BMC Genomics最新文献

{"title":"Identification of lncRNAs involved in the hair follicle cycle transition of cashmere goats in response to photoperiod change.","authors":"Min Yang, Yingying Li, Qianqian Liang, Huajiao Dong, Yuehui Ma, Göran Andersson, Erik Bongcam-Rudloff, Hafiz Ishfaq Ahmad, Xuefeng Fu, Jilong Han","doi":"10.1186/s12864-025-11675-x","DOIUrl":"10.1186/s12864-025-11675-x","url":null,"abstract":"<p><strong>Background: </strong>Cashmere goats, as one of the important domesticated animal species, are known for their high-quality fiber. The growth of cashmere has seasonal variations caused by photoperiodic changes, but the molecular genetic mechanisms underlying this phenotype including the functional role of long non-coding RNAs (lncRNA) is still poorly understood.</p><p><strong>Results: </strong>In this study, we analyzed the RNA-seq dataset of 39 Cashmere goat skin samples including all different growth stages and identified 1591 lncRNAs. These lncRNAs exhibited growth stage-specific expression patterns. Combining shortened light and hair follicle growth cycles, we found that 68% of differentially photo-responsive lncRNAs showed similar expression trends during transition phase I (early anagen to anagen phase). This suggests that the mechanism of light-controlled induction of hair follicles from early anagen to anagen is similar to that of transition phase I. According to weighted gene co-expression network analyses (WGCNA) analysis, it was found that two gene clusters and 10 hub lncRNAs participated in the transformation of hair follicle cycle, inducing hair follicles to enter the full growth phase in advance. These hub lncRNAs may regulate the development cycle of hair follicles through cis- or trans-regulation on clock genes, SLC superfamily genes, fibroblast growth factor genes.</p><p><strong>Conclusions: </strong>This study identified the key lncRNAs and target genes probably participating in the transformation of hair follicle cycle. This study will help further elucidate the role of lncRNAs in the hair follicle cycle and development.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"487"},"PeriodicalIF":3.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12080124/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs.","authors":"Hongwei Yin, Qianyi Zhao, Liu Yang, Guoqiang Yi, Wenye Yao, Lingzhao Fang, Lijing Bai","doi":"10.1186/s12864-025-11490-4","DOIUrl":"10.1186/s12864-025-11490-4","url":null,"abstract":"<p><strong>Background: </strong>Topologically associating domains (TADs) are functional units that organize chromosomes into 3D structures of interacting chromatin, and play a crucial role in regulating gene expression by constraining enhancer-promoter contacts. Evidence suggests that deletion of TAD boundaries can lead to aberrant expression of neighboring genes. In our study, we analyzed high-throughput chromatin conformation capture (Hi-C) datasets from publicly available sources, integrating 71 datasets across five tissues in six pig breeds.</p><p><strong>Results: </strong>Our comprehensive analysis revealed 65,843 TADs in pigs, and we found that TAD boundaries are enriched for expression Quantitative Trait Loci (eQTL), splicing Quantitative Trait Loci (sQTL), Loss-of-Function variants (LoFs), and other regulatory variants. Genes within conserved TADs are associated with fundamental biological functions, while those in dynamic TADs may have tissue-specific roles. Specifically, we observed differential expression of the NCOA2 gene within dynamic TADs. This gene is highly expressed in adipose tissue, where it plays a crucial role in regulating lipid metabolism and maintaining energy homeostasis. Additionally, differential expression of the BMPER gene within dynamic TADs is associated with its role in modulating the activities of bone morphogenetic proteins (BMPs)-critical growth factors involved in bone and cartilage development.</p><p><strong>Conclusion: </strong>Our investigations have shed light on the pivotal roles of TADs in governing gene expression and even influencing traits. Our study has unveiled a holistic interplay between chromatin interactions and gene regulation across various tissues and pig breeds. Furthermore, we anticipate that incorporating markers, such as structural variants (SVs), and phenotypes will enhance our understanding of their intricate interactions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"484"},"PeriodicalIF":3.5,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079826/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Negative effect of seasonal heat stress on testis morphology and transcriptomes in Angora rabbit.","authors":"Haisheng Ding, Yuanlang Wang, Huiling Zhao, Jinzi Wang, Dongwei Huang","doi":"10.1186/s12864-025-11659-x","DOIUrl":"https://doi.org/10.1186/s12864-025-11659-x","url":null,"abstract":"<p><strong>Background: </strong>The temperature of testes exposed to hyperthermic conditions can affect livestock reproductive performance. This study aimed to explore the difference in semen quality, testicular morphological structure, and gene expression profiles of testes of Angora rabbits in spring (no heat stress), summer (intense heat stress), and autumn (no heat stress) seasons.