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. 2017 Sep 29;7:12478. doi: 10.1038/s41598-017-12778-6

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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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SNP-based GWAS for grain shape (GS) and association signals detected on chromosome 3, 5, 7, 10 and 11. GS being a derived trait from the ratio of GL to GWi, association signals detected in both GL and GWi were expected to show up in GS. Results showed that the cloned genes for GWi (GW5) and GL (GS3) were detected, and new candidate loci in chromosomes 3, 7 and 11 detected previously in GW and GL GWAS were also detected in japonica (A,D), indica (B,E) and all (C,F combined) panel (left side) in raw (left) and cooked grain (right), respectively. A new locus in chromosome 10 (GS_c10.1) was also detected. Horizontal red and blue line represents the genome-wide significant threshold −log₁₀(P) value of 7 and 5, respectively.