentation. This perspective article outlines the major challenges in this amazing field that offer an enormous potential for basic biomedical sciences as well as related translational approaches if they are tackled in a multidisciplinary discourse.

Stage‐by‐stage exploration of normal embryonic development in the Arabian killifish, Aphanius dispar

AbstractBackgroundArabian killifish, Aphanius dispar, lives in marine coastal areas of the Middle East, as well as in streams that experience a wide range of salinities and temperatures. It has been used as a mosquito control agent and for studying the toxicities of environmental pollutants. A. dispar's eggshell (chorion) and embryos are highly transparent and are suitable for high resolution microscopic observations, offering excellent visibility of live tissues.ResultsIn this study, the staging of normal embryonic development of A. dispar was described and investigated at different temperatures. Embryonic development was then examined under different thermal environments from 26 to 34°C. Our data suggest that temperature has a significant effect on embryonic development, with accelerated development at higher temperatures.ConclusionA. dispar exhibits broad thermal tolerance and extended independent feeding capabilities, making it a promising model organism for toxicology and pathogenesis studies conducted over an extended period of time (12 days post‐fertilization).

Immobilization secondary to cell death of muscle precursors with a dual transcriptional signature contributes to the emu wing skeletal pattern

Limb reduction has occurred multiple times in tetrapod history. Among ratites, wing reductions range from mild vestigialization to complete loss, with emus (Dromaius novaehollandiae) serving as a model for studying the genetic mechanisms behind limb reduction. Here, we explore the developmental mechanisms underlying wing reduction in emu. Our analyses reveal that immobilization resulting from the absence of distal muscles contributes to skeletal shortening, fusion and left-right intraindividual variation. Expression analysis and single cell-RNA sequencing identify muscle progenitors displaying a dual lateral plate mesodermal and myogenic signature. These cells aggregate at the proximal region of wing buds and undergo cell death. We propose that this cell death, linked to the lack of distal muscle masses, underlines the morphological features and variability in skeletal elements due to reduced mechanical loading. Our results demonstrate that differential mobility during embryonic development may drive morphological diversification in vestigial structures.

Role of hedgehog signaling in the pathogenesis and therapy of heterotopic ossification

Heterotopic ossification (HO) is a pathological process that generates ectopic bone in soft tissues. Hedgehog signaling (Hh signaling) is a signaling pathway that plays an important role in embryonic development and involves three ligands: sonic hedgehog (Shh), Indian hedgehog (Ihh) and desert hedgehog (Dhh). Hh signaling also has an important role in skeletal development. This paper discusses the effects of Hh signaling on the process of HO formation and describes several signaling molecules that are involved in Hh-mediated processes: parathyroid Hormone-Related Protein (PTHrP) and Fkbp10 mediate the expression of Hh during chondrogenesic differentiation. Extracellular signal-regulated kinase (ERK), GNAs and Yes-Associated Protein (YAP) interact with Hh signaling to play a role in osteogenic differentiation. Runt-Related Transcription Factor 2 (Runx2), Mohawk gene (Mkx) and bone morphogenetic protein (BMP) mediate Hh signaling during both chondrogenic and osteogenic differentiation. This paper also discusses possible therapeutic options for HO, lists several Hh inhibitors and explores whether they could serve as emerging targets for the treatment of HO.

Effects of different temperatures on the embryonic development of the Lebranche mullet Mugil liza.

We herein investigated the influence of temperature on theembryonic development (from fertilisation to hatching) of Mugil liza larvae. For this purpose, oocytes (>600 μm) and sperm were obtained from breeding stock at the laboratory of marine fish culture (LAPMAR). After fertilisation, 1200 eggs were distributed in 12 cylindrical experimental units of 400 mL under four different temperatures 18, 22, 26 and 30 ºC, all in triplicate. Every 15 min until hatching, about 10 eggs were randomly sampled in each treatment. The eggs were visualized and photographed, and the classification of embryonic stages was performed. Temperature influenced the main events of the embryonic development of M. liza. More accelerated development was observed according to the increase in temperature until the gastrula phase. At temperatures of 22 and 26 °C, embryonic development occurred from fertilisation to hatching of the larvae. In the 18 °C treatment, it was verified that most of the embryos ceased development during the final phase of cleavage and the beginning of blastula formation, while in the 30 °C treatment patterns of embryo malformation were also verified, with erratic divisions of the blastomeres, resulting in irregular cells. Unlike what was observed at a temperature of 18 °C, none of the embryos incubated at 30 °C reached the blastopore closure phase, stopping in the gastrula. The larvae hatched in the treatments at 22 and 26 °C were viable and exhibited intense swimming, with a large amount of reserve material (yolk) and an evident drop of oil.

