{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T12:39:16Z","timestamp":1786711156056,"version":"build-2736575974"},"reference-count":40,"publisher":"MDPI AG","issue":"16","license":[{"start":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T00:00:00Z","timestamp":1786665600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008118","name":"Natural Science Foundation of Shandong Province","doi-asserted-by":"publisher","award":["ZR2023MC143"],"award-info":[{"award-number":["ZR2023MC143"]}],"id":[{"id":"10.13039\/501100008118","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32372098"],"award-info":[{"award-number":["32372098"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["32372098"],"award-info":[{"award-number":["32372098"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>Spike density is an important component of wheat spike architecture and is determined by the combined effects of spike-axis elongation and spikelet number. In this study, we characterized an ethyl methanesulfonate (EMS)-induced recessive dense-spike mutant, ds, which was obtained from EMS mutagenesis of the wheat cultivar YN21 in 2013 and displays a field-visible compact spike architecture associated with a shortened spike axis, reduced spike internode spacing, and increased spikelet number. Genetic analysis showed that all F1 plants exhibited normal spikes and that segregation in the F2 population fitted a 3:1 ratio, supporting control by a single recessive nuclear gene. Through genome-wide marker-based linkage screening, enlarged-population validation, and fine mapping, ds was delimited to an approximately 864.819 kb interval between ID2B2796 and ID2B7615 on chromosome 2B. This interval contains 11 high-confidence annotated genes, including F-box protein, actin, ubiquitin-conjugating enzyme, ribosomal protein L16, RecX, plant cysteine oxidase, PI4KII\u03b3, and two adjacent GA3OX-family-related genes. Integrated RNA-seq and RT-qPCR analyses showed that the two adjacent GA3OX-family-related genes were expressed in young spikes and exhibited reduced expression in ds-sib relative to WT-sib. These expression data support their retention as plausible, non-exclusive candidates but do not establish causality. Transcriptome analysis further revealed changes in hormone-related pathways, cell-wall organization, carbohydrate metabolism, and transcription-factor regulation. These results provide a reliable genetic basis for further molecular cloning of ds and suggest that altered hormone- and growth-related transcriptional responses may be associated with dense-spike formation in wheat.<\/jats:p>","DOI":"10.3390\/plants15162470","type":"journal-article","created":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T11:57:46Z","timestamp":1786708666000},"page":"2470","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Characterization and Fine Mapping of ds, a Recessive Dense-Spike Mutant Associated with Shortened Spike Axis and Increased Spikelet Number in Wheat"],"prefix":"10.3390","volume":"15","author":[{"given":"Xiangtai","family":"Che","sequence":"first","affiliation":[{"name":"School of Life Sciences, Yantai University, Yantai 264005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuo","family":"Li","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Yantai University, Yantai 264005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaoyuan","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Yantai University, Yantai 264005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-1329-4178","authenticated-orcid":false,"given":"Luxue","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Yantai University, Yantai 264005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Ning","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Yantai University, Yantai 264005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinwei","family":"Feng","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Yantai University, Yantai 264005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Yantai University, Yantai 264005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanhu","family":"Guo","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Yantai University, Yantai 264005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haotong","family":"Sun","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Yantai University, Yantai 264005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingquan","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Yantai University, Yantai 264005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiancheng","family":"Song","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Yantai University, Yantai 264005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Zhao","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Yantai University, Yantai 264005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Yantai University, Yantai 264005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1111\/jipb.12732","article-title":"Genetic pathways controlling inflorescence architecture and development in wheat and barley","volume":"61","author":"Gauley","year":"2019","journal-title":"J. Integr. Plant Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"5182","DOI":"10.1073\/pnas.1815465116","article-title":"Unleashing floret fertility in wheat through the mutation of a homeobox gene","volume":"116","author":"Sakuma","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1105\/tpc.17.00961","article-title":"TEOSINTE BRANCHED1 regulates inflorescence architecture and development in bread wheat (Triticum aestivum)","volume":"30","author":"Dixon","year":"2018","journal-title":"Plant Cell"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1585","DOI":"10.1038\/s41598-020-80473-0","article-title":"Linkage mapping identifies a non-synonymous mutation in FLOWERING LOCUS T (FT-B1) increasing spikelet number per spike in wheat","volume":"11","author":"Brassac","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_5","first-page":"1883","article-title":"Molecular and genetic pathways for optimizing spikelet number, fertility, and yield in wheat","volume":"18","author":"Yuan","year":"2020","journal-title":"Plant Biotechnol. J."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1534\/genetics.105.044727","article-title":"Molecular characterization of the major wheat domestication gene Q","volume":"172","author":"Simons","year":"2006","journal-title":"Genetics"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2071","DOI":"10.1007\/s00122-018-3133-3","article-title":"Phenotypic and genetic analysis of spike and kernel characteristics in wheat reveals long-term genetic trends of grain yield components","volume":"131","author":"Leiser","year":"2018","journal-title":"Theor. Appl. Genet."