{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T02:13:17Z","timestamp":1788228797855,"version":"build-2803163510"},"reference-count":196,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T00:00:00Z","timestamp":1788134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Major Science and Technology Projects of Yunnan Province","award":["202502AE090026"],"award-info":[{"award-number":["202502AE090026"]}]},{"name":"Major Science and Technology Projects of Yunnan Province","award":["202202AE090005"],"award-info":[{"award-number":["202202AE090005"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>RNA-omics technologies have expanded poultry transcriptome research beyond tissue-level gene abundance. They now resolve intact transcripts, RNA chemical modifications, cellular origins, and spatial locations. This review centers on a core question: what specific, previously inaccessible RNA information does each RNA-omics technology provide? Based on their primary measurement targets, we categorize these technologies into four groups: bulk transcriptome and small RNA sequencing for analyzing gene expression and regulatory RNA networks; long-read and direct RNA sequencing for resolving transcript isoforms; epitranscriptomic methods for detecting RNA modifications; and single-cell and spatial transcriptomics for identifying the cellular origins and spatial distributions of signals. Methods for resolving RNA structure, RNA\u2013protein interactions, and translation status (e.g., structure probing, CLIP-type mapping, and ribosome profiling) remain in their infancy in poultry, leaving translation and RNA\u2013protein regulation largely unmeasured in tissues such as the oviduct, the lipogenic liver and nucleated erythrocytes. For each category, we discuss its direct measurement targets and primary outputs, the additional information it provides compared to established methods, representative applications in poultry, and its inherent limitations. Building on this framework, we discuss how to select and combine technologies based on specific research questions and summarize their applications in studies of production performance and product quality, reproduction, and health and resilience. Different technologies measure distinct types of RNA features and are not simply interchangeable. Future research must place greater emphasis on matching technologies to scientific questions, integrating complementary data, and improving three foundations: the annotation of poultry transcripts and non-coding RNAs, standardized analytical pipelines, and functional validation systems.<\/jats:p>","DOI":"10.3390\/ani16172700","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T01:05:26Z","timestamp":1788224726000},"page":"2700","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Advances in Poultry RNA-Omics Research: Technologies, RNA Information Layers, and Applications in Complex Traits"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-3477-8493","authenticated-orcid":false,"given":"Wenbin","family":"Dao","sequence":"first","affiliation":[{"name":"Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simeng","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2355-9777","authenticated-orcid":false,"given":"Xinyang","family":"Fan","sequence":"additional","affiliation":[{"name":"Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2127-0379","authenticated-orcid":false,"given":"Yongwang","family":"Miao","sequence":"additional","affiliation":[{"name":"Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"6248","DOI":"10.3390\/cimb46060373","article-title":"The omics revolution in understanding chicken reproduction: A comprehensive review","volume":"46","author":"Wadood","year":"2024","journal-title":"Curr. Issues Mol. Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: A revolutionary tool for transcriptomics","volume":"10","author":"Wang","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"104643","DOI":"10.1016\/j.psj.2024.104643","article-title":"Omics based technology application in poultry meat research","volume":"104","author":"Zhou","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1080\/03079457.2022.2086447","article-title":"Omics technologies in poultry health and productivity\u2014Part 1: Current use in poultry research","volume":"51","author":"Dehau","year":"2022","journal-title":"Avian Pathol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s13059-016-0881-8","article-title":"A survey of best practices for RNA-seq data analysis","volume":"17","author":"Conesa","year":"2016","journal-title":"Genome Biol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/s41576-019-0150-2","article-title":"RNA sequencing: The teenage years","volume":"20","author":"Stark","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"5650","DOI":"10.1038\/s41467-020-19015-1","article-title":"Benchmarking of cell type deconvolution pipelines for transcriptomics data","volume":"11","author":"Powell","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/nature07509","article-title":"Alternative isoform regulation in human tissue transcriptomes","volume":"456","author":"Wang","year":"2008","journal-title":"Nature"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1186\/s13059-022-02811-x","article-title":"The genetic and biochemical determinants of mRNA degradation rates in mammals","volume":"23","author":"Agarwal","year":"2022","journal-title":"Genome Biol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/s41576-020-00295-8","article-title":"The epitranscriptome beyond m6A","volume":"22","author":"Wiener","year":"2021","journal-title":"Nat. Rev. Genet."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"100385","DOI":"10.1016\/j.xgen.2023.100385","article-title":"Gene expression and RNA splicing explain large proportions of the heritability for complex traits in cattle","volume":"3","author":"Xiang","year":"2023","journal-title":"Cell Genom."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e70131","DOI":"10.1002\/age.70131","article-title":"Heritability Patterns of Protein-Coding Genes Expression: Insights from the Pig Genotype-Tissue Expression Project","volume":"57","author":"Su","year":"2026","journal-title":"Anim. Genet."