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While measuring root systems under field conditions is labor\u2010intensive, most quantitative trait loci (QTLs) related to root traits have been detected under artificial conditions. However, QTLs identified under artificial conditions may not always manifest the expected effects that are observed under field conditions. To address this issue, we developed RSApaddy3D, a rapid phenotyping method for rice root systems, using X\u2010ray computed tomography (CT) volumes of soil blocks collected from paddies. RSApaddy3D employs 2\u2010dimensional kernel filters tailored to extract disk\u2010shaped fragments from the CT volumes. Tubular root fragments are expected to exhibit disk\u2010shaped cross\u2010sections along the <jats:italic>x<\/jats:italic>\u2010, <jats:italic>y<\/jats:italic>\u2010, or <jats:italic>z<\/jats:italic>\u2010axes. By applying these filters along all three axes and integrating the results, 3\u2010dimensional root fragments can be accurately extracted. Furthermore, vectorizing the root system enables geometrical removal of the roots of neighboring individuals. We conducted a genome\u2010wide association study (GWAS) of root diameter, number, and growth angle in 133 Japanese rice varieties and detected three QTLs (<jats:italic>qNCR1<\/jats:italic>, <jats:italic>qNCR2<\/jats:italic>, and <jats:italic>qRGA1<\/jats:italic>) that were associated with each trait. This process was completed within 10 person\u2010days from soil monolith collection in the paddy to the GWAS. Without RSApaddy3D, roots would need to be washed from the soil monolith and measured, which is estimated to require &gt;500 person\u2010days. Therefore, RSApaddy3D was approximately 50\u00d7 more labor\u2010saving. In summary, we have demonstrated that RSApaddy3D is an efficient method for phenotyping rice root systems under field conditions.<\/jats:p>","DOI":"10.1111\/tpj.17171","type":"journal-article","created":{"date-parts":[[2024,11,25]],"date-time":"2024-11-25T15:15:02Z","timestamp":1732547702000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Detection of quantitative trait loci for rice root systems grown in paddies based on nondestructive phenotyping using X\u2010ray computed tomography"],"prefix":"10.1111","volume":"121","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6295-2208","authenticated-orcid":false,"given":"Shota","family":"Teramoto","sequence":"first","affiliation":[{"name":"Institute of Crop Sciences National Agriculture &amp; Food Research Organization  Tsukuba Ibaraki 305\u20108602 Japan"},{"name":"Research Center for Agricultural Information Technology National Agriculture &amp; Food Research Organization  Tsukuba Ibaraki 305\u20108517 Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4006-954X","authenticated-orcid":false,"given":"Yusaku","family":"Uga","sequence":"additional","affiliation":[{"name":"Institute of Crop Sciences National Agriculture &amp; Food Research Organization  Tsukuba Ibaraki 305\u20108602 Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,11,25]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep05563"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00438\u2010019\u201001563\u2010x"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12284\u2010017\u20100184\u2010z"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.2134\/asaspecpub50.c9"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-67282-8"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.fcr.2016.04.008"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.3390\/s130302830"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598\u2010020\u201076949\u20108"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11104\u2010015\u20102379\u20107"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/erz383"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102164\u201012\u2010387"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2019.00204"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.plaphy.2024.108386"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.2134\/agronj1955.00021962004700100006x"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11104\u2010019\u201004053\u20106"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2301054120"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010020\u20102649\u20102"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13007\u2010020\u201000612\u20106"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/ers150"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/erad390"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11104\u2010010\u20100675\u20109"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.15226"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2016.01584"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2005911117"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12284\u2010015\u20100049\u20102"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2016.01335"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1111\/jipb.12434"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.1104\/pp.109.1.7"},{"key":"e_1_2_9_30_1","doi-asserted-by":"publisher","DOI":"10.1049\/iet-ipr:20080080"},{"key":"e_1_2_9_31_1","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.2001.05566"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00122\u2010021\u201003819\u2010w"},{"key":"e_1_2_9_33_1","unstructured":"Okuta R. 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