{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T14:06:38Z","timestamp":1788876398263,"version":"build-2803163510"},"reference-count":47,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T00:00:00Z","timestamp":1788825600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100017666","name":"Agricultural Variety Improvement Project of Shandong Province","doi-asserted-by":"publisher","award":["2024LZGC010"],"award-info":[{"award-number":["2024LZGC010"]}],"id":[{"id":"10.13039\/501100017666","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017666","name":"Agricultural Variety Improvement Project of Shandong Province","doi-asserted-by":"publisher","award":["2024LZGC030"],"award-info":[{"award-number":["2024LZGC030"]}],"id":[{"id":"10.13039\/501100017666","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Modern Agro-industry Technology Research System of Shandong Province","award":["SDAIT-28-01"],"award-info":[{"award-number":["SDAIT-28-01"]}]},{"name":"Modern Agro-industry Technology Research System of Shandong Province","award":["SDAIT-28-06"],"award-info":[{"award-number":["SDAIT-28-06"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Curr. Issues Mol. Biol.","CIMB"],"abstract":"<jats:p>Glycosyltransferases (GTs) are key enzymes that catalyze the transfer of sugar moieties to diverse acceptor molecules and play important roles in a wide range of biological processes, including plant growth, development, and environmental adaptation. However, glycosyltransferase family 4 (GT4), the second-largest GT family, remains poorly characterized in soybean. In this study, we identified 60 GT4 family members in the soybean genome based on sequence information from the CAZy database and systematically characterized their phylogenetic relationships, genomic organization, and expression patterns by integrating genomic and multidimensional transcriptomic data. Furthermore, using a previously established soybean ethyl methanesulfonate (EMS) mutant population, we identified GmSPS8 as a candidate gene potentially involved in the regulation of seed weight. Notably, natural variation and haplotype analyses revealed that GmSPS8 is located within a genomic region subject to domestication selection, suggesting its potential involvement in the evolutionary selection of soybean seed size. In sum, we systematically characterized the soybean GT4 gene family and identified GmSPS8 as a potential domestication-associated candidate gene for seed weight regulation, providing new insights into the functional characterization of soybean GT4 family members and the identification and utilization of genes associated with soybean yield-related traits.<\/jats:p>","DOI":"10.3390\/cimb48090918","type":"journal-article","created":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T12:51:48Z","timestamp":1788871908000},"page":"918","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome-Wide Identification of the Glycosyltransferase 4 Family and Characterization of GmSPS8 Associated with Seed Weight in Soybean"],"prefix":"10.3390","volume":"48","author":[{"given":"Hongxiang","family":"Cao","sequence":"first","affiliation":[{"name":"College of Agronomy, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-0055-4353","authenticated-orcid":false,"given":"Luqi","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Agronomy, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Kaibo","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Agronomy, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"}]},{"given":"Su","family":"Ma","sequence":"additional","affiliation":[{"name":"College of Agronomy, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"formal-analysis","vocabulary":"credit"}]},{"given":"Miao","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Agronomy, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Yongjing","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Agronomy, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0530-7987","authenticated-orcid":false,"given":"Yongbin","family":"Zhuang","sequence":"additional","affiliation":[{"name":"College of Agronomy, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"formal-analysis","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5508-9941","authenticated-orcid":false,"given":"Baoyin","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Agronomy, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Jinfei","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Agronomy, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Dajian","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Agronomy, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7898-800X","authenticated-orcid":false,"given":"Xiaoming","family":"Li","sequence":"additional","affiliation":[{"name":"College of Agronomy, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1146\/annurev.biochem.76.061005.092322","article-title":"Glycosyltransferases: Structures, functions, and mechanisms","volume":"77","author":"Lairson","year":"2008","journal-title":"Annu. Rev. Biochem."},{"key":"ref_2","first-page":"1","article-title":"Enzyme nomenclature. Recommendations 1992. Supplement 4: Corrections and additions","volume":"250","author":"Barrett","year":"1997","journal-title":"Eur. J. Biochem."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"8350","DOI":"10.1039\/C5CS00600G","article-title":"Glycosyltransferases: Mechanisms and applications in natural product development","volume":"44","author":"Liang","year":"2015","journal-title":"Chem. Soc. Rev."