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.1038\/s41592-024-02298-3","article-title":"Systematic assessment of long-read RNA-seq methods for transcript identification and quantification","volume":"21","author":"Wang","year":"2024","journal-title":"Nat. Methods"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.gpb.2015.08.002","article-title":"PacBio Sequencing and its Applications","volume":"13","author":"Rhoads","year":"2015","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"7198","DOI":"10.1038\/s41467-021-27393-3","article-title":"RNA modifications detection by comparative Nanopore direct RNA sequencing","volume":"12","author":"Leger","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/nature11112","article-title":"Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq","volume":"485","author":"Dominissini","year":"2012","journal-title":"Nature"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1126\/science.aaf2403","article-title":"Visualization and analysis of gene expression in tissue sections by spatial transcriptomics","volume":"353","author":"Vickovic","year":"2016","journal-title":"Science"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/nmeth.1315","article-title":"mRNA-Seq whole-transcriptome analysis of a single cell","volume":"6","author":"Tang","year":"2009","journal-title":"Nat. Methods"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1126\/science.1168978","article-title":"Genome-Wide analysis in vivo of translation with nucleotide resolution using ribosome profiling","volume":"324","author":"Ingolia","year":"2009","journal-title":"Science"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/nature14263","article-title":"Structural imprints in vivo decode RNA regulatory mechanisms","volume":"519","author":"Spitale","year":"2015","journal-title":"Nature"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1534\/g3.116.035923","article-title":"A new chicken genome assembly provides insight into avian genome structure","volume":"7","author":"Warren","year":"2017","journal-title":"G3 Genes Genomes Genet."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"6588","DOI":"10.1038\/s41598-024-56705-y","article-title":"Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues","volume":"14","author":"Degalez","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Woo, S.J., Songodan, T., and Han, J.Y. (2026). Unique chicken B cell development: Species-specific mechanisms and contradictory requirements of B cell receptor for post-hatched B cell development. Front. Immunol., 17.","DOI":"10.3389\/fimmu.2026.1755331"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Scanes, C.G. (2020). Avian Physiology: Are Birds Simply Feathered Mammals?. Front. Physiol., 11.","DOI":"10.3389\/fphys.2020.542466"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"D982","DOI":"10.1093\/nar\/gkaf731","article-title":"The ChickenGTEx portal: A pan-tissue catalogue of regulatory variants shaping transcriptomic and phenotypic diversity","volume":"54","author":"Hou","year":"2026","journal-title":"Nucleic Acids Res."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Guan, D., Halstead, M.M., Islas-Trejo, A.D., Goszczynski, D.E., Cheng, H.H., Ross, P.J., and Zhou, H. (2022). Prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing. Front. Genet., 13.","DOI":"10.3389\/fgene.2022.997460"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1298","DOI":"10.1038\/s41588-025-02155-9","article-title":"Genetic regulation of gene expression across multiple tissues in chickens","volume":"57","author":"Guan","year":"2025","journal-title":"Nat. Genet."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Lu, Y., Li, M., Gao, Z., Ma, H., Chong, Y., Hong, J., Wu, J., Wu, D., Xi, D., and Deng, W. (2024). Innovative insights into Single-Cell technologies and Multi-Omics integration in livestock and poultry. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms252312940"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"32508","DOI":"10.1021\/acs.jafc.5c13040","article-title":"Single-Cell Multi-Omics sequencing technologies and their applications in livestock and poultry research","volume":"73","author":"Cao","year":"2025","journal-title":"J. Agric. Food Chem."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"International Chicken Genome Sequencing Consortium (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695\u2013716.","DOI":"10.1038\/nature03154"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e2216641120","DOI":"10.1073\/pnas.2216641120","article-title":"Evolutionary analysis of a complete chicken genome","volume":"120","author":"Huang","year":"2023","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"Trapnell","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1038\/s41576-025-00828-z","article-title":"Transcriptomics in the era of long-read sequencing","volume":"26","author":"Liu","year":"2025","journal-title":"Nat. Rev. Genet."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"6590","DOI":"10.1038\/s41598-020-63355-3","article-title":"Limits in the detection of m6A changes using MeRIP\/m6A-seq","volume":"10","author":"McIntyre","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1111\/age.13469","article-title":"Core competing endogenous RNA network based on mRNA and non-coding RNA expression profiles in chicken fatty liver","volume":"55","author":"Xiao","year":"2024","journal-title":"Anim. Genet."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Lei, Q., Hu, X., Han, H., Wang, J., Liu, W., Zhou, Y., Cao, D., Li, F., and Liu, J. (2022). Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods. BMC Genom., 23.","DOI":"10.1186\/s12864-022-08525-5"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"20861","DOI":"10.1038\/s41598-021-00176-y","article-title":"Analysis of potential regulatory LncRNAs and CircRNAs in the oxidative myofiber and glycolytic myofiber of chickens","volume":"11","author":"Ju","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Jin, Y., Dong, J., Li, J., Huang, M., Wang, D., and Tan, X. (2025). Novel insights into the molecular mechanisms of chicken breast muscle development by integrating Non-Coding RNA and mRNA profiles. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26178181"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Jia, Q.-H., Cao, Y.-Z., Xing, Y.-X., Guan, H.-B., Ma, C.-L., Li, X., Tian, W.-H., Li, Z.-J., Tian, Y.-D., and Li, G.-X. (2024). LncRNA lncLLM facilitates lipid deposition by promoting the ubiquitination of MYH9 in chicken LMH cells. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms251910316"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1111\/age.13405","article-title":"LncRNA ENSGALG00000021686 regulates fat metabolism in chicken hepatocytes via miR-146b\/AGPAT2 pathway","volume":"55","author":"Xing","year":"2024","journal-title":"Anim. Genet."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Nguyen, T.V., Tat, T.H., and Do, D.N. (2025). MiRNAs in poultry health and production: Progress and challenges. Animals, 15.","DOI":"10.3390\/ani15223230"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Gu, L., Jiang, Q., Chen, Y., Zheng, X., Zhou, H., and Xu, T. (2022). Transcriptome-wide study revealed m6A and miRNA regulation of embryonic breast muscle development in Wenchang chickens. Front. Vet. Sci., 9.","DOI":"10.3389\/fvets.2022.934728"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Kuo, R.I., Tseng, E., Eory, L., Paton, I.R., Archibald, A.L., and Burt, D.W. (2017). Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human. BMC Genom., 18.","DOI":"10.1186\/s12864-017-3691-9"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"3972","DOI":"10.1038\/s41467-024-48117-3","article-title":"Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data","volume":"15","author":"Su","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Zhao, Y., Wang, Y., Ren, Y., Liu, L., Wang, T., Liu, L., and Li, X. (2025). Direct RNA sequencing reveals chicken post-transcriptional modifications in response to Campylobacter jejuni inoculation. BMC Genom., 26.","DOI":"10.1186\/s12864-025-11564-3"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/nmeth.4577","article-title":"Highly parallel direct RNA sequencing on an array of nanopores","volume":"15","author":"Garalde","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Zhang, Y., Chen, Y., Ji, H., Niu, Y., He, L., Wang, W., Yu, T., Han, R., Tian, Y., and Liu, X. (2025). Dynamic m6A modification landscape during the egg laying process of chickens. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26041677"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"106892","DOI":"10.1016\/j.psj.2026.106892","article-title":"Screening of m6A methylated genes associated with preovulatory follicle development in Bashang long-tailed chicken","volume":"105","author":"Duan","year":"2026","journal-title":"Poult. Sci."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Zhao, Q., Yao, Z., Chen, L., He, Y., Xie, Z., Zhang, H., Lin, W., Chen, F., Xie, Q., and Zhang, X. (2022). Transcriptome-Wide dynamics of m6A methylation in tumor livers induced by ALV-J infection in chickens. Front. Immunol., 13.","DOI":"10.3389\/fimmu.2022.868892"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1261\/rna.079615.123","article-title":"The importance of m6A topology in chicken embryo mRNA: A precise mapping of m6A at the conserved chicken \u03b2-actin zipcode","volume":"29","author":"Baron","year":"2023","journal-title":"RNA"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1906","DOI":"10.1038\/s41467-023-37596-5","article-title":"Systematic comparison of tools used for m6A mapping from nanopore direct RNA sequencing","volume":"14","author":"Zhong","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"bbae001","DOI":"10.1093\/bib\/bbae001","article-title":"Benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing","volume":"25","author":"Maestri","year":"2024","journal-title":"Brief. Bioinform."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"e63907","DOI":"10.7554\/eLife.63907","article-title":"A cell atlas of the chick retina based on single-cell transcriptomics","volume":"10","author":"Yamagata","year":"2021","journal-title":"eLife"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1771","DOI":"10.1038\/s41467-021-21892-z","article-title":"Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis","volume":"12","author":"Mantri","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Feregrino, C., Sacher, F., Parnas, O., and Tschopp, P. (2019). A single-cell transcriptomic atlas of the developing chicken limb. BMC Genom., 20.","DOI":"10.1186\/s12864-019-5802-2"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"105095","DOI":"10.1016\/j.psj.2025.105095","article-title":"Spatial transcriptomic differences in the breast muscle of grower broilers at 21 and 28 days of age","volume":"104","author":"Choi","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"104669","DOI":"10.1016\/j.psj.2024.104669","article-title":"Single-cell RNA sequencing of the spleen reveals differences in Salmonella typhimurium infection mechanisms between different chicken breeds","volume":"104","author":"Zhang","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Tu, J.-H., Liu, B.-G., Lin, B.-J., Liu, H.-C., Guo, S.-C., Ouyang, Q.-Y., Fang, L.-Z., He, X., Song, Z.-H., and Zhang, H.-H. (2025). Single-cell transcriptomic atlas of the chicken cecum reveals cellular responses and state shifts during Eimeria tenella infection. BMC Genom., 26.","DOI":"10.1186\/s12864-025-11302-9"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"e70093","DOI":"10.1002\/imt2.70093","article-title":"Single-nucleus RNA sequencing reveals RUNX1 regulation of muscle hypertrophy through PI3K\/AKT\/mTOR pathway","volume":"4","author":"Wang","year":"2025","journal-title":"iMeta"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"3450","DOI":"10.1038\/s41598-024-53904-5","article-title":"Spatial transcriptomics reveals alterations in perivascular macrophage lipid metabolism in the onset of Wooden Breast myopathy in broiler chickens","volume":"14","author":"Wang","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Blech-Hermoni, Y., Dasgupta, T., Coram, R.J., and Ladd, A.N. (2016). Identification of Targets of CUG-BP, Elav-Like Family Member 1 (CELF1) Regulation in Embryonic Heart Muscle. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0149061"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1038\/nmeth.3810","article-title":"Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)","volume":"13","author":"Pratt","year":"2016","journal-title":"Nat. Methods"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/nmeth.4437","article-title":"Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations","volume":"14","author":"Sage","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Bakken, T.E., Hodge, R.D., Miller, J.A., Yao, Z., Nguyen, T.N., Aevermann, B., Barkan, E., Bertagnolli, D., Casper, T., and Dee, N. (2018). Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0209648"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"8353","DOI":"10.1038\/s41467-023-43458-x","article-title":"High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis","volume":"14","author":"Janesick","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.1038\/s41588-025-02193-3","article-title":"High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer","volume":"57","author":"Oliveira","year":"2025","journal-title":"Nat. Genet."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1038\/nature12894","article-title":"Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo","volume":"505","author":"Rouskin","year":"2014","journal-title":"Nature"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1038\/s41597-019-0293-1","article-title":"Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos","volume":"6","author":"Yin","year":"2019","journal-title":"Sci. Data"},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Wu, J., Liu, S., Jiang, D., Zhou, Y.N., Jiang, H., Xiao, X., Zha, B., Fang, Y., Huang, J., and Hu, X. (2024). Exploring gene expression and alternative splicing in Duck embryonic myoblasts via Full-Length transcriptome sequencing. Vet. Sci., 11.","DOI":"10.3390\/vetsci11120601"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1186\/s40104-022-00710-6","article-title":"The m6A methylation regulates gonadal sex differentiation in chicken embryo","volume":"13","author":"Li","year":"2022","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Wang, Z., Ju, X., Li, S., Yu, J., Yang, X., Cai, D., Li, K., Gonzalez, J.M., Nie, Q., and Li, Z. (2025). METTL3 facilitates the translation of CircSIK2 during chicken myogenesis in an m6A dependent manner. PLoS Genet., 21.","DOI":"10.1371\/journal.pgen.1011934"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"105216","DOI":"10.1016\/j.psj.2025.105216","article-title":"METTL3-dependent m6A modification of GHR mRNA regulates mitochondrial function through mitochondrial biogenesis during myoblast differentiation","volume":"104","author":"Zhao","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"102793","DOI":"10.1016\/j.psj.2023.102793","article-title":"RNA N6-methyladenosine profiling reveals differentially methylated genes associated with intramuscular fat metabolism during breast muscle development in chicken","volume":"102","author":"Yu","year":"2023","journal-title":"Poult. Sci."