Transcriptome analysis of the effects of high temperature on zygotic genome activation in porcine embryos

Damage to the development of porcine gametes and embryos caused by high temperatures (HT) is one of the main reasons for the decline in the economic benefits of the livestock industry. Zygotic genome activation (ZGA) marks the beginning of gene expression programs in mammalian pre-implantation embryos. In pigs, ZGA occurs at the 4-cell (4 C) stage, indicating that correct gene expression at this stage plays an important regulatory role in embryonic development. However, the effect of the HT environment on early porcine embryonic development and the RNA expression profile of ZGA remain unclear. In this study, we compared the RNA transcription patterns of porcine 4 C embryos under normal and HT conditions using RNA-seq and identified 326 differentially expressed genes (DEGs). These changes were mainly related to DNA polymerase activity, DNA replication, and nucleotidyltransferase activity. In addition, entries for reverse transcription and endonuclease activity were enriched, indicating that ZGA interfered under HT conditions. Further comparison of the experimental results with the porcine ZGA gene revealed 39 ZGA genes among the DEGs. KEGG and GSEA analysis showed that the oxidative phosphorylation pathway was significantly enriched and signaling pathways related to energy metabolism were significantly downregulated. We also found that NDUFA6 and CDKN1A were located at the center of the protein-protein interaction network diagram of the DEGs. In summary, HT conditions affect mitochondrial function and oxidative phosphorylation levels, and lead to changes in the expression pattern of ZGA in early porcine embryos, with its hub genes NDUFA6 and CDKN1A.

Two-way Dispatched function in Sonic hedgehog shedding and transfer to high-density lipoproteins

The Sonic hedgehog (Shh) signaling pathway controls embryonic development and tissue homeostasis after birth. This requires regulated solubilization of dual-lipidated, firmly plasma membrane-associated Shh precursors from producing cells. Although it is firmly established that the resistance-nodulation-division transporter Dispatched (Disp) drives this process, it is less clear how lipidated Shh solubilization from the plasma membrane is achieved. We have previously shown that Disp promotes proteolytic solubilization of Shh from its lipidated terminal peptide anchors. This process, termed shedding, converts tightly membrane-associated hydrophobic Shh precursors into delipidated soluble proteins. We show here that Disp-mediated Shh shedding is modulated by a serum factor that we identify as high-density lipoprotein (HDL). In addition to serving as a soluble sink for free membrane cholesterol, HDLs also accept the cholesterol-modified Shh peptide from Disp. The cholesteroylated Shh peptide is necessary and sufficient for Disp-mediated transfer because artificially cholesteroylated mCherry associates with HDL in a Disp-dependent manner, whereas an N-palmitoylated Shh variant lacking C-cholesterol does not. Disp-mediated Shh transfer to HDL is completed by proteolytic processing of the palmitoylated N-terminal membrane anchor. In contrast to dual-processed soluble Shh with moderate bioactivity, HDL-associated N-processed Shh is highly bioactive. We propose that the purpose of generating different soluble forms of Shh from the dual-lipidated precursor is to tune cellular responses in a tissue-type and time-specific manner.

Two-way Dispatched function in Sonic hedgehog shedding and transfer to high-density lipoproteins

