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. 2019 Jan 3;10:24. doi: 10.1038/s41467-018-07974-5

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — GWAS analysis of Tos17 and Karma TE families. GWAS analysis for Tos17 (a) and Karma (b) TE families. Manhattan plot represents the log10 p value for each association between the single-nucleotide polymorhisms and the TE insertion (see Methods). TE insertion-SNP association p value >6 are significative. c, d The TE insertion distribution in rice traditional varieties (Fig. 3) reflects a polymorphism in TE copy number along rice varieties, considered a quantitative phenotype