},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Chakraborty, P., Kuo, R.I., Wu, Z., Morris, K.M., Dutia, B.M., Kaiser, P., and Smith, J. (2022). The role of dendritic cells in the host response to Marek\u2019s disease virus (MDV) as shown by transcriptomic analysis of susceptible and resistant birds. Pathogens, 11.","DOI":"10.3390\/pathogens11111340"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"109009","DOI":"10.1016\/j.isci.2024.109009","article-title":"Spatial and single-nucleus transcriptomics decoding the molecular landscape and cellular organization of avian optic tectum","volume":"27","author":"Liao","year":"2024","journal-title":"iScience"},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Zhao, W., He, X., Hoadley, K.A., Parker, J.S., Hayes, D.N., and Perou, C.M. (2014). Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling. BMC Genom., 15.","DOI":"10.1186\/1471-2164-15-419"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1016\/j.ymeth.2012.07.030","article-title":"Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing","volume":"58","author":"Hafner","year":"2012","journal-title":"Methods"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1080\/15476286.2021.2012632","article-title":"Comparative analysis of circular RNA enrichment methods","volume":"19","author":"Shi","year":"2022","journal-title":"RNA Biol."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nature11928","article-title":"Circular RNAs are a large class of animal RNAs with regulatory potency","volume":"495","author":"Memczak","year":"2013","journal-title":"Nature"},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Li, B., and Dewey, C.N. (2011). RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-323"},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Zhang, C., Zhang, B., Lin, L.-L., and Zhao, S. (2017). Evaluation and comparison of computational tools for RNA-seq isoform quantification. BMC Genom., 18.","DOI":"10.1186\/s12864-017-4002-1"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1016\/j.cell.2011.07.014","article-title":"A ceRNA hypothesis: The rosetta stone of a hidden RNA language?","volume":"146","author":"Salmena","year":"2011","journal-title":"Cell"},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Wang, X., Lin, J., Jiao, Z., Zhang, L., Guo, D., An, L., Xie, T., and Lin, S. (2023). Circular RNA circIGF2BP3 promotes the proliferation and differentiation of chicken primary myoblasts. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms242115545"},{"key":"ref_84","doi-asserted-by":"crossref","unstructured":"Sarma, A., Suri, P., Justice, M., Angamuthu, R., and Pushparaj, S. (2025). An emphasis on the role of long Non-Coding RNAs in viral gene expression, pathogenesis, and innate immunity in viral chicken diseases. Non-Coding RNA, 11.","DOI":"10.3390\/ncrna11030042"},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Grushina, V.A., Gagarina, V.S., Prasolov, D.E., Kolpakov, F.A., Gusev, O.A., and Pintus, S.S. (2025). Prediction of enhancer RNAs in chicken genome. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms262210986"},{"key":"ref_86","doi-asserted-by":"crossref","unstructured":"Han, J.H., Lee, H.J., and Kim, T.H. (2023). Characterization of transcriptional enhancers in the chicken genome using CRISPR-mediated activation. Front. Genome Ed., 5.","DOI":"10.3389\/fgeed.2023.1269115"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"104612","DOI":"10.1016\/j.psj.2024.104612","article-title":"Emerging roles of circular RNAs on the regulation of production traits in chicken","volume":"104","author":"You","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_88","doi-asserted-by":"crossref","unstructured":"Shi, H., He, Y., Li, X., Du, Y., Zhao, J., and Ge, C. (2022). Regulation of Non-Coding RNA in the Growth and Development of Skeletal Muscle in Domestic Chickens. Genes, 13.","DOI":"10.3390\/genes13061033"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1126\/science.1229386","article-title":"Precise maps of RNA polymerase reveal how promoters direct initiation and pausing","volume":"339","author":"Kwak","year":"2013","journal-title":"Science"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"1845","DOI":"10.1126\/science.1162228","article-title":"Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters","volume":"322","author":"Core","year":"2008","journal-title":"Science"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"Langfelder, P., and Horvath, S. (2008). WGCNA: An R package for weighted correlation network analysis. BMC Bioinform., 9.","DOI":"10.1186\/1471-2105-9-559"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1016\/j.molcel.2014.09.018","article-title":"Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition","volume":"56","author":"Bosson","year":"2014","journal-title":"Mol. Cell"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1016\/j.molcel.2014.03.045","article-title":"Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance","volume":"54","author":"Denzler","year":"2014","journal-title":"Mol. Cell"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/nrg.2016.20","article-title":"Endogenous microRNA sponges: Evidence and controversy","volume":"17","author":"Thomson","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"e58","DOI":"10.1093\/nar\/gkv1458","article-title":"Comparison of circular RNA prediction tools","volume":"44","author":"Hansen","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1038\/nbt.2705","article-title":"A single-molecule long-read survey of the human transcriptome","volume":"31","author":"Sharon","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"106240","DOI":"10.1016\/j.psj.2025.106240","article-title":"Emerging technologies in poultry genomics: Unlocking innovation for the future of sustainable production","volume":"105","author":"Zhou","year":"2026","journal-title":"Poult. Sci."