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Sequence comparison of DEGs and other reported yield related genes for polymorphism

HG Haritha Guttikonda
ST Shashi Rekha Thummala
SA Surekha Agarwal
SM Satendra K Mangrauthia
RR Rajeshwari Ramanan
SN Sarla Neelamraju
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In order to identify polymorphism between KMR3 and IL50-13, we performed BLASTN analysis of 136 DEGs including 78 DEGs of qyld2.1, 25 DEGs of qyld8.2, 12 DEGs showing high fold expression and 21 reported yield related gene sequences against the scaffolds obtained by whole-genome sequencing of the restorers KMR3 (without O. rufipogon) and IL50-13 [IET21943 = RPBio4919-50-13] (with O. rufipogon). The comparison was done by considering the gene sequence corresponding to Nipponbare and its gene sequence was used to obtain the corresponding gene sequences from the scaffolds of the two restorers KMR3 and IL50-13. The orthologous genomic regions were available for all genes analysed. Further we also analyzed the effect of identified SNPs/InDels in the coding region that could affect the expression of the genes showing polymorphism and also the effect of the variants in the 2 kb upstream and downstream regions of the given genes using the SnpEff software (Wayne State University, Detroit MI USA)79. The DEGs along with their gene and chromosome names and their corresponding coordinates are given in Supplementary Table S3.

Copyright and License information: The Author(s) ©2020
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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