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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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Detailed sequence collinearity in chromosomes 3, 5, 7, 10 and 11 between indica and japonica reference genomes. Circos plots showed syntenic relationship of five chromosomes (physical size shown in Mb) within indica and japonica subspecies based on protein sequence alignment. Conserved regions were shown in green while black lines represented the break points. The positions of genes that have been cloned for grain width, length and shape were also labeled in the synteny map. Blue and green boxes represented regions in the respective chromosome where GWAS peaks were detected; blue were for SNP-based GWAS, while green were for those done using indels. It was evident that most of the cloned/characterized genes for grain size and shape were in collinearity between indica and japonica.