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/S0022-2836(03)00307-3","article-title":"An evolving hierarchical family classification for glycosyltransferases","volume":"328","author":"Coutinho","year":"2003","journal-title":"J. Mol. Biol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1042\/bj3260929u","article-title":"A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities","volume":"326","author":"Campbell","year":"1997","journal-title":"Biochem. J."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"D571","DOI":"10.1093\/nar\/gkab1045","article-title":"The carbohydrate-active enzyme database: Functions and literature","volume":"50","author":"Drula","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1146\/annurev.cellbio.22.022206.160206","article-title":"Cellulose synthesis in higher plants","volume":"22","author":"Somerville","year":"2006","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Wang, Y., Li, H., Chang, J., Zhang, Y., Li, J., Jia, S., and Shi, Y. (2024). Genome-wide identification and analysis of glycosyltransferases in Colletotrichum graminicola. Microorganisms, 12.","DOI":"10.3390\/microorganisms12122551"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1093\/pcp\/pct173","article-title":"UGT74D1 catalyzes the glucosylation of 2-oxindole-3-acetic acid in the auxin metabolic pathway in Arabidopsis","volume":"55","author":"Tanaka","year":"2014","journal-title":"Plant Cell Physiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"46629","DOI":"10.1038\/srep46629","article-title":"Differences in salicylic acid glucose conjugations by UGT74F1 and UGT74F2 from Arabidopsis thaliana","volume":"7","author":"Iancu","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"101261","DOI":"10.1016\/j.xplc.2025.101261","article-title":"Two pathogen-inducible UDP-glycosyltransferases, UGT73C3 and UGT73C4, catalyze the glycosylation of pinoresinol to promote plant immunity in Arabidopsis","volume":"6","author":"Zhao","year":"2025","journal-title":"Plant Commun."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1046\/j.1365-313x.2001.01161.x","article-title":"Two glucosyltransferases are involved in detoxification of benzoxazinoids in maize","volume":"28","author":"Hu","year":"2001","journal-title":"Plant J."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-020-16403-5","article-title":"UDP-glucosyltransferase regulates seed size and abiotic stress tolerance associated with metabolic flux redirection in rice","volume":"11","author":"Dong","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1111\/plb.12627","article-title":"Ectopic expression of glycosyltransferase UGT76E11 increases flavonoid accumulation and enhances abiotic stress tolerance in Arabidopsis","volume":"20","author":"Li","year":"2018","journal-title":"Plant Biol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"108182","DOI":"10.1016\/j.biotechadv.2023.108182","article-title":"The function of UDP-glycosyltransferases in plants and their possible use in crop protection","volume":"67","author":"Gharabli","year":"2023","journal-title":"Biotechnol. Adv."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2799","DOI":"10.1093\/jxb\/ers001","article-title":"Over-expression of a putative poplar glycosyltransferase gene, PtGT1, in tobacco increases lignin content and causes early flowering","volume":"63","author":"Wang","year":"2012","journal-title":"J. Exp. Bot."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1111\/tpj.15549","article-title":"Natural variation of ZmCGT1 is responsible for isoorientin accumulation in maize silk","volume":"109","author":"Sun","year":"2022","journal-title":"Plant J."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"18335","DOI":"10.1021\/acs.jafc.4c05068","article-title":"Sucrose phosphate synthase genes in plants: Its role and practice for crop improvement","volume":"72","author":"Li","year":"2024","journal-title":"J. Agric. Food Chem."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Stein, O., and Granot, D. (2019). An Overview of Sucrose Synthases in Plants. Front. Plant Sci., 10.","DOI":"10.3389\/fpls.2019.00095"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Shen, J., Xu, Y., Yuan, S., Jin, F., Huang, Y., Chen, H., Shan, Z., Yang, Z., Chen, S., and Zhou, X. (2023). Genome-Wide Identification of GmSPS Gene Family in Soybean and Expression Analysis in Response to Cold Stress. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms241612878"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"W200","DOI":"10.1093\/nar\/gky448","article-title":"HMMER web server: 2018 update","volume":"46","author":"Potter","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.1016\/j.molp.2023.09.010","article-title":"TBtools-II: A \u201cone for all, all for one\u201d bioinformatics platform for biological big-data mining","volume":"16","author":"Chen","year":"2023","journal-title":"Mol. Plant"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"W39","DOI":"10.1093\/nar\/gkv416","article-title":"The MEME Suite","volume":"43","author":"Bailey","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1435","DOI":"10.1111\/pbi.13844","article-title":"iSoybean: A database for the mutational fingerprints of soybean","volume":"20","author":"Zhang","year":"2022","journal-title":"Plant Biotechnol. J."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"W296","DOI":"10.1093\/nar\/gky427","article-title":"Swiss-model: Homology modelling of protein structures and complexes","volume":"46","author":"Andrew","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2206","DOI":"10.1038\/s41596-024-00968-2","article-title":"Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX","volume":"19","author":"Wang","year":"2024","journal-title":"Nat. Protoc."