</p><p><strong>Results: </strong>Heat stress during summer significantly reduced semen quality and damaged testicular morphology and spermatogenesis, which recovered to normal levels in autumn, although semen quality recovery was notably slow. RNA-Seq analysis showed that the expression levels of 8703 genes changed significantly in summer, but their expression levels in autumn returned to those in spring, which was consistent with the testicular morphology analysis results in different seasons. Enrichment analysis revealed that the DEGs were primarily associated with spermatogenesis, sperm motility, spermatid development, cell death, regulation of apoptotic processes, and responses to external stimuli. The MAPK, Rap1, TNF, Ras, Apoptosis, and Wnt signaling pathways regulated reproduction under heat stress. In addition, minimal variations in testicular morphology and gene expression profiles were observed between autumn and spring. Gene expression pattern analysis showed that genes with high expression in summer mainly participated in the regulation of cell apoptosis, immunity, and response to heat stress, whereas genes with low expression in summer mainly participated in the regulation of spermatogenesis.</p><p><strong>Conclusions: </strong>This study investigated the influence of different seasons on the reproductive performance of male Angora rabbits and provided initial insights into the molecular regulatory mechanisms underlying the testicular response to heat stress during summer.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"478"},"PeriodicalIF":3.5,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12076845/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic structure of yellow lupin (Lupinus luteus): genome organization, evolution, gene family expansion, metabolites and protein synthesis.","authors":"J Eduardo Martinez-Hernandez, Haroldo Salvo-Garrido, Daniela Levicoy, Peter D S Caligari, Annally Rupayán, Tomas Moyano, Makarena Carrasco, Sebastián Hernandez, Grace Armijo-Godoy, Fernando Westermeyer, Giovanni Larama","doi":"10.1186/s12864-025-11678-8","DOIUrl":"https://doi.org/10.1186/s12864-025-11678-8","url":null,"abstract":"<p><p>Yellow lupin (Lupinus luteus) gives valuable high-quality protein and has good sustainability due to its ability in nitrogen fixation and exudation of organic acids, which reduces the need for chemical-based phosphate fertilization in acid soils. However, the crop needs further improvements to contribute in a major way to sustainable agriculture and food security.In this study, we present the first chromosome-level genome assembly of L. luteus. The results provide insights into its genomic organization, evolution, and functional attributes. Using integrated genomic approaches, we unveil the genetic bases governing its adaptive responses to environmental stress, delineating the intricate interplay among alkaloid biosynthesis, mechanisms of pathogen resistance, and secondary metabolite transporters. Our comparative genomic analysis of closely related species highlights recent speciation events within the Lupinus genus, exposing extensive synteny preservation alongside notable structural alterations, particularly chromosome translocations. Remarkable expansions of gene families implicated in terpene metabolism, stress responses, and conglutin proteins were identified, elucidating the genetic basis of L. luteus' superior nutritional profile and defensive capabilities. Additionally, a diverse array of disease resistance-related (R) genes was uncovered, alongside the characterization of pivotal enzymes governing quinolizidine alkaloid biosynthesis, thus shedding light on the molecular mechanisms underlying \"bitterness\" in lupin seeds.This comprehensive genomic analysis serves as a valuable resource to improve this species in terms of resilience, yield, and seed protein levels to contribute to food and feed to face the worldwide challenge of sustainable agriculture and food security.