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"3359","DOI":"10.1038\/s41467-019-11272-z","article-title":"A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes","volume":"10","author":"Soneson","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"102789","DOI":"10.1016\/j.omtn.2025.102789","article-title":"Using RNA-targeting CRISPR-Cas13 and engineered U1 systems to target ABCA4 splice variants in Stargardt disease","volume":"37","author":"Liou","year":"2026","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"gkaf1447","DOI":"10.1093\/nar\/gkaf1447","article-title":"Junction-targeting designs limit the application of CRISPR-Cas13d in circular RNA perturbation studies","volume":"54","author":"Valbuena","year":"2026","journal-title":"Nucleic Acids Res."},{"key":"ref_102","doi-asserted-by":"crossref","unstructured":"Han, X., Zhou, X., Liu, J., Zou, Y., Pang, Y., Li, R., Wang, X., Cheng, B., Cao, Z., and Luan, P. (2026). PLIN1a: The principal protein isoform that performs the function of chicken PLIN1. Front. Cell Dev. Biol., 14.","DOI":"10.3389\/fcell.2026.1896814"},{"key":"ref_103","first-page":"21628","article-title":"Chicken PPAR\u03b3 Undergoes Alternative Polyadenylation to Produce Five 3\u2032 UTR Isoforms with Distinct Regulatory Functions","volume":"74","author":"Mu","year":"2026","journal-title":"J. Agric. Food Chem."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"6410","DOI":"10.1016\/j.psj.2020.09.086","article-title":"Peroxisome proliferator-activated receptor \u03b3 isoforms differentially regulate preadipocyte proliferation, apoptosis, and differentiation in chickens","volume":"99","author":"Mu","year":"2020","journal-title":"Poult. Sci."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1186\/s12711-023-00849-4","article-title":"Comparative analyses of dynamic transcriptome profiles highlight key response genes and dominant isoforms for muscle development and growth in chicken","volume":"55","author":"Wang","year":"2023","journal-title":"Genet. Sel. Evol."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.ygcen.2018.12.011","article-title":"Changes in prolactin receptor homodimer availability may cause late feathering in chickens","volume":"272","author":"Okamura","year":"2019","journal-title":"Gen. Comp. Endocrinol."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/j.gene.2013.11.037","article-title":"Molecular characterization and differential expression of multiple goose dopamine D2 receptors","volume":"535","author":"Wang","year":"2014","journal-title":"Gene"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"2236","DOI":"10.1016\/j.molcel.2022.05.029","article-title":"Hidden codes in mRNA: Control of gene expression by m6A","volume":"82","author":"Murakami","year":"2022","journal-title":"Mol. Cell"},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1038\/nchembio.1432","article-title":"A METTL3\u2013METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation","volume":"10","author":"Liu","year":"2014","journal-title":"Nat. Chem. Biol."},{"key":"ref_110","doi-asserted-by":"crossref","unstructured":"Cheng, B., Leng, L., Li, Z., Wang, W., Jing, Y., Li, Y., Wang, N., Li, H., and Wang, S. (2021). Profiling of RNA N6-methyladenosine methylation reveals the critical role of m6A in chicken adipose deposition. Front. Cell Dev. Biol., 9.","DOI":"10.3389\/fcell.2021.590468"},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nature12730","article-title":"N6-methyladenosine-dependent regulation of messenger RNA stability","volume":"505","author":"Wang","year":"2014","journal-title":"Nature"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.1101\/gr.277704.123","article-title":"Allele-specific RNA N6-methyladenosine modifications reveal functional genetic variants in human tissues","volume":"33","author":"Cao","year":"2023","journal-title":"Genome Res."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"1210","DOI":"10.1038\/s41587-022-01243-z","article-title":"m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome","volume":"40","author":"Hu","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/s41587-022-01487-9","article-title":"Absolute quantification of single-base m6A methylation in the mammalian transcriptome using GLORI","volume":"41","author":"Liu","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","article-title":"Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets","volume":"161","author":"Macosko","year":"2015","journal-title":"Cell"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1038\/s41587-019-0071-9","article-title":"A comparison of single-cell trajectory inference methods","volume":"37","author":"Saelens","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"3224","DOI":"10.1038\/s41467-022-30755-0","article-title":"Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data","volume":"13","author":"Dimitrov","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"106475","DOI":"10.1016\/j.psj.2026.106475","article-title":"Single-cell transcriptomics reveals diversity and conservation of chicken lymphocytes","volume":"105","author":"Liu","year":"2026","journal-title":"Poult. Sci."},{"key":"ref_119","doi-asserted-by":"crossref","unstructured":"Maxwell, M., S\u00f6derlund, R., H\u00e4rtle, S., and Wattrang, E. (2024). Single-cell RNA-seq mapping of chicken peripheral blood leukocytes. BMC Genom., 25.","DOI":"10.1186\/s12864-024-10044-4"},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"103979","DOI":"10.1016\/j.psj.2024.103979","article-title":"Single-nucleus transcriptome reveals cell dynamic response of liver during the late chick embryonic development","volume":"103","author":"Wang","year":"2024","journal-title":"Poult. Sci."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1016\/j.cell.2022.04.003","article-title":"Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays","volume":"185","author":"Chen","year":"2022","journal-title":"Cell"},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"1484","DOI":"10.1038\/s41596-020-0292-x","article-title":"CellPhoneDB: Inferring cell\u2013cell communication from combined expression of multi-subunit ligand\u2013receptor complexes","volume":"15","author":"Efremova","year":"2020","journal-title":"Nat. Protoc."},{"key":"ref_123","doi-asserted-by":"crossref","unstructured":"Wang, J., Adelson, D.L., Yilmaz, A., Sze, S.-H., Jin, Y., and Zhu, J.J. (2005). Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics. BMC Genom., 6.","DOI":"10.1186\/1471-2164-6-45"},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"109880","DOI":"10.1016\/j.isci.2024.109880","article-title":"Single-cell transcriptomic reveals a cell atlas and diversity of chicken amygdala responded to social hierarchy","volume":"27","author":"Chen","year":"2024","journal-title":"iScience"},{"key":"ref_125","doi-asserted-by":"crossref","unstructured":"Chen, B., Ji, H., Duan, X.