{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T18:15:45Z","timestamp":1788804945886,"version":"build-2803163510"},"reference-count":48,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2022,6,19]],"date-time":"2022-06-19T00:00:00Z","timestamp":1655596800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Key-Area Research and Development Program of Guangdong Province","award":["2020B020220001"],"award-info":[{"award-number":["2020B020220001"]}]},{"name":"Key-Area Research and Development Program of Guangdong Province","award":["No.Y2017PT52"],"award-info":[{"award-number":["No.Y2017PT52"]}]},{"name":"Central Public-Interest Scientific Institution Basal Research Fund","award":["2020B020220001"],"award-info":[{"award-number":["2020B020220001"]}]},{"name":"Central Public-Interest Scientific Institution Basal Research Fund","award":["No.Y2017PT52"],"award-info":[{"award-number":["No.Y2017PT52"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>The stem diameter, an important agronomic trait, affects cucumber growth and yield. However, no genes responsible for cucumber stem diameter have been identified yet. In this study, the stem diameter of 88 cucumber core germplasms were measured in spring 2020, autumn 2020 and autumn 2021, and a genome-wide association study (GWAS) was carried out based on the gene sequence and stem diameter of core germplasms. A total of eight loci (gSD1.1, gSD2.1, gSD3.1, gSD3.2, gSD4.1, gSD5.1, gSD5.2, and gSD6.1) significantly associated with cucumber stem diameter were detected. Of these, five loci (gSD1.1, gSD2.1, gSD3.1, gSD5.2, and gSD6.1) were repeatedly detected in two or more seasons and were considered as robust and reliable loci. Based on the linkage disequilibrium sequences of the associated SNP loci, 37 genes were selected. By further investigating the five loci via analyzing Arabidopsis homologous genes and gene haplotypes, five genes (CsaV3_1G028310, CsaV3_2G006960, CsaV3_3G009560, CsaV3_5G031320, and CsaV3_6G031260) showed variations in amino acid sequence between thick stem lines and thin stem lines. Expression pattern analyses of these genes also showed a significant difference between thick stem and thin stem lines. This study laid the foundation for gene cloning and molecular mechanism study of cucumber stem development.<\/jats:p>","DOI":"10.3390\/genes13061095","type":"journal-article","created":{"date-parts":[[2022,6,19]],"date-time":"2022-06-19T10:14:52Z","timestamp":1655633692000},"page":"1095","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Genome-Wide Association Studies Reveal Candidate Genes Related to Stem Diameter in Cucumber (Cucumis sativus L.)"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3402-3094","authenticated-orcid":false,"given":"Yingying","family":"Yang","sequence":"first","affiliation":[{"name":"Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8035-8656","authenticated-orcid":false,"given":"Shaoyun","family":"Dong","sequence":"additional","affiliation":[{"name":"Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Miao","sequence":"additional","affiliation":[{"name":"Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoping","family":"Liu","sequence":"additional","affiliation":[{"name":"Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuonan","family":"Dai","sequence":"additional","affiliation":[{"name":"Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangsheng","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xingfang","family":"Gu","sequence":"additional","affiliation":[{"name":"Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengping","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,6,19]]},"reference":[{"key":"ref_1","unstructured":"(2022, April 12). FAOSTAT. Available online: http:\/\/www.fao.org\/faostat\/en\/#data."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1146\/annurev-arplant-042817-040422","article-title":"Genetic Regulation of Shoot Architecture","volume":"69","author":"Wang","year":"2018","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_3","first-page":"44","article-title":"Analysis on Heterosis and Combining Ability of Six Mini-cucumber Inbred Lines","volume":"20","author":"Yang","year":"2016","journal-title":"J. Changjiang Veg."},{"key":"ref_4","first-page":"1297","article-title":"Effects of Different LED Light Qualities on Cucumber Seedling Growth and Chlorophyll Fluorescence Parameters","volume":"46","author":"Cao","year":"2013","journal-title":"Sci. Agric. Sin."},{"key":"ref_5","first-page":"590","article-title":"Effect of organic manuring and mineral fertilizer on the growth, yield and economics of soybean [Glycine max (L.) Merrill]","volume":"5","author":"Tomar","year":"2009","journal-title":"Int. J. Agric. Sciences."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"129","DOI":"10.3923\/pjbs.2015.129.134","article-title":"Effect of Bio-fertilizer and Chemical Fertilizer on Growth and Yield in Cucumber (Cucumis sativus) in Green House Condition","volume":"18","author":"Kamil","year":"2015","journal-title":"Pak. J. Biol. Sci."