The Sonic hedgehog (Shh) signaling pathway controls embryonic development and tissue homeostasis after birth. This requires regulated solubilization of dual-lipidated, firmly plasma membrane-associated Shh precursors from producing cells. Although it is firmly established that the resistance-nodulation-division transporter Dispatched (Disp) drives this process, it is less clear how lipidated Shh solubilization from the plasma membrane is achieved. We have previously shown that Disp promotes proteolytic solubilization of Shh from its lipidated terminal peptide anchors. This process, termed shedding, converts tightly membrane-associated hydrophobic Shh precursors into delipidated soluble proteins. We show here that Disp-mediated Shh shedding is modulated by a serum factor that we identify as high-density lipoprotein (HDL). In addition to serving as a soluble sink for free membrane cholesterol, HDLs also accept the cholesterol-modified Shh peptide from Disp. The cholesteroylated Shh peptide is necessary and sufficient for Disp-mediated transfer because artificially cholesteroylated mCherry associates with HDL in a Disp-dependent manner, whereas an N-palmitoylated Shh variant lacking C-cholesterol does not. Disp-mediated Shh transfer to HDL is completed by proteolytic processing of the palmitoylated N-terminal membrane anchor. In contrast to dual-processed soluble Shh with moderate bioactivity, HDL-associated N-processed Shh is highly bioactive. We propose that the purpose of generating different soluble forms of Shh from the dual-lipidated precursor is to tune cellular responses in a tissue-type and time-specific manner.

The correlation between embryo rescue and hormonal changes in seedless grapes

After normal pollination and fertilization of pseudoparthenocarpic seedless grapes, their embryos often stop developing due to certain developmental factors, resulting in embryo abortion. Hybrid breeding using seedless grapes as the maternal parent requires embryo rescue breeding technology. This technology plays a crucial role in seedless grape breeding. Although previous studies have extensively explored this technology, knowledge regarding its impact on embryo abortion and the effectiveness of rescue techniques remains limited. This study aimed to investigate the correlation between embryo rescue and hormonal changes in seedless grapes. Four Eurasian seedless grape cultivars, “Thompson Seedless,” “Flame Seedless,” “Heshi Seedless,” and “Ruby Seedless,” were selected for examination. We investigated endogenous hormone levels, including indole-3-acetic acid (IAA), gibberellic acid (GA3), and abscisic acid (ABA), in both berries and in vitro ovules during the most suitable embryo rescue time for these cultivars. Based on the observed fluctuations in endogenous hormone levels and previous research findings, appropriate doses of exogenous hormones, such as IAA, GA3, and ABA, were applied during seedless grape embryo rescue. The results indicated significant differences in endogenous hormone levels between berries with varying ovule counts of the same cultivar and ovules cultured in vitro, suggesting a hormonal influence on ovule abortion and embryo development in seedless grapes. Further research has identified effective ratios of exogenous hormones: 30 mg·L–1 IAA + 30 mg·L–1 ABA for berry ovule development, 1.0 mg·L–1 IAA + 2.0 mg·L–1 6-benzylaminopurine (6-BA) + 1.0 mg·L–1 GA3 + 1.0 mg·L-1 ABA for in vitro ovule development, and 1.0 mg·L–1 IAA + 2.0 mg·L–1 6-BA + 1.0 mg·L–1 GA3 for embryo germination and seedling formation. In summary, hormonal changes significantly influence ovule and embryo development and are closely related to seedless grape embryo rescue breeding. This study deepened our understanding of the correlation between seedless grape embryo rescue and hormonal changes. It also resulted in the successful production of a batch of embryo rescue seedlings, further improving embryo rescue breeding technology and providing new germplasm materials for developing new seedless grape cultivars.

Effect of temperature on the embryonic and larvae development of discus fish Symphysodon aequifasciatus and time of first feeding.

This study aimed to analyze the influence of different temperatures on the embryonic and larval development of discus fish Symphysodon aequifasciatus and determine the time required for the beginning of exogenous feeding. Eggs and larvae were obtained from natural spawns and distributed in five treatments: 24.0, 26.0, 28.0, 30.0, and 32.0°C. To assess the developmental stages and embryonic structures, samples were taken at regular intervals and checked under an optical microscope. At the end of the experimental period, statistical analysis was performed, followed by Tukey's test. As a result, it was possible to observe the significant effects of temperature on the variables. It was noted that the temperature accelerated the embryonic and larval development of the discus and also contributed to a reduction in the time between the incubation period and the feeding transition. It was also noted that the incubation of eggs and larvae at a temperature of 24.0°C can cause damage to embryos, such as malformation of the body as well as anomalies in the circulatory system.

