Differentially abundant proteins associated with heterosis in the primary roots of popcorn.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29758068", "kind": "science-record", "revision": 8, "content_hash": "sha256:da8183a7584384e8f6d3367bdb78325ce031f6501204e442462100a2a6740e4a", "created_at": "2026-11-01T15:40:33Z", "updated_at": "2026-11-01T22:43:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Differentially abundant proteins associated with heterosis in the primary roots of popcorn.", "doi": "10.1371/journal.pone.0197114", "pmid": "29758068", "authors": ["Mathias F Rockenbach", "Caio C G Corrêa", "Angelo S Heringer", "Ismael L J Freitas", "Claudete Santa-Catarina", "Antônio T do Amaral-Júnior", "Vanildo Silveira"], "journal": "PloS one", "year": 2018, "abstract": "Although heterosis has significantly contributed to increases in worldwide crop production, the molecular mechanisms regulating this phenomenon are still unknown. In the present study, we used a comparative proteomic approach to explore hybrid vigor via the proteome of both the popcorn L54 ♀ and P8 ♂ genotypes and the resultant UENF/UEM01 hybrid cross. To analyze the differentially abundant proteins involved in heterosis, we used the primary roots of these genotypes to analyze growth parameters and extract proteins. The results of the growth parameter analysis showed that the mid- and best-parent heterosis were positive for root length and root dry matter but negative for root fresh matter, seedling fresh matter, and protein content. The comparative proteomic analysis identified 1343 proteins in the primary roots of hybrid UENF/UEM01 and its parental lines; 220 proteins were differentially regulated in terms of protein abundance. The mass spectrometry proteomic data are available via ProteomeXchange with identifier \"PXD009436\". A total of 62 regulated proteins were classified as nonadditive, of which 53.2% were classified as high parent abundance (+), 17.8% as above-high parent abundance (+ +), 16.1% as below-low parent abundance (- -), and 12.9% as low parent abundance (-). A total of 22 biological processes were associated with nonadditive proteins; processes involving translation, ribosome biogenesis, and energy-related metabolism represented 45.2% of the nonadditive proteins. Our results suggest that heterosis in the popcorn hybrid UENF/UEM01 at an early stage of plant development is associated with an up-regulation of proteins related to synthesis and energy metabolism.", "claims": [{"id": "claim-method", "statement": "Based on the results of the ANOVA (p<0.05), differentially abundant proteins were considered up-regulated if their fold change (FC) was greater than 1.5 and down-regulated if their FC was less than 0.667.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29758068", "locator": "sections[8] \"Protein identification and functional classification\" paragraph 2", "quote": "Based on the results of the ANOVA (p<0.05), differentially abundant proteins were considered up-regulated if their fold change (FC) was greater than 1.5 and down-regulated if their FC was less than 0.667."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomic data are available via ProteomeXchange with identifier “PXD009436”.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29758068", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The mass spectrometry proteomic data are available via ProteomeXchange with identifier “PXD009436”."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used ANOVA and t-tests to identify differentially abundant and nonadditively regulated proteins, found that early heterosis was associated with increased abundance of proteins related to synthesis and energy metabolism, and deposited the mass-spectrometry proteomic data in ProteomeXchange under identifier “PXD009436”.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:29758068"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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"8.2", "-23.9", "2.4", "-22.2", "-7.2"]], "row_count": 7, "column_count": 6, "numeric_cells": 32, "header_rows": 1, "locator": "section[10]/table-wrap[1]#pone.0197114.t001"}}, {"id": "asset:table:pmid:29758068:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:88d46461096ee78b59d4589875a5af1c8611e157e2e914c64aa4602f859675c5", "bytes": 9330, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#pone.0197114.t002", "version": null, "note": "Nonadditively regulated proteins identified in the primary roots of the popcorn hybrid UENF/UEM01 at the 5th DAS.", "structure": {"pmcid": "PMC5951555", "section_index": 11, "section_title": "Proteomic profiles", "row_count": 64, "column_count": 12}, "table": {"label": "Table 2", "caption": "Nonadditively regulated proteins identified in the primary roots of the popcorn hybrid UENF/UEM01 at the 5th DAS.", "rows": [["Accession", "Protein Description", "Peptide Count", "Confidence Score", "Normalized Total Ion Count (TIC)", "Fold ChangeHybrid/Mean Parental Lines", "T-test Value", "Nonadditive Class*", "Biological Process", "Reference"], ["Mean L54", "Mean P8", "Mean Hybrid"], ["C4J5M2", "AP-3 complex subunit delta", "3", "13.5", "12722.8", "11454.0", "19641.4", "1.62", "0.030", "(+)", "Vesicle-mediated Transport", ""], ["B4FID1", "40S ribosomal S17-4", "2", "19.9", "9047.2", "7494.7", "15426.1", "1.87", "0.004", "(+)", "Translation", "Marcon et al.2013"], ["B6T1F1", "60S ribosomal L19-3", "4", "43.9", "1318.4", "1689.8", "2299.6", "1.53", "0.026", "(+)", "Translation", "Marcon et al.2013"], ["B6T379", "40S ribosomal S15", "2", "20.0", "23540.8", "23639.4", "38381.3", "1.63", "0.019", "(+)", "Translation", "Guo et al.2013"], ["B4FNW1", "triosephosphate cytosolic", "14", "138.8", "20680.5", "14836.1", "34631.0", "1.95", "0.041", "(+)", "Small Molecule Metabolic Process", 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD009436"], "resolved_accessions": ["PXD009436"], "statements": ["The mass spectrometry proteomic data are available via ProteomeXchange with identifier “PXD009436”."], "basis": "The paper names PXD009436 in ProteomeXchange Consortium and the accession resolves in the repository. 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The mass spectrometry proteomic data are available via ProteomeXchange with"], "order_basis": "paper_text_order:255", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Based on the results of the ANOVA (p<0.05), differentially abundant proteins were considered up-regulated if their fold change (FC) was greater than 1.5 and down-regulated if their FC was less than 0.667."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}