Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq.

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The present investigation was aimed to identify the differentially expressed genes (DEGs), metabolic gene networks and metabolic pathways in bovine liver transcriptome of young bulls. In this study, we comparatively analyzed the bovine liver transcriptome of dairy (Polish Holstein Friesian (HF); n = 6), beef (Hereford; n = 6), and dual purpose (Polish-Red; n = 6) cattle breeds. This study identified 895, 338, and 571 significant (p < 0.01) differentially expressed (DE) gene-transcripts represented as 745, 265, and 498 hepatic DE genes through the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-HF versus Polish-Red breeds comparisons, respectively. By combining all breeds comparisons, 75 hepatic DE genes (p < 0.01) were identified as commonly shared among all the three breed comparisons; 70, 160, and 38 hepatic DE genes were commonly shared between the following comparisons: (i) Polish-Red versus Hereford and Polish-HF versus Hereford; (ii) Polish-Red versus Hereford and Polish-HF versus Polish-Red; and (iii) Polish-HF versus Hereford and Polish-HF versus Polish-Red, respectively. A total of 440, 82, and 225 hepatic DE genes were uniquely observed for the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-Red versus Polish-HF comparisons, respectively. Gene ontology (GO) analysis identified top-ranked enriched GO terms (p < 0.01) including 17, 16, and 31 functional groups and 151, 61, and 140 gene functions that were DE in all three breed liver transcriptome comparisons. Gene network analysis identified several potential metabolic pathways involved in glutamine family amino-acid, triglyceride synthesis, gluconeogenesis, p38MAPK cascade regulation, cholesterol biosynthesis (Polish-Red versus Hereford); IGF-receptor signaling, catecholamine transport, lipoprotein lipase, tyrosine kinase binding receptor (Polish-HF versus Hereford), and PGF-receptor binding, (Polish-HF versus Polish-Red). Validation results showed that the relative expression values were consistent to those obtained by RNA-seq, and significantly correlated between the quantitative reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson's r > 0.90). Our results provide new insights on bovine liver gene expressions among dairy versus dual versus beef breeds by identifying the large numbers of DEGs markers submitted to NCBI gene expression omnibus (GEO) accession number GSE114233, which can serve as useful genetic tools to develop the gene assays for trait-associated studies as well as, to effectively implement in genomics selection (GS) cattle breeding programs in Poland.", "claims": [{"id": "claim-data-access", "statement": "The FASTQ sequencing data of this present study were deposited in the NCBI database under submission number: SRS1296732 (http://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=312148) [31] and the gene expression data of investigated animals (n = 18) were deposited in the NCBI database under submission number: GSE 114233 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114233) and summarized in Table 2.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30934933", "locator": "sections[5] \"2.3. 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No.", "Breed", "Web-Link"], ["CP19", "GSM3138303", "Polish Red", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138303"], ["CP20", "GSM3138304", "Polish Red", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138304"], ["CP21", "GSM3138305", "Polish Red", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138305"], ["CP22", "GSM3138306", "Polish Red", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138306"], ["CP23", "GSM3138307", "Polish Red", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138307"], ["CP24", "GSM3138308", "Polish Red", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138308"], ["CP27", "GSM3138309", "Polish HF", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138309"], ["CP28", "GSM3138310", "Polish HF", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138310"], ["CP29", "GSM3138311", "Polish HF", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138311"], ["CP30", "GSM3138312", "Polish HF", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138312"], ["CP31", "GSM3138313", "Polish HF", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138313"], ["CP32", "GSM3138314", "Polish HF", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138314"], ["CP35", "GSM3138315", "Hereford", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138315"], ["CP36", "GSM3138316", "Hereford", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138316"], ["CP37", "GSM3138317", "Hereford", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138317"], ["CP38", "GSM3138318", "Hereford", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138318"], ["CP39", "GSM3138319", "Hereford", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138319"], ["CP40", "GSM3138320", "Hereford", "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3138320"]], "row_count": 19, "column_count": 4, "numeric_cells": 54, "header_rows": 1, "locator": "section[5]/table-wrap[1]#vetsci-06-00036-t002"}}, {"id": "asset:table:pmid:30934933:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:88e39165b32a1e9078fadc4ea25b46a6478185e97e764e01187b10157e7c5648", "bytes": 1979, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#vetsci-06-00036-t003", "version": null, "note": "List of selected DE gene-transcripts for the validation of RNA-seq experiment by qRT-PCR.", "structure": {"pmcid": "PMC6631511", "section_index": 8, "section_title": "2.6. Validation of DE Gene-Transcripts Using RT-PCR/qPCR", "row_count": 15, "column_count": 9}, "table": {"label": "Table 3", "caption": "List of selected