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/j.gpb.2021.12.002","article-title":"KaKs_calculator 3.0: Calculating selective pressure on coding and non-coding sequences","volume":"20","author":"Zhang","year":"2022","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1016\/j.cell.2024.10.050","article-title":"A spatially resolved multi-omic single-cell atlas of soybean development","volume":"188","author":"Zhang","year":"2025","journal-title":"Cell"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Hao","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Zhang, R., Jia, G., and Diao, X. (2023). geneHapR: An R package for gene haplotypic statistics and visualization. BMC Bioinform., 24.","DOI":"10.1186\/s12859-023-05318-9"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The Variant Call Format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"W216","DOI":"10.1093\/nar\/gkac194","article-title":"DAVID: A web server for functional enrichment analysis and functional annotation of gene lists","volume":"50","author":"Sherman","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1002\/pro.4218","article-title":"PANTHER: Making genome-scale phylogenetics accessible to all","volume":"31","author":"Thomas","year":"2022","journal-title":"Protein Sci."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1805","DOI":"10.1016\/j.cj.2025.08.013","article-title":"Identification of a major QTL and its candidate genes controlling stem strength in soybean via QTL mapping and GWAS","volume":"13","author":"Liu","year":"2025","journal-title":"Crop J."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"6519","DOI":"10.1016\/j.cell.2025.09.007","article-title":"Genomic atlas of 8,105 accessions reveals stepwise domestication, global dissemination, and improvement trajectories in soybean","volume":"188","author":"Zhu","year":"2025","journal-title":"Cell"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1939","DOI":"10.1002\/cbic.201000201","article-title":"Glycosyltransferases and their assays","volume":"11","author":"Wagner","year":"2010","journal-title":"ChemBioChem"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"e2303836120","DOI":"10.1073\/pnas.2303836120","article-title":"Dynamics of cis-regulatory sequences and transcriptional divergence of duplicated genes in soybean","volume":"120","author":"Fang","year":"2023","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Krishnamurthy, P., Tsukamoto, C., and Ishimoto, M. (2020). Reconstruction of the evolutionary histories of UGT gene superfamily in legumes clarifies the functional divergence of duplicates in specialized metabolism. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21051855"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1104\/pp.107.106955","article-title":"Antisense repression of the Medicago truncatula nodule-enhanced sucrose synthase leads to a handicapped nitrogen fixation mirrored by specific alterations in the symbiotic transcriptome and metabolome","volume":"145","author":"Baier","year":"2007","journal-title":"Plant Physiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1094\/MPMI-11-18-0322-R","article-title":"Digalactosyldiacylglycerol synthase gene MtDGD1 plays an essential role in nodule development and nitrogen fixation","volume":"32","author":"Si","year":"2019","journal-title":"Mol. Plant Microbe Interact."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1111\/j.1365-313X.2009.03817.x","article-title":"Arabidopsis NF-YB subunits LEC1 and LEC1-LIKE activate transcription by interacting with seed-specific ABRE-binding factors","volume":"58","author":"Yamamoto","year":"2009","journal-title":"Plant J."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1104\/pp.99.2.434","article-title":"Evidence for the involvement of sucrose phosphate synthase in the pathway of sugar accumulation in sucrose-accumulating tomato fruits","volume":"99","author":"Dali","year":"1992","journal-title":"Plant Physiol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1104\/pp.76.2.424","article-title":"Biochemical Basis for Effects of K-Deficiency on Assimilate Export Rate and Accumulation of Soluble Sugars in Soybean Leaves","volume":"76","author":"Huber","year":"1984","journal-title":"Plant Physiol."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Du, Y., Zhao, Q., Chen, L., Yao, X., Zhang, H., Wu, J., and Xie, F. (2020). Effect of Drought Stress during Soybean R2\u2013R6 Growth Stages on Sucrose Metabolism in Leaf and Seed. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21020618"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1007\/BF00194429","article-title":"Sucrose synthase catalyses a readily reversible reaction in vivo in developing potato tubers and other plant tissues","volume":"189","author":"Geigenberger","year":"1993","journal-title":"Planta"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1093\/pcp\/pcj068","article-title":"The three maize sucrose synthase isoforms differ in distribution, localization, and phosphorylation","volume":"47","author":"Duncan","year":"2006","journal-title":"Plant Cell Physiol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1093\/mp\/ssr090","article-title":"Overexpression of a potato sucrose synthase gene in cotton accelerates leaf expansion, reduces seed abortion, and enhances fiber production","volume":"5","author":"Xu","year":"2012","journal-title":"Mol. Plant"}],"container-title":["Current Issues in Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1467-3045\/48\/9\/918\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T13:07:24Z","timestamp":1788872844000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1467-3045\/48\/9\/918"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,8]]},"references-count":47,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["cimb48090918"],"URL":"https:\/\/doi.org\/10.3390\/cimb48090918","relation":{},"ISSN":["1467-3045"],"issn-type":[{"value":"1467-3045","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,8]]}}}