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Essential oil compounds, including atractylodin, hinesol, \u03b2-eudesmol, and atractylon, are key determinants of crude drug quality. Conventional breeding of A. lancea is difficult because of its perennial growth. In this study, a chromosome-scale reference genome of A. lancea (4.79 Gb) was generated, and genome-wide association studies (GWAS) and genomic predictions of essential oil compounds were conducted to explore the potential for genome-assisted breeding. Genotyping of 480 lines using double-digest restriction-site\u2013associated DNA-sequencing yielded 29,136 high-quality SNPs. All the compounds showed high genomic heritability (h2 = 0.758\u20130.915), indicating strong genetic control. Despite the high genomic heritability, GWAS detected only one weak association with atractylon and no significant loci for the three compounds. However, genomic prediction achieved moderate to high accuracy across multiple models, particularly the ridge regression, genomic best linear unbiased prediction, and Bayesian approaches. The prediction accuracy, measured as the Pearson correlation coefficient between the observed and predicted values, exceeded 0.6 for all four essential oil compounds. These results demonstrate the efficacy of genomic selection for improving essential oil compound levels in A. lancea and provide a foundation for genome-assisted breeding of medicinal plants with long breeding cycles.<\/jats:p>","DOI":"10.1093\/dnares\/dsag014","type":"journal-article","created":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T11:52:22Z","timestamp":1788954742000},"source":"Crossref","is-referenced-by-count":0,"title":["Chromosome-scale genome assembly and genomic prediction of essential oil compounds in\n                    <i>Atractylodes lancea<\/i>\n                    for genomics-assisted breeding"],"prefix":"10.1093","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4861-0612","authenticated-orcid":false,"given":"Takahiro","family":"Tsusaka","sequence":"first","affiliation":[{"name":"Botanical Raw Materials Cultivation Technology Development Department, Tsumura & Co., Ami , Ibaraki 300-1192 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7880-6221","authenticated-orcid":false,"given":"Kenta","family":"Shirasawa","sequence":"additional","affiliation":[{"name":"Kazusa DNA Research Institute Department of Frontier Research and Development, , Chiba 292-0818 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-2895-5890","authenticated-orcid":false,"given":"Yunjia","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong , Shatin ,","place":["Hong Kong"]},{"name":"The State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong , Shatin ,","place":["Hong Kong"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0489-3884","authenticated-orcid":false,"given":"Ting-Fung","family":"Chan","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong , Shatin ,","place":["Hong Kong"]},{"name":"The State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong , Shatin ,","place":["Hong Kong"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5217-1800","authenticated-orcid":false,"given":"Hiroki","family":"Yamaji","sequence":"additional","affiliation":[{"name":"Botanical Raw Materials Cultivation Technology Development Department, Tsumura & Co., Ami , Ibaraki 300-1192 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9555-5054","authenticated-orcid":false,"given":"Sachiko","family":"Isobe","sequence":"additional","affiliation":[{"name":"Kazusa DNA Research Institute Department of Frontier Research and Development, , Chiba 292-0818 ,","place":["Japan"]},{"name":"Graduate School of Agricultural and Life Sciences, University of Tokyo , Tokyo 113-8657 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,10]]},"reference":[{"key":"2026092404083854900_dsag014-B1","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1248\/bpb.29.315","article-title":"Identification of medicinal Atractylodes based on ITS sequences of nrDNA","volume":"29","author":"Shiba","year":"2006","journal-title":"Biol Pharm Bull."},{"key":"2026092404083854900_dsag014-B2","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1248\/yakushi1947.103.4_442","article-title":"Studies of crude drugs about its origin, process and quality. 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