DE gene-transcripts for the validation of RNA-seq experiment by qRT-PCR.", "rows": [["Gene Full Name", "Calpain 11", "Calpain 2", "Insulin Like Growth Factor Binding Protein 1", "Insulin Like Growth Factor Binding Protein 2", "Insulin Like Growth Factor I", "Insulin Like Growth Factor Binding Protein, Acid Labile Subunit (IGFALS)", "Somatotropin", "Family with Sequence Similarity 13 Member A"], ["Gene symbol", "CAPN11", "CAPN2", "IGFBP1", "IGFBP2", "IGF-I", "IGFALS", "GH", "FAM13A"], ["Forward primer", "GAACCTTCAA", "CCAACATTGA", "TAGCGTAAAT", "GTGCAAGAT", "GAGTGCAGG", "CAGGTAACA", "AGCCATCTG", "CCTTTCTATTT"], ["CTGTCAAGCG", "CGAGATTGACA", "TGGCAGGGAA", "GTCTCTGAACG", "AAACAAGAACT", "AGCTGGCCTA", "TTGTTTGCCC", "GAGCAGTGCC"], ["Reverse primer", "TTGAGTCGGT", "ATTGTCTGCA", "ACACTGTGTT", "TGCTCGTTGT", "TTGGTAGGT", "GTGGTCCAG", "TATTAGGAAA", "CTGAGTCCTCT"], ["TCTGGCTTAT", "ACTCAAAGGC", "CCCATGTTTG", "AGAAGAGATGA", "CTTCTGGTGTT", "GTAGAGTTTCT", "GGACAGTGGGAG", "GAACTTTGG"], ["Ensembl Gene ID", "ENSBTAG000", "ENSBTAG000", "ENSBTAG00", "ENSBTAG00", "ENSBTAG00", "ENSBTAG000", "ENSBTAG00", "ENSBTAG000"], ["21066", "12778", "46768", "5596", "11082", "33299", "17220", "11187"], ["Ensembl Transcript ID", "ENSBTAT00", "ENSBTAT00", "ENSBTAT00", "ENSBTAT000", "ENSBTAT00", "ENSBTAT000", "ENSBTAT00", "ENSBTAT00"], ["4690", "47532", "64194", "7349", "14713", "47326", "22885", "14855"], ["BTA chromosome", "23", "16", "4", "2", "5", "25", "19", "6"], ["Gene Start (bp)", "17,807,298", "27,781,671", "76,720,883", "1.05E + 08", "66,532,877", "1,366,647", "48,768,618", "37,355,568"], ["Gene End (bp)", "17,820,479", "27,840,009", "76,725,301", "1.05E + 08", "66,604,734", "1,368,479", "48,772,014", "37,457,493"], ["Transcript Start (bp)", "17,807,298", "27,781,671", "76,720,883", "1.05E + 08", "66,532,877", "1,366,647", "48,768,618", "37,355,568"], ["Transcript length", "2675", "3179", "917", "1141", "862", "1833", "817", "5125"]], "row_count": 15, "column_count": 9, "numeric_cells": 79, "header_rows": 1, "locator": "section[8]/table-wrap[1]#vetsci-06-00036-t003"}}], "gaps": ["asset:data:geo:GSE114233 not downloaded", "asset:data:geo:GSE114233 licence not read", "asset:data:geo:SRS1296732 not downloaded", "asset:data:geo:SRS1296732 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "deseq2", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "DEseq"}}, {"id": "method-2", "family": "differential_expression", "specific": "edger", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "EdgeR"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: deseq2."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["SRS1296732", "GSE114233"], "resolved_accessions": ["GSE114233"], "statements": ["The FASTQ sequencing data of this present study were deposited in the NCBI database under submission number: SRS1296732 (http://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=312148) [31] and the gene expression data of investigated animals (n = 18) were deposited in the NCBI database under submission number: GSE 114233 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114233) and summarized in Table 2."], "basis": "The paper names GSE114233 in NCBI Sequence Read Archive (SRA) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:30934933", "data:geo:GSE114233", "asset:table:pmid:30934933:1", "asset:table:pmid:30934933:2", "asset:table:pmid:30934933:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE114233"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:43:22Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 51086, "completion_tokens": 2398, "cached_tokens": 17160}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:30934933", "type": "paper", "label": "pmid:30934933"}, {"id": "source:pmid:30934933", "type": "manuscript", "label": "PMID 30934933 full text"}, {"id": "data:geo:GSE114233", "type": "dataset", "label": "GEO GSE114233"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30934933", "type": "paper", "label": "pmid:30934933"}, {"id": "source:pmid:30934933", "type": "manuscript", "label": "PMID 30934933 full text"}, {"id": "data:geo:GSE114233", "type": "dataset", "label": "GEO GSE114233"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30934933", "type": "extraction", "used": ["source:pmid:30934933"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE114233", "type": "accession_resolution", "used": ["data:geo:GSE114233"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:30934933", "parent_hash": "sha256:af7adc181fdd5da9caeea9ddfd14c54cc82c53de564a667761eff31cd1e029f6", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE114233 licence not read", "asset:data:geo:GSE114233 not downloaded", "asset:data:geo:SRS1296732 licence not read", "asset:data:geo:SRS1296732 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["iver Transcriptome among Cattle Breeds Using RNA-seq.", "values were consistent to those obtained by RNA-seq, and significantly correlated between the qu", "tive reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson's r > 0.90). Our results provide ne", ", we comparatively analyzed the bovine liver transcriptome of dairy (Polish Holstein Friesian (HF); n ="], "order_basis": "paper_text_order:29", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["the quantitative reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson's r > 0.90). Our resul", "e quantitative reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson's r > 0.90). Our resul", "eq, and significantly correlated between the quantitative reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson's r > 0.90).", "was made by quantitation of libraries using qPCR according to the Illumina sequencing library"], "order_basis": "paper_text_order:2212", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["DEseq"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}