},{"key":"ref_7","first-page":"302","article-title":"Genetic Analysis of Plant Type Traits of Muskmelon","volume":"23","author":"Qi","year":"2015","journal-title":"J. Agric. Biotechnol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"4109","DOI":"10.1038\/s41598-021-83548-8","article-title":"Genetic analysis and QTL mapping of yield and fruit traits in bitter gourd (Momordica charantia L.)","volume":"11","author":"Rao","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_9","first-page":"198","article-title":"Genetic Analysis and QTL Mapping of Important Agronomic Traits of Chieh-qua","volume":"3","author":"Lin","year":"2019","journal-title":"Chin. Hortic. Soc."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1270\/jsbbs.58.453","article-title":"Detecting QTLs for plant architecture traits in cucumber (Cucumis sativus L.)","volume":"58","author":"Li","year":"2008","journal-title":"Breed. Sci."},{"key":"ref_11","unstructured":"Wang, L.J., Yuan, J.J., Zheng, S.L., Kong, F.L., Zhong, L., Cheng, Q.B., and Dou, P. (2016). A crop stem thickness measurement caliper. (CN205102741U[P]), CN Patent."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.hpj.2019.12.002","article-title":"Advance of horticultural plant genomes","volume":"5","author":"Zhang","year":"2019","journal-title":"Hortic. Plant J."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1126\/science.1259215","article-title":"Biosynthesis, regulation, and domestication of bitterness in cucumber","volume":"346","author":"Shang","year":"2014","journal-title":"Science"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1007\/s00122-018-3191-6","article-title":"Novel loci fsd6.1 and Csgl3 regulate ultra-high fruit spine density in cucumber","volume":"132","author":"Bo","year":"2019","journal-title":"Theor. Appl. Genet."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Bo, K., Wei, S., Wang, W., Miao, H., Dong, S., Zhang, S., and Gu, X. (2019). QTL mapping and genome-wide association study reveal two novel loci associated with green flesh color in cucumber. BMC Plant Biol., 19.","DOI":"10.1186\/s12870-019-1835-6"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1038\/s41438-018-0080-8","article-title":"The USDA cucumber (Cucumis sativus L.) collection: Genetic diversity, population structure, genome-wide association studies, and core collection development","volume":"5","author":"Wang","year":"2018","journal-title":"Hortic. Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1007\/s00122-017-3022-1","article-title":"QTL mapping of downy and powdery mildew resistances in PI 197088 cucumber with genotyping-by-sequencing in RIL population","volume":"131","author":"Wang","year":"2018","journal-title":"Theor. Appl. Genet."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Liu, X.P., Lu, H.W., Liu, P.N., Miao, H., Bai, Y.L., Gu, X., and Zhang, S.P. (2020). Identification of novel loci and candidate genes for cucumber downy mildew resistance using GWAS. Plants, 9.","DOI":"10.21203\/rs.3.rs-41473\/v1"},{"key":"ref_19","first-page":"1371","article-title":"Genome-wide association study of powdery mildew resistance of cucumber core germplasms","volume":"48","author":"Jia","year":"2021","journal-title":"Acta Hortic. Sin."},{"key":"ref_20","first-page":"1606","article-title":"Evaluation and genome-wide association study (GWAS) of low-temperature tolerance at seedling stage in cucumber core germplasm","volume":"20","author":"Wang","year":"2019","journal-title":"J. Plant Genet. Resour."},{"key":"ref_21","first-page":"335","article-title":"Evaluation and genome-wide association study (GWAS) of thermotolerance for cucumber at the germination stage","volume":"20","author":"Zhang","year":"2019","journal-title":"J. Plant Genet. Resour."},{"key":"ref_22","first-page":"1223","article-title":"Evaluation and genome-wide association study (GWAS) of seedling thermotolerance in cucumber core germplasm","volume":"20","author":"Wei","year":"2019","journal-title":"J. Plant Genet. Resour."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Lv, J., Qi, J.J., Shi, Q.X., Shen, D., Zhang, S.P., Shao, G.J., Li, H., Sun, Z.Y., Weng, Y.Q., and Shang, Y. (2012). Genetic diversity and population structure of cucumber (Cucumis sativus L.). PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0046919"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1510","DOI":"10.1038\/ng.2801","article-title":"A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity","volume":"45","author":"Qi","year":"2013","journal-title":"Nat. Genet."},{"key":"ref_25","unstructured":"SAS Institute (2012). SAS\/OR 9.3 User\u2019s Guide: Mathematical Programming Examples, SAS Institute."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Yan, Q. (2021). Research on differential privacy decision tree method based on Pearson correlation coefficient. [Master\u2019s Thesis, Guangxi Normal University].","DOI":"10.1109\/ICIST52614.2021.9440604"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1016\/j.molp.2020.06.009","article-title":"TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data","volume":"13","author":"Chen","year":"2020","journal-title":"Mol. Plant"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: A tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1038\/nmeth.1681","article-title":"FaST linear mixed models for genome-wide association studies","volume":"8","author":"Lippert","year":"2011","journal-title":"Nat. Methods"},{"key":"ref_30","unstructured":"Yin, L. (2018). CMplot: Circle Manhattan Plot, GitHub, Inc."