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"477"},"PeriodicalIF":3.5,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12076967/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterizing differences in the muscle transcriptome between cattle with alternative LCORL-NCAPG haplotypes.","authors":"Fernanda Martins Rodrigues, Leif E Majeres, Anna C Dilger, Joshua C McCann, Christopher J Cassady, Dan W Shike, Jonathan E Beever","doi":"10.1186/s12864-025-11665-z","DOIUrl":"https://doi.org/10.1186/s12864-025-11665-z","url":null,"abstract":"<p><strong>Background: </strong>The LCORL-NCAPG locus is a major quantitative trait locus (QTL) on bovine chromosome 6 (BTA6) that influences growth and carcass composition in cattle. To further understand the molecular mechanism responsible for the phenotypic changes associated with this locus, twenty-four Charolais-sired calves were selected for muscle transcriptome analysis based on alternative homozygous LCORL-NCAPG haplotypes (i.e., 12 \"QQ\" and 12 \"qq\", where \"Q\" is a haplotype harboring variation associated with increased growth). At 300 days of age, a biopsy of the longissimus dorsi muscle was collected from each animal for RNA sequencing.</p><p><strong>Results: </strong>Gene expression analysis identified 733 genes as differentially expressed between QQ and qq animals (q-value < 0.05). Notably, LCORL and genes known to be important regulators of growth such as IGF2 were upregulated in QQ individuals, while genes associated with adiposity such as FASN and LEP were downregulated, reflecting the increase in lean growth associated with this locus. Gene set enrichment analysis demonstrated QQ individuals had downregulation of pathways associated with adipogenesis, alongside upregulation of transcripts for cellular machinery essential for protein synthesis and energy metabolism, particularly ribosomal and mitochondrial components.</p><p><strong>Conclusions: </strong>The differences in the muscle transcriptome between QQ and qq animals imply that muscle hypertrophy may be metabolically favored over accumulation of fat in animals with the QQ haplotype. Our findings also suggest this haplotype could be linked to a difference in LCORL expression that potentially influences the downstream transcriptional effects observed, though further research will be needed to confirm the molecular mechanisms underlying the associated changes in phenotype.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"479"},"PeriodicalIF":3.5,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12076881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mapping-based genome size estimation.","authors":"Shakunthala Natarajan, Jessica Gehrke, Boas Pucker","doi":"10.1186/s12864-025-11640-8","DOIUrl":"https://doi.org/10.1186/s12864-025-11640-8","url":null,"abstract":"<p><p>While the size of chromosomes can be measured under a microscope, obtaining the exact size of a genome remains a challenge. Biochemical methods and k-mer distribution-based approaches allow only estimations. An alternative approach to estimate the genome size based on high contiguity assemblies and read mappings is presented here. Analyses of Arabidopsis thaliana and Beta vulgaris data sets are presented to show the impact of different parameters. Oryza sativa, Brachypodium distachyon, Solanum lycopersicum, Vitis vinifera, and Zea mays were also analyzed to demonstrate the broad applicability of this approach. Further, MGSE was also used to analyze Escherichia coli, Saccharomyces cerevisiae, and Caenorhabditis elegans datasets to show its utility beyond plants. Mapping-based Genome Size Estimation (MGSE) and additional scripts are available on GitHub: https://github.com/bpucker/MGSE . MGSE predicts genome sizes based on short reads or long reads requiring a minimal coverage of 5-fold.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"482"},"PeriodicalIF":3.5,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079912/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distribution of runs of homozygosity in Lactuca species and its implications for plant breeding and evolutionary conservation.","authors":"Qianqian Zhang, Wenjun Lv, Defu Liu, Xueying Xie, Ke Yang, You Tang, Johann Solkner","doi":"10.1186/s12864-025-11674-y","DOIUrl":"https://doi.org/10.1186/s12864-025-11674-y","url":null,"abstract":"<p><p>Runs of homozygosity (ROH) have been extensively investigated to uncover the genomic inbred regions that reflect past population and breeding histories. In this study, we have explored the distribution and number of ROH in different Lactuca species including the cultivated lettuce varieties and their wild relatives. Next generation sequencing (NGS) technology provides the