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. 2017 Aug 9;7:7635. doi: 10.1038/s41598-017-06742-7

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© The Author(s) 2017

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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GWAS results. (a) Total original phenotype variance of F1 hybrids explained by QTLs identified in F1 GWAS. (b) Total BPaV variance explained by QTLs identified in BPaV GWAS. (c) Total SCA variance explained by QTLs identified in SCA GWAS. (d) Frequency distribution of QTLs identified in F1 GWAS, BPaV GWAS, and SCA GWAS based on the variance explained by each QTL. The vertical dashed lines represent the average variance explained for the three QTL groups. (e,f) Manhattan plots of HD GWAS results for the CS dataset (E) and LS dataset (F). (g,h) Manhattan plots of SNPP GWAS results for the CS dataset (g) and LS dataset (h). Y-axis, RMIP in resample GWAS; red dashed lines, shared QTLs among different GWAS categories; open symbols, GWAS signals disappeared when using corresponding original F1 hybrid phenotypes as covariates.