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Cultivated oats (\n                    <jats:italic>Avena sativa<\/jats:italic>\n                    L.) are categorized into hulled and naked types based on lemma morphology, and naked oats possess superior processing and nutritional quality. Here, we decipher the genetic architecture of 666 globally collected oat accessions via population structure, genetic diversity and gene flow analyses, revealing genetic admixture and lineage differentiation driven by geographic isolation and divergent selection. Population evolutionary analyses indicate that Chinese naked oat landraces diverge from the Central and Eastern Eurasian hulled oats 6124 generations ago and undergo secondary domestication in North China under strong artificial selection. Multi-environment phenotyping of 19 traits from 2010 to 2021 reveals that hulled oats outperform in grain size and yield, while naked oats have higher crude protein (+25.5%) and crude fat (+16.9%). Genome-wide scans identify 883 directional selection genes related to nutrient metabolism, whereas balancing selection on carbon metabolism genes restricts yield potential. Furthermore, integrated GWAS identify three favorable haplotypes associated with favorable agronomic and quality traits, providing key genetic resources for oat molecular breeding.\n                  <\/jats:p>","DOI":"10.1038\/s42003-026-10626-w","type":"journal-article","created":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T09:45:54Z","timestamp":1783763154000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Investigation of naked oat (Avena sativa ssp. nuda) domestication provides insights into yield and nutritional gaps in oats"],"prefix":"10.1038","volume":"9","author":[{"given":"Xiaolong","family":"Dong","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaiquan","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zilin","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6463-8180","authenticated-orcid":false,"given":"Wubishet A.","family":"Bekele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinkun","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laichun","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaotian","family":"Liang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinyi","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunlong","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongjie","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xingjia","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuzhen","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-7454-7699","authenticated-orcid":false,"given":"Ruizhen","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9523-2319","authenticated-orcid":false,"given":"Changzhong","family":"Ren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3304-3301","authenticated-orcid":false,"given":"Yuanying","family":"Peng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,11]]},"reference":[{"key":"10626_CR1","doi-asserted-by":"crossref","first-page":"1936","DOI":"10.1126\/science.1123604","volume":"311","author":"C Li","year":"2006","unstructured":"Li, C., Zhou, A. & Sang, T. 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Wild and Cultivated Oats, Section Euavena Griseb (All-Union Institute of Applied Botany and New Cultures Press, 1930)."},{"key":"10626_CR5","unstructured":"Food and Agriculture Organization of the United Nations. FAOSTAT: Crop Production Dataset (QCL). https:\/\/www.fao.org\/faostat\/en\/#data\/QCL (Accessed 20 February 2022)."},{"key":"10626_CR6","unstructured":"Baum, B. R. Oats: Wild and Cultivated. A Monograph of the Genus Avena L. (Poaceae) (Department of Agriculture Press, 1977."},{"key":"10626_CR7","unstructured":"Frey, K. J. National Plant Breeding Study I: Human and Financial Resources Devoted to Plant Breeding Research and Development in the United States in 1994 (No. 98) (Iowa State University Press, 1996)."},{"key":"10626_CR8","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1111\/j.1469-8137.1996.tb01141.x","volume":"134","author":"HJ Ougham","year":"1996","unstructured":"Ougham, H. J., Latipova, G. & Valentine, J. Morphological and biochemical characterization of spikelet development in naked oats (Avena sativa). N. Phytol. 134, 5\u201312 (1996).","journal-title":"N. Phytol."},{"key":"10626_CR9","doi-asserted-by":"publisher","first-page":"662","DOI":"10.1007\/s13197-013-1072-1","volume":"52","author":"P Rasane","year":"2015","unstructured":"Rasane, P., Jha, A., Sabikhi, L., Kumar, A. & Unnikrishnan, V. S. Nutritional advantages of oats and opportunities for its processing as value added foods \u2013 a review. J. Food Sci. Technol. 52, 662\u2013675 (2015).","journal-title":"J. Food Sci. Technol."},{"key":"10626_CR10","doi-asserted-by":"crossref","first-page":"510","DOI":"10.2134\/agronj1994.00021962008600030010x","volume":"86","author":"P Peltonen-Sainio","year":"1994","unstructured":"Peltonen-Sainio, P. Yield component differences between naked and conventional oat. Agron. J. 86, 510\u2013513 (1994).","journal-title":"Agron. 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