Pipeline publication

[…] owing quantile normalization algorithm. Lines with contrasting phenotypes were selected for expression analysis and the log2 transform value has been shown as heat map using Genesis tool63 with variance of ±3., SNP-seek database64 was used to determine the enrichment of the phenotype discriminating haplotype blocks in each of the different subspecies represented in the complete 3,000 rice genomes panel. The distribution representation of the haplotype blocks in each subspecies was calculated and visualized as percentages., We used reference protein sequences of japonica and indica, adapted from reference genomes of MSU version 7 and gramene database, respectively. We followed the all-to-all blastP of respective protein sequence using NCBI-BLAST-2.2.28+ tool65. A stringent criterion of e-value of e-30 was used in blast alignment of protein sequence within japonica and indica considering their genetic similarity at sub-species level. Subsequently, collinearity was established using MCScanX66 with the threshold of 10 genes constructing each collinear block. On the basis of these outcomes, colinearity was identified and represented in the form of circos67 that further overlaid with genomic region corresponding to cloned and characterized genes regulating grain size and shape and significant genomic region regulating grain width detected as an outcome of GWAS., , Electronic supplementary material , Supplementary information accompanies this paper at 10.1038/s41598-017-12778-6., Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations., The authors thank Dr. Hei Leung, International Rice Research Institute, Philippines for insightful comments and helpful discussions. We acknowledge the Advanced Science and Technology Institute of Department of Science and Te […]

Pipeline specifications

Software tools BLASTP, MCScanX, Circos
Organisms Oryza sativa