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1534\/genetics.115.176628","article-title":"The genetic basis of composite spike form in barley and \u2018miracle-wheat\u2019","volume":"201","author":"Poursarebani","year":"2015","journal-title":"Genetics"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1104\/pp.114.250043","article-title":"FRIZZY PANICLE drives supernumerary spikelets in bread wheat","volume":"167","author":"Dobrovolskaya","year":"2015","journal-title":"Plant Physiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"14229","DOI":"10.1038\/s41598-022-18614-w","article-title":"Overexpression of the WAPO-A1 gene increases the number of spikelets per spike in bread wheat","volume":"12","author":"Wittern","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"2296","DOI":"10.1093\/plcell\/koab119","article-title":"Ectopic expression of Triticum polonicum VRT-A2 underlies elongated glumes and grains in hexaploid wheat in a dosage-dependent manner","volume":"33","author":"Adamski","year":"2021","journal-title":"Plant Cell"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1536","DOI":"10.1093\/plphys\/kiac156","article-title":"High expression of the MADS-box gene VRT2 increases the number of rudimentary basal spikelets in wheat","volume":"189","author":"Backhaus","year":"2022","journal-title":"Plant Physiol."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Chen, H., Zhang, X., Xu, S., Song, C., and Mao, H. (2023). TaSPL17s act redundantly with TaSPL14s to control spike development and their elite haplotypes may improve wheat grain yield. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1229827"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1038\/22307","article-title":"\u2018Green revolution\u2019 genes encode mutant gibberellin response modulators","volume":"400","author":"Peng","year":"1999","journal-title":"Nature"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1146\/annurev.arplant.59.032607.092804","article-title":"Gibberellin metabolism and its regulation","volume":"59","author":"Yamaguchi","year":"2008","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1104\/pp.110.161554","article-title":"Gibberellin\u2013GID1\u2013DELLA: A pivotal regulatory module for plant growth and development","volume":"154","author":"Sun","year":"2010","journal-title":"Plant Physiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1242\/dev.087650","article-title":"Gibberellin signaling in plants","volume":"140","author":"Achard","year":"2013","journal-title":"Development"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1146\/annurev-arplant-042809-112308","article-title":"Auxin biosynthesis and its role in plant development","volume":"61","author":"Zhao","year":"2010","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1146\/annurev-cellbio-101011-155741","article-title":"Hormonal interactions in the regulation of plant development","volume":"28","author":"Vanstraelen","year":"2012","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1146\/annurev.arplant.59.032607.092902","article-title":"Molecular basis of plant architecture","volume":"59","author":"Wang","year":"2008","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1038\/ncb2546","article-title":"Brassinosteroid, gibberellin, and phytochrome impinge on a common transcription module in Arabidopsis","volume":"14","author":"Bai","year":"2012","journal-title":"Nat. Cell Biol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"850","DOI":"10.1038\/nrm1746","article-title":"Growth of the plant cell wall","volume":"6","author":"Cosgrove","year":"2005","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2206","DOI":"10.1126\/science.1102765","article-title":"Toward a systems approach to understanding plant cell walls","volume":"306","author":"Somerville","year":"2004","journal-title":"Science"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1104\/pp.110.161240","article-title":"Plant cell walls","volume":"154","author":"Keegstra","year":"2010","journal-title":"Plant Physiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1146\/annurev-arplant-042811-105449","article-title":"Growth control and cell wall signaling in plants","volume":"63","author":"Wolf","year":"2012","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1146\/annurev-arplant-043015-112222","article-title":"Biosynthesis of the plant cell wall matrix polysaccharide xyloglucan","volume":"67","author":"Pauly","year":"2016","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_27","unstructured":"International Wheat Genome Sequencing Consortium (IWGSC) (2018). Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, 361, eaar7191."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1111\/tpj.15289","article-title":"Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly","volume":"107","author":"Zhu","year":"2021","journal-title":"Plant J."},{"key":"ref_29","first-page":"3345","article-title":"GIBBERELLIN 3-OXIDASE genes regulate height and grain size in bread wheat","volume":"76","author":"Phillips","year":"2025","journal-title":"J. Exp. Bot."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1965","DOI":"10.1016\/j.molp.2021.10.006","article-title":"WheatOmics: A platform combining multiple omics data to accelerate functional genomics studies in wheat","volume":"14","author":"Ma","year":"2021","journal-title":"Mol. Plant"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2172","DOI":"10.1104\/pp.15.01667","article-title":"expVIP: A customizable RNA-seq data analysis and visualization platform","volume":"170","author":"Borrill","year":"2016","journal-title":"Plant Physiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1038\/nrg3745","article-title":"Using next-generation sequencing to isolate mutant genes from forward genetic screens","volume":"15","author":"Schneeberger","year":"2014","journal-title":"Nat. Rev. Genet."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Uauy, C., Paraiso, F., Colasuonno, P., Tran, R.K., Tsai, H., Berardi, S., Comai, L., and Dubcovsky, J. (2009). A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheat. BMC Plant Biol., 9.","DOI":"10.1186\/1471-2229-9-115"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"You, J., Liu, H., Wang, S., Luo, W., Gou, L., Tang, H., Mu, Y., Deng, M., Jiang, Q., and Chen, G. (2021). Spike density quantitative trait loci detection and analysis in tetraploid and hexaploid wheat recombinant inbred line populations. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.796397"},{"key":"ref_35","first-page":"11","article-title":"A rapid DNA isolation procedure for small quantities of fresh leaf tissue","volume":"19","author":"Doyle","year":"1987","journal-title":"Phytochem. Bull."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"4321","DOI":"10.1093\/nar\/8.19.4321","article-title":"Rapid isolation of high molecular weight plant DNA","volume":"8","author":"Murray","year":"1980","journal-title":"Nucleic Acids Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: A fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_39","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_40","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: An R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"}],"container-title":["Plants"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/16\/2470\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T12:09:00Z","timestamp":1786709340000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/16\/2470"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,14]]},"references-count":40,"journal-issue":{"issue":"16","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["plants15162470"],"URL":"https:\/\/doi.org\/10.3390\/plants15162470","relation":{},"ISSN":["2223-7747"],"issn-type":[{"value":"2223-7747","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,14]]}}}