Extracellular vesicles affecting embryo development in vitro: a potential culture medium supplement

Extracellular vesicles (EVs) are nanometer-sized lipid bilayer vesicles released by cells, playing a crucial role in mediating cellular communication. This review evaluates the effect of EVs on early embryonic development in vitro by systematically searching the literature across three databases, Embase, PubMed, and Scopus, from inception (Embase, 1947; PubMed, 1996; and Scopus, 2004) to 30 June 2024. A total of 28 studies were considered relevant and included in this review. The EVs included in these investigations have been recovered from a range of sources, including oviduct fluid, follicular fluid, uterine fluid, seminal plasma, embryos, oviduct epithelial cells, endometrial epithelial cells, amniotic cells, and endometrial-derived mesenchymal stem cells collected primarily from mice, rabbits, cattle and pigs. This diversity in EV sources highlights the broad interest and potential applications of EVs in embryo culture systems. These studies have demonstrated that supplementation with EVs derived from physiologically normal biofluids and cells to the embryo culture medium system has positive effects on embryonic development. Conversely, EVs derived from cells under pathological conditions have shown a negative impact. This finding underscores the importance of the source and condition of EVs used in culture media. Further, the addition of EVs as a culture medium supplement holds significant therapeutic potential for optimizing in vitro embryo culture systems. In conclusion, this evaluation offers a thorough assessment of the available data on the role of EVs in embryo culture media and highlights the potential and challenges of using EVs in vitro embryo production.

OVO positively regulates essential maternal pathways by binding near the transcriptional start sites in the Drosophila female germline

Differentiation of female germline stem cells into a mature oocyte includes the expression of RNAs and proteins that drive early embryonic development in Drosophila. We have little insight into what activates the expression of these maternal factors. One candidate is the zinc-finger protein OVO. OVO is required for female germline viability and has been shown to positively regulate its own expression, as well as a downstream target, ovarian tumor, by binding to the transcriptional start site (TSS). To find additional OVO targets in the female germline and further elucidate OVO’s role in oocyte development, we performed ChIP-seq to determine genome-wide OVO occupancy, as well as RNA-seq comparing hypomorphic and wild type rescue ovo alleles. OVO preferentially binds in close proximity to target TSSs genome-wide, is associated with open chromatin, transcriptionally active histone marks, and OVO-dependent expression. Motif enrichment analysis on OVO ChIP peaks identified a 5’-TAACNGT-3’ OVO DNA binding motif spatially enriched near TSSs. However, the OVO DNA binding motif does not exhibit precise motif spacing relative to the TSS characteristic of RNA polymerase II complex binding core promoter elements. Integrated genomics analysis showed that 525 genes that are bound and increase in expression downstream of OVO are known to be essential maternally expressed genes. These include genes involved in anterior/posterior/germ plasm specification (bcd, exu, swa, osk, nos, aub, pgc, gcl), egg activation (png, plu, gnu, wisp, C(3)g, mtrm), translational regulation (cup, orb, bru1, me31B), and vitelline membrane formation (fs(1)N, fs(1)M3, clos). This suggests that OVO is a master transcriptional regulator of oocyte development and is responsible for the expression of structural components of the egg as well as maternally provided RNAs that are required for early embryonic development.

Temporal BMP4 effects on mouse embryonic and extraembryonic development.

The developing placenta, which in mice originates through the extraembryonic ectoderm (ExE), is essential for mammalian embryonic development. Yet unbiased characterization of the differentiation dynamicsof the ExE and its interactions with the embryo proper remains incomplete. Here we develop a temporal single-cell model of mouse gastrulation that maps continuous and parallel differentiation in embryonic and extraembryonic lineages. This is matched with a three-way perturbation approach to target signalling from the embryo proper, the ExE alone, or both. We show that ExE specification involves early spatial and transcriptional bifurcation of uncommitted ectoplacental cone cells and chorion progenitors. Early BMP4 signalling from chorion progenitors is required for proper differentiation of uncommitted ectoplacental cone cells and later for their specification towards trophoblast giant cells. We also find biphasic regulation by BMP4 in the embryo. The early ExE-originating BMP4 signal is necessary for proper mesoendoderm bifurcation and forallantois and primordial germ cell specification. However, commencing at embryonic day 7.5, embryo-derived BMP4 restricts the primordial germ cell pool size by favouring differentiation of their extraembryonic mesoderm precursors towards an allantois fate. ExE and embryonic tissues are therefore entangled in time, space and signalling axes, highlighting the importance of their integrated understanding and modelling in vivo and in vitro.