},{"key":"ref_31","unstructured":"(2022, April 12). Available online: http:\/\/cucurbitgenomics.org\/."},{"key":"ref_32","unstructured":"(2021, December 09). TAIR. Available online: https:\/\/www.arabidopsis.org\/."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1007\/s00122-018-3074-x","article-title":"Combined fine mapping, genetic diversity, and transcriptome profiling reveals that the auxin transporter gene ns plays an important role in cucumber fruit spine development","volume":"131","author":"Xie","year":"2018","journal-title":"Theor. Appl. Genet."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Jaro\u0161ov\u00e1, J., and Kundu, J.K. (2010). Research article Validation of reference genes as internal control for studying viral infections in cereals by quantitative real-time RT-PCR. BMC Plant Biol., 10.","DOI":"10.1186\/1471-2229-10-146"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"5928","DOI":"10.1128\/jb.170.12.5928-5930.1988","article-title":"Two cellular components, PrlA and SecB, that recognize different sequence determinants are required for efficient protein export","volume":"170","author":"Trun","year":"1989","journal-title":"J. Bacteriol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1105\/tpc.107.057448","article-title":"HD-ZIP III Activity Is Modulated by Competitive Inhibitors via a Feedback Loop in Arabidopsis Shoot Apical Meristem Development","volume":"20","author":"Kim","year":"2008","journal-title":"Plant Cell"},{"key":"ref_37","first-page":"701","article-title":"Cell wall composition and penetration resistance against the fungal pathogen Colletotrichum higginsianum are affected by impaired starch turnover in Arabidopsis mutants","volume":"68","author":"Engelsdorf","year":"2017","journal-title":"J. Exp. Bot."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Schweingruber, F.H., and B\u00f6rner, A. (2018). Stem anatomical structures of major taxonomic units. The Plant Stem, Springer.","DOI":"10.1007\/978-3-319-73524-5"},{"key":"ref_39","unstructured":"Huang, J. (2010). The Comparative Anatomical Observation of Cucumber. [Ph.D. Dissertation, Northeast Agricultural University]."},{"key":"ref_40","unstructured":"Hu, D.Y. (2014). Studies of the Mechanisms of Improvement in the Growth of Autumn Cucumbers and Soil Environment with Aerated Irrigation. [Ph.D. Dissertation, Hunan Agricultural University]."},{"key":"ref_41","first-page":"33","article-title":"Morphology of Cucumber Plants as Influenced by Pranic Agriculture","volume":"11","author":"Jois","year":"2016","journal-title":"Asian J. Agric. Res."},{"key":"ref_42","first-page":"47","article-title":"Effect of compound microbial agents on growth and quality of cucumber in greenhouse","volume":"26","author":"Lv","year":"2020","journal-title":"Anhui Agric. Sci. Bull."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1002\/pmic.200300413","article-title":"Proteomic analysis of changes in the extracellular matrix of arabidopsis cell suspension cultures induced by fungal elicitors","volume":"3","author":"Ndimba","year":"2010","journal-title":"Proteomics"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1105\/tpc.19.00486","article-title":"A Large Transposon Insertion in the stiff1 Promoter Increases Stalk Strength in Maize","volume":"32","author":"Zhang","year":"2020","journal-title":"Plant Cell"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1016\/S0092-8674(00)81703-1","article-title":"Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem","volume":"95","author":"Mayer","year":"1998","journal-title":"Cell"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1111\/jipb.13185","article-title":"Loss of Gn1a\/OsCKX2 confers heavy-panicle rice with excellent lodging resistance","volume":"64","author":"Tu","year":"2022","journal-title":"J. Integr. Plant Biol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"4807","DOI":"10.1093\/jxb\/erz208","article-title":"Elevated CO2-induced changes in mesophyll conductance and anatomical traits in wild type and carbohydrate-metabolism mutants of Arabidopsis","volume":"70","author":"Mizokami","year":"2019","journal-title":"J. Exp. Bot."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"3005","DOI":"10.1093\/jxb\/eru137","article-title":"Members of the tomato FRUITFULL MADS-box family regulate style abscission and fruit ripening","volume":"65","author":"Wang","year":"2014","journal-title":"J. Exp. Bot."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/13\/6\/1095\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T23:35:13Z","timestamp":1760139313000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/13\/6\/1095"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,19]]},"references-count":48,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2022,6]]}},"alternative-id":["genes13061095"],"URL":"https:\/\/doi.org\/10.3390\/genes13061095","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,19]]}}}