-C., Hu, C., Zhi, Y., Qin, P., Liu, X., Tian, W., Tian, Y., and Kang, X. (2025). Single-cell transcriptome profiling of peripheral blood mononuclear cells reveals immune cell heterogeneity in chickens. J. Integr. Agric., in press.","DOI":"10.1016\/j.jia.2025.05.016"},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1186\/s13578-021-00728-9","article-title":"From nasal to basal: Single-cell sequencing of the bursa of Fabricius highlights the IBDV infection mechanism in chickens","volume":"11","author":"Shah","year":"2021","journal-title":"Cell Biosci."},{"key":"ref_127","doi-asserted-by":"crossref","unstructured":"Qu, X., Li, X., Li, Z., Liao, M., and Dai, M. (2022). Chicken peripheral blood mononuclear cells response to avian leukosis virus subgroup J infection assessed by Single-Cell RNA sequencing. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.800618"},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"5355","DOI":"10.1038\/s41598-023-32308-x","article-title":"The immune cell landscape and response of Marek\u2019s disease resistant and susceptible chickens infected with Marek\u2019s disease virus","volume":"13","author":"Warren","year":"2023","journal-title":"Sci. Rep."},{"key":"ref_129","doi-asserted-by":"crossref","unstructured":"Wang, S., Huang, T., Xie, Z., Wan, L., Ren, H., Wu, T., Xie, L., Luo, S., Li, M., and Xie, Z. (2023). Transcriptomic and translatomic analyses reveal insights into the signaling pathways of the innate immune response in the spleens of SPF chickens infected with avian reovirus. Viruses, 15.","DOI":"10.3390\/v15122346"},{"key":"ref_130","doi-asserted-by":"crossref","unstructured":"Chai, R., Xiao, C., Yang, Z., Du, W., Lv, K., Zhang, J., and Yang, X. (2024). Identification of genes associated with sperm storage capacity in hens at different times after insemination by RNA-seq and Ribo-seq. BMC Genom., 25.","DOI":"10.1186\/s12864-024-10472-2"},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1038\/s41586-025-09256-9","article-title":"A male-essential miRNA is key for avian sex chromosome dosage compensation","volume":"645","author":"Fallahshahroudi","year":"2025","journal-title":"Nature"},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1186\/s40104-026-01421-y","article-title":"Integrative analysis of RNA-seq and Ribo-seq reveals that lncRNA regulates chicken myogenesis through encoding peptide","volume":"17","author":"Niu","year":"2026","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nrg.2016.49","article-title":"Coming of age: Ten years of next-generation sequencing technologies","volume":"17","author":"Goodwin","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/s41576-023-00580-2","article-title":"Methods and applications for single-cell and spatial multi-omics","volume":"24","author":"Vandereyken","year":"2023","journal-title":"Nat. Rev. Genet."},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1016\/j.jgg.2025.10.004","article-title":"A universal and cost-efficient sample labeling approach for multiplexed single-cell RNA-seq based on recombinant HUH-endonuclease-agglutinin tagging","volume":"53","author":"Zhang","year":"2026","journal-title":"J. Genet. Genom."},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"117793221989905","DOI":"10.1177\/1177932219899051","article-title":"Multi-omics data integration, interpretation, and its application","volume":"14","author":"Subramanian","year":"2020","journal-title":"Bioinform. Biol. Insights"},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1038\/s43588-021-00086-z","article-title":"Undisclosed, unmet and neglected challenges in multi-omics studies","volume":"1","author":"Tarazona","year":"2021","journal-title":"Nat. Comput. Sci."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"104811","DOI":"10.1016\/j.psj.2025.104811","article-title":"The m6A modification regulates the composition of myofiber types in chicken skeletal muscle","volume":"104","author":"Shan","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"101250","DOI":"10.1016\/j.xgen.2026.101250","article-title":"FastGxC: Fast and powerful context-specific eQTL mapping in bulk and single-cell data","volume":"6","author":"Krockenberger","year":"2026","journal-title":"Cell Genom."},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"1438","DOI":"10.1038\/s41588-022-01153-5","article-title":"A multi-tissue atlas of regulatory variants in cattle","volume":"54","author":"Liu","year":"2022","journal-title":"Nat. Genet."},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"107132","DOI":"10.1016\/j.psj.2026.107132","article-title":"The current and future perspective of ChickenGTEx project and its applications in precision breeding","volume":"105","author":"Fang","year":"2026","journal-title":"Poult. Sci."},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"100","DOI":"10.12688\/f1000research.10571.2","article-title":"Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis","volume":"6","author":"Weirather","year":"2017","journal-title":"F1000Research"},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1038\/s41592-022-01480-9","article-title":"Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution","volume":"19","author":"Li","year":"2022","journal-title":"Nat. Methods"},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"1517","DOI":"10.1038\/s41587-021-00965-w","article-title":"Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq","volume":"39","author":"Philpott","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1038\/s41467-023-35958-7","article-title":"scm6A-seq reveals single-cell landscapes of the dynamic m6A during oocyte maturation and early embryonic development","volume":"14","author":"Yao","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"3092","DOI":"10.1038\/s41467-020-16937-8","article-title":"Harmonization of quality metrics and power calculation in multi-omic studies","volume":"11","author":"Tarazona","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s13567-023-01144-2","article-title":"Temporal transcriptome profiling of floating apical out chicken enteroids suggest stability and reproducibility","volume":"54","author":"Nash","year":"2023","journal-title":"Vet. Res."