The efficacy of orally administered L-carnitine in alleviating ovarian dysfunctions has laid the foundation for targeted in vivo use: a study employing self-control and propensity score matching

ObjectiveThis study aimed to evaluate the effectiveness of oral L-carnitine administration in patients after treatment failure to lay the groundwork for targeted in vivo use.Methods and materialsA total of 515 In Vitro Fertilization (IVF) patients undergoing subsequent cycles were included after applying exclusion criteria. They were divided into a control group of 362 patients and a study group of 153 patients who received oral L-carnitine until oocyte retrieval.140 patients were matched according to maternal age, infertility duration, body mass index (BMI), day three top-quality embryos rate, by propensity score matching (PSM). The study investigated the relationship between L-carnitine treatment and in vivo oocyte maturation, normal fertilization, and subsequent embryo development.ResultsFollowing PSM, initial differences in BMI and Day3 top-quality embryo rate between groups were nullified, we created two comparable cohorts with highly similar characteristics. In the subsequent cycles, the study group showed significant improvements in in vivo oocyte maturation rate at retrieval (p=0.002), normal in vitro fertilization rate (p=0.003), blastocyst formation rate (p=0.003), and usable blastocyst rate compared to controls. Although there was no significant difference in the top-quality embryo rate on Day 3, the study group showed a 10% increase in the upper quartile (55.35% vs. 66.67%). The cumulative clinical pregnancy and live birth rates showed a significant improvement (59.82% vs. 68.42%,p=0.004, 47.41% vs. 59.80%, p=0.002). Furthermore, self-control analysis revealed substantial enhancements (p<0.001) in all outcome measures following L-carnitine administration, resulting in the birth of 74 healthy neonates without congenital anomalies.ConclusionWe theorized that daily oral intake of L-carnitine before oocyte retrieval could boost oocyte quality and embryonic development, thus improving IVF outcomes. Ongoing investigations hold the potential to offer valuable insights into the applications and mechanisms underlying the therapeutic effectiveness of L-carnitine.

Dynamic Transcriptome Profile Analysis of Mechanisms Related to Melanin Deposition in Chicken Muscle Development

The pectoral muscle is an important component of skeletal muscle. The blackness of pectoral muscles can directly affect the economic value of black-boned chickens. Although the genes associated with melanogenesis in mammals and birds have been thoroughly investigated, only little is known about the key genes involved in muscle hyperpigmentation during embryonic development. Here, we analyzed melanin deposition patterns in the pectoral muscle of Yugan black-boned chickens and compared differentially expressed genes (DEGs) between the muscles of Wenchang (non-black-boned chickens) and Yugan black-boned chickens on embryonic days 9, 13, 17, and 21. Melanin pigments were found to gradually accumulate in the muscle fibers over time. Using RNA-seq, there were 40, 97, 169, and 94 genes were identified as DEGs, respectively, between Yugan black-boned chicken muscles and Wenchang chickens at embryonic day 9, 13, 17, and 21 stages (fold change ≥2.0, false discovery rate (FDR) < 0.05). Thirteen DEGs, such as MSTRG.720, EDNRB2, TYRP1, and DCT, were commonly identified among the time points observed. These DEGs were mainly involved in pigmentation, melanin biosynthetic and metabolic processes, and secondary metabolite biosynthetic processes. Pathway analysis of the DEGs revealed that they were mainly associated with melanogenesis and tyrosine metabolism. Moreover, weighted gene co-expression network analysis (WGCNA) was used to detect core modules and central genes related to melanogenesis in the muscles of black-boned chickens. A total of 24 modules were identified. Correlation analysis indicated that one of them (the orange module) was positively correlated with muscle pigmentation traits (r > 0.8 and p < 0.001). Correlations between gene expression and L* values of the breast muscle were investigated in Yugan and Taihe black-boned chickens after hatching. The results confirmed that EDNRB2, GPNMB, TRPM1, TYR, and DCT expression levels were significantly associated with L* values (p < 0.01) in black-boned chickens (p < 0.05). Our results suggest that EDNRB2, GPNMB, TRPM1, TYR, and DCT are the essential genes regulating melanin deposition in the breast muscle of black-boned chickens. MSTRG.720 is a potential candidate gene involved in melanin deposition in the breast muscles of Yugan black-boned chickens.