unique opportunity to study the genomes with resolution up to per-base-pair and we could compute ROH in the highest accuracy using NGS data. Our study reveals that Lactuca sativa has the longest average ROH length and fewest number of ROHs, while wild species show shorter, more numerous ROHs as expected. We found that these cultivated varieties exhibit relatively stable number of ROH and ROH lengths, with the largest median ROH count observed in Oilseed and the largest average ROH length in Crisphead. There is a significant proportion of medium-length ROHs (100 kb-1 Mb) enriched in L. sativa and L. serriola, with the highest number observed in L. serriola, while L. saligna has more short ROHs (< 10 KB), and the highest number of ROHs in the 10 KB-100 KB range were observed in Butterhead, with Stalk and Oilseed showing fewer and shorter ROHs overall. It suggests that Stalk and Oilseed were still in a process of breeding. The comparison between PLINK computation and our developed in-house algorithm shows that PLINK tends to detect longer ROH, whereas our algorithm adopts a more conservative approach, resulting in fewer and shorter ROH segments detected with higher precision more suitable for NGS data. We further analyze the distribution of ROH hotspots with a higher frequency occurred across cultivated species genomes, which has identified key genes such as DREB2B, NHL12, RPV1, and EIX2, which play crucial roles in plant stress tolerance and immune responses, enhancing adaptability to extreme environments and providing resistance to various diseases. These findings provide fresh scientific insights into lettuce breeding, germplasm conservation, and sustainable production, highlighting the importance of understanding and managing genetic diversity in global agricultural practices.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"481"},"PeriodicalIF":3.5,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12076861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental acclimatization of the relatively high latitude scleractinian coral Pavona decussata: integrative perspectives on seasonal subaerial exposure and temperature fluctuations.","authors":"Man Zhang, Shan Huang, Li Luo, Kefu Yu","doi":"10.1186/s12864-025-11660-4","DOIUrl":"https://doi.org/10.1186/s12864-025-11660-4","url":null,"abstract":"<p><strong>Background: </strong>Coral reefs are being increasingly threatened due to global climate change. However, some coral species have shown strong tolerance despite living in marginal environments. The species Pavona decussata from Weizhou Island in the South China Sea experiences subaerial exposure in summer and winter due to extreme low tides, and their environmental acclimatization to this aerial exposure remains unexplored.</p><p><strong>Results: </strong>Here we aimed to explore the molecular mechanism of P. decussata under season or subaerial exposure background through physiological and multi-omics integrative analyses. Specifically, corals with a history of seasonal air exposure underwent comprehensive changes in energy metabolism and defense mechanisms compared to permanently submerged corals. In summer, corals experiencing subaerial exposure enhanced antioxidant defense by increasing the activities of the enzymes T-SOD and CAT, and the coral-associated bacterial community shifted toward the class Alphaproteobacteria that may have provided corals with resistance to environmental stresses. Moreover, the decrease in the transcript levels of the TCA cycle and the increase in metabolite content of ornithine suggested an alteration in energy metabolic pathways. Corals with an air-exposed background may have enhanced energy reserves in winter, as indicated by a higher content of Chl a and a rebound in coral-associated bacterial community toward the class Gammaproteobacteria. Furthermore, accumulation of the metabolite leukotriene D4 and activation of the TGF-beta signaling pathway suggested higher anti-inflammatory requirements and positive regulation by innate immunity.</p><p><strong>Conclusions: </strong>This study provides insights into the acclimatization of P. decussata to seasonal environmental fluctuations and demonstrates that relatively high-latitude corals possess the plasticity and acclimatory capacity to adapt to marginal environments.