},{"key":"ref_148","doi-asserted-by":"crossref","unstructured":"Xing, Y., Ma, C., Guan, H., Shen, J., Shen, Y., Li, G., Sun, G., Tian, Y., Kang, X., and Liu, X. (2025). Multi-Omics insights into regulatory mechanisms underlying differential deposition of intramuscular and abdominal fat in chickens. Biomolecules, 15.","DOI":"10.3390\/biom15010134"},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"105058","DOI":"10.1016\/j.psj.2025.105058","article-title":"Identification of key genes associated with residual feed intake in small-sized meat ducks through integrated analysis of mRNA and miRNA transcriptomes","volume":"104","author":"Geng","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_150","doi-asserted-by":"crossref","unstructured":"Xiong, H., Li, W., Wang, L., Wang, X., Tang, B., Cui, Z., and Liu, L. (2024). Whole transcriptome analysis revealed the regulatory network and related pathways of non-coding RNA regulating ovarian atrophy in broody hens. Front. Vet. Sci., 11.","DOI":"10.3389\/fvets.2024.1399776"},{"key":"ref_151","doi-asserted-by":"crossref","unstructured":"Li, P., Chu, C., Hu, L., Zhang, G., Wu, P., and Zhang, Q. (2025). Whole transcriptome sequencing reveals the functional regulation of chicken reproduction by lncRNAs, miRNAs, and mRNAs across the hypothalamus-pituitary-ovary axis. Front. Vet. Sci., 12.","DOI":"10.3389\/fvets.2025.1687863"},{"key":"ref_152","doi-asserted-by":"crossref","unstructured":"Powell, A.A., Velleman, S.G., Strasburg, G.M., Abrahante Llor\u00e9ns, J.E., and Reed, K.M. (2024). Circular RNA expression in turkey skeletal muscle satellite cells is significantly altered by thermal challenge. Front. Physiol., 15.","DOI":"10.3389\/fphys.2024.1476487"},{"key":"ref_153","doi-asserted-by":"crossref","unstructured":"Zhai, B., Zhao, Y., Fan, S., Yuan, P., Li, H., Li, S., Li, Y., Zhang, Y., Huang, H., and Li, H. (2021). Differentially expressed lncRNAs related to the development of abdominal fat in Gushi chickens and their interaction regulatory network. Front. Genet., 12.","DOI":"10.3389\/fgene.2021.802857"},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"105542","DOI":"10.1016\/j.psj.2025.105542","article-title":"Decoding chicken growth regulation through multi-omics insights and emerging genetic tools for growth optimization","volume":"104","author":"Nawaz","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"781","DOI":"10.3382\/ps\/peu008","article-title":"Ovarian follicle selection and granulosa cell differentiation","volume":"94","author":"Johnson","year":"2015","journal-title":"Poult. Sci."},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"810","DOI":"10.3382\/ps\/peu042","article-title":"Control of the reproductive axis: Balancing act between stimulatory and inhibitory input","volume":"94","year":"2015","journal-title":"Poult. Sci."},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"1879","DOI":"10.1007\/s00018-019-03360-6","article-title":"Zygotic genome activation in the chicken: A comparative review","volume":"77","author":"Rengaraj","year":"2020","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"105430","DOI":"10.1016\/j.psj.2025.105430","article-title":"Single-cell RNA sequencing uncovers cellular heterogeneity of granulosa cells and provides a signature for follicular development in chicken","volume":"104","author":"Yu","year":"2025","journal-title":"Poult. Sci."},{"key":"ref_159","doi-asserted-by":"crossref","unstructured":"Ran, M., Hu, S., Ouyang, Q., Xie, H., Zhang, X., Lin, Y., Li, X., Hu, J., Li, L., and He, H. (2023). miR-202-5p inhibits lipid metabolism and steroidogenesis of goose hierarchical granulosa cells by targeting ACSL3. Animals, 13.","DOI":"10.3390\/ani13030325"},{"key":"ref_160","doi-asserted-by":"crossref","unstructured":"Yu, H., Mi, C., Wang, Q., Zou, W., Dai, G., Zhang, T., Zhang, G., Xie, K., Wang, J., and Shi, H. (2021). Comprehensive analyses of circRNA expression profiles and function prediction in chicken cecums after Eimeria tenella infection. Front. Cell. Infect. Microbiol., 11.","DOI":"10.3389\/fcimb.2021.628667"},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/nature16547","article-title":"Dual RNA-seq unveils noncoding RNA functions in host\u2013pathogen interactions","volume":"529","author":"Westermann","year":"2016","journal-title":"Nature"},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1017\/S0031182021000111","article-title":"Dual RNA-Seq transcriptome analysis of chicken macrophage-like cells (HD11) infected in vitro with Eimeria tenella","volume":"148","author":"Sandholt","year":"2021","journal-title":"Parasitology"},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"1279","DOI":"10.1080\/1828051X.2024.2395855","article-title":"Synbiotic modulate the host immune response to Salmonella typhimurium infection in commercial and indigenous chicken","volume":"23","author":"Elsharkawy","year":"2024","journal-title":"Ital. J. Anim. Sci."},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"5993","DOI":"10.1128\/IAI.00695-07","article-title":"Chicken cecum immune response to Salmonella enterica serovars of different levels of invasiveness","volume":"75","author":"Berndt","year":"2007","journal-title":"Infect. Immun."},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"110475","DOI":"10.1016\/j.ygeno.2022.110475","article-title":"Comparative RNA-Seq analysis reveals insights in Salmonella disease resistance of chicken; and database development as resource for gene expression in poultry","volume":"114","author":"Dar","year":"2022","journal-title":"Genomics"},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1098\/rstb.2008.0184","article-title":"Decomposing health: Tolerance and resistance to parasites in animals","volume":"364","author":"Graham","year":"2009","journal-title":"Philos. Trans. R. Soc. B Biol. Sci."},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"100286","DOI":"10.1016\/j.animal.2021.100286","article-title":"Review: Livestock disease resilience: From individual to herd level","volume":"15","author":"Knap","year":"2021","journal-title":"Animal"},{"key":"ref_168","doi-asserted-by":"crossref","unstructured":"Azli, B., Salim, N.F., Hair-Bejo, M., Omar, A.R., Mohamed Sohaimi, N., Clifford, U.C., Abdul Hamid, N.A.W., and Mat Isa, N. (2025). Temporal dynamics of chicken host\u2019s molecular response against Fowl adenovirus serotype 8b infection via RNA-sequencing. BMC Genom., 26.","DOI":"10.1186\/s12864-025-11853-x"},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1101\/gr.222976.117","article-title":"SQANTI: Extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification","volume":"28","author":"Tardaguila","year":"2018","journal-title":"Genome Res."},{"key":"ref_170","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1126\/science.1251385","article-title":"Comparative genomics reveals insights into avian genome evolution and adaptation","volume":"346","author":"Zhang","year":"2014","journal-title":"Science"},{"key":"ref_171","doi-asserted-by":"crossref","unstructured":"Foissac, S., Djebali, S., Munyard, K., Vialaneix, N., Rau, A., Muret, K., Esquerr\u00e9, D., Zytnicki, M., Derrien, T., and Bardou, P. (2019). Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biol., 17.","DOI":"10.1186\/s12915-019-0726-5"},{"key":"ref_172","doi-asserted-by":"crossref","unstructured":"Tixier-Boichard, M., Fabre, S., Dhorne-Pollet, S., Goubil, A., Acloque, H., Vincent-Naulleau, S., Ross, P., Wang, Y., Chanthavixay, G., and Cheng, H. (2021). Tissue resources for the functional annotation of animal genomes. Front. Genet., 12.","DOI":"10.3389\/fgene.2021.666265"},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1146\/annurev-animal-020518-114913","article-title":"Functional annotation of animal genomes (FAANG): Current achievements and roadmap","volume":"7","author":"Giuffra","year":"2019","journal-title":"Annu. Rev. Anim. Biosci."},{"key":"ref_174","doi-asserted-by":"crossref","unstructured":"The FAANG Consortium, Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., and Clarke, L. (2015). Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biol., 16, 57.","DOI":"10.1186\/s13059-015-0622-4"},{"key":"ref_175","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.1016\/j.ajhg.2024.05.012","article-title":"From complete genomes to pangenomes","volume":"111","author":"Miga","year":"2024","journal-title":"Am. J. Hum. Genet."},{"key":"ref_176","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/s40104-024-01141-1","article-title":"Near telomere-to-telomere genome assemblies of Silkie Gallus gallus and Mallard Anas platyrhynchos restored the structure of chromosomes and \u201cmissing\u201d genes in birds","volume":"16","author":"Zhao","year":"2025","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"ref_177","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1038\/s41586-022-04558-8","article-title":"A joint NCBI and EMBL-EBI transcript set for clinical genomics and research","volume":"604","author":"Morales","year":"2022","journal-title":"Nature"},{"key":"ref_178","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1038\/s41467-021-21038-1","article-title":"A practical solution to pseudoreplication bias in single-cell studies","volume":"12","author":"Zimmerman","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_179","doi-asserted-by":"crossref","first-page":"5692","DOI":"10.1038\/s41467-021-25960-2","article-title":"Confronting false discoveries in single-cell differential expression","volume":"12","author":"Squair","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1261\/rna.053959.115","article-title":"How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?","volume":"22","author":"Schurch","year":"2016","journal-title":"RNA"},{"key":"ref_181","doi-asserted-by":"crossref","unstructured":"Ellegren, H., Hultin-Rosenberg, L., Brunstr\u00f6m, B., Dencker, L., Kultima, K., and Scholz, B. (2007). Faced with inequality: Chicken do not have a general dosage compensation of sex-linked genes. BMC Biol., 5.","DOI":"10.1186\/1741-7007-5-40"},{"key":"ref_182","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1534\/genetics.115.179234","article-title":"Conservation of Regional Variation in Sex-Specific Sex Chromosome Regulation","volume":"201","author":"Wright","year":"2015","journal-title":"Genetics"},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"ref_184","doi-asserted-by":"crossref","unstructured":"Acharya, M., Arsi, K., Donoghue, A.M., Liyanage, R., and Rath, N.C. (2020). Production and characterization of avian crypt-villus enteroids and the effect of chemicals. BMC Vet. Res., 16.","DOI":"10.1186\/s12917-020-02397-1"},{"key":"ref_185","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1186\/s13567-021-01010-z","article-title":"Novel chicken two-dimensional intestinal model comprising all key epithelial cell types and a mesenchymal sub-layer","volume":"52","author":"Orr","year":"2021","journal-title":"Vet. Res."},{"key":"ref_186","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/ng.3506","article-title":"Integrative approaches for large-scale transcriptome-wide association studies","volume":"48","author":"Gusev","year":"2016","journal-title":"Nat. Genet."},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"e2514736122","DOI":"10.1073\/pnas.2514736122","article-title":"Integrating extensive functional annotations and multiomics of cattle enhances climate resilience prediction and mapping","volume":"122","author":"Xiang","year":"2025","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/s12711-025-00966-2","article-title":"Comparison of genomic prediction accuracies in dairy cattle lactation traits using five classes of functional variants versus generic SNP","volume":"57","author":"Alemu","year":"2025","journal-title":"Genet. Sel. Evol."},{"key":"ref_189","doi-asserted-by":"crossref","first-page":"5686","DOI":"10.1038\/s41467-026-72470-0","article-title":"Improving genomic prediction accuracy of complex traits by integrating massive types of functional annotation information","volume":"17","author":"Tang","year":"2026","journal-title":"Nat. Commun."},{"key":"ref_190","doi-asserted-by":"crossref","first-page":"101742","DOI":"10.1016\/j.animal.2025.101742","article-title":"Using transcriptomic data to improve the prediction of immunity traits in pigs","volume":"20","author":"Haas","year":"2026","journal-title":"Animal"},{"key":"ref_191","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1186\/s40104-026-01477-w","article-title":"From linear models to deep learning: Statistical advances in genomic selection for animal breeding","volume":"17","author":"Zhang","year":"2026","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"ref_192","doi-asserted-by":"crossref","unstructured":"He, J., Shi, N., Yao, H., Li, J., Wang, Y., and Zhang, J. (2025). Genome editing in the chicken: From PGC-mediated germline transmission to advanced applications. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26199426"},{"key":"ref_193","doi-asserted-by":"crossref","first-page":"106722","DOI":"10.1016\/j.psj.2026.106722","article-title":"High genotoxicity of CRISPR\/Cas9 versus limited efficacy of CRISPRi in chicken primordial germ cells","volume":"105","author":"Zhang","year":"2026","journal-title":"Poult. Sci."},{"key":"ref_194","doi-asserted-by":"crossref","first-page":"1104","DOI":"10.1017\/S0031182025100619","article-title":"Cultivating the endogenous life cycle of Eimeria tenella in chicken intestinal organoids","volume":"152","author":"Teng","year":"2025","journal-title":"Parasitology"},{"key":"ref_195","doi-asserted-by":"crossref","first-page":"11362","DOI":"10.1038\/s41598-025-95721-4","article-title":"Cellular landscape of avian intestinal organoids revealed by single cell transcriptomics","volume":"15","author":"Sun","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_196","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.1093\/biolre\/ioaf274","article-title":"Turkey oviduct epithelial organoids express region-associated markers and avian influenza virus receptors","volume":"114","author":"Santativongchai","year":"2026","journal-title":"Biol. Reprod."}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/17\/2700\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T01:16:41Z","timestamp":1788225401000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/17\/2700"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,31]]},"references-count":196,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ani16172700"],"URL":"https:\/\/doi.org\/10.3390\/ani16172700","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,31]]}}}