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"483"},"PeriodicalIF":3.5,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12080138/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The CNV map construction and ROH analysis of Pinan cattle.","authors":"Xingya Song, Zijing Zhang, Shengyan Xing, Xian Liu, Yuqiao Zhang, Jiamei Wang, Shijie Lyu, Xiangnan Wang, Xingshan Qi, Weidong Ma, Chuzhao Lei, Eryao Wang, Yongzhen Huang","doi":"10.1186/s12864-025-11626-6","DOIUrl":"https://doi.org/10.1186/s12864-025-11626-6","url":null,"abstract":"<p><p>Pinan cattle, as the progeny of crossbreeding improvement between Nanyang cattle and Piedmontese, have attracted attention for their excellent growth performance. In this study, we constructed a copy number variation map by whole genome resequencing of 132 Pinan cattle. In the genome of Pinan cattle, deletion-type copy number variants occupied a higher proportion and only 3.31% of CNVRs overlapped with exonic regions. It showed that Pinan cattle was clearly distinguishable from other breeds and Pinan cattle was closer to Nanyang cattle by population genetic structure analysis based on CNVRs. The degree of inbreeding in the Pinan cattle population was explored by ROH analysis, which showed that the degree of inbreeding in Pinan cattle was lower than that in European beef cattle, suggesting that the risk of inbreeding was low. Candidate genes related to muscle development (CADM3, CNTFR, DOCK3), reproductive traits (SCAPER), embryonic development (RERE) and immune traits (CD84) were identified by V_ST selection analysis, ROH islands and iHS selection analysis, which provided a new scientific basis for the genetic basis of the excellent traits in Pinan cattle.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"480"},"PeriodicalIF":3.5,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12077032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High temporal-resolution transcriptome landscape reveals the biological process and regulatory genes of melanin deposition in breast muscle of Silkie chickens during embryonic development.","authors":"Xinting Yang, Bowen Ma, Qingyu Zhao, Yaxiong Jia, Qingshi Meng, Yuchang Qin, Chaohua Tang, Junmin Zhang","doi":"10.1186/s12864-025-11654-2","DOIUrl":"10.1186/s12864-025-11654-2","url":null,"abstract":"<p><strong>Background: </strong>Abnormal deposition of melanin in skeletal muscle is an interesting phenomenon and the Silkie is the most typical example. Melanin deposition involves multiple steps such as neural crest cell migration, melanocyte differentiation, melanosome assembly and melanin biosynthesis, which have already occurred during the embryonic stage of Silkies. However, there is no comprehensive understanding of the dynamic changes in the biological processes and regulatory mechanism underlying melanin deposition in skeletal muscle during chicken embryonic development.</p><p><strong>Results: </strong>In this study, high-performance liquid chromatography (HPLC) was used to accurately measure the melanin content in breast muscle across 13 embryonic time points. There was no melanin in breast muscle on embryonic day 8 (E08) to E10, a trace amount of melanin on E11 to E16 and a large amount of melanin on E17 to E21. According to melanin content and deposition pattern, the melanin deposition process in breast muscle was further divided into five stages, including E08 to E10, E11 to E14, E15 to E16, E17 to E18, and E19 to E21. High temporal-resolution transcriptome analysis was performed in the breast muscle of Silkies across 13 embryonic time points. The protein-coding genes (PCGs) and transcriptional factors (TFs) significantly specifically expressed at these five stages were identified. Among these stage-specific genes, stage-specific DEGs between Silkies and Wenchang chickens without melanosis were further screened at each stage. During E08 to E10, three stage-specific DEGs and one stage-specific TF act on neural crest cell migration and melanocyte stem cell differentiation. During E17 to E21, nine stage-specific DEGs and one stage-specific TF act on melanosome assembly and melanin biosynthesis. During E19 to E21, one stage-specific DEG enhances melanin biosynthesis. These stage-specific DEGs and TFs all affect the final melanin content of breast muscle.</p><p><strong>Conclusions: </strong>This study reveals the critical stage of melanin deposition in breast muscle during the embryonic development, and identified the biological processes and functional genes at each stage. This study provides novel insights into the biological process and regulatory mechanism of melanin deposition in skeletal muscle and provides a reference for breeding Silkies with high muscle melanin content.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"476"},"PeriodicalIF":3.5,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12070674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143969889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}