Version 1
: Received: 6 March 2020 / Approved: 7 March 2020 / Online: 7 March 2020 (09:03:34 CET)
How to cite:
Kumar, D.; Das, P.K.; Singha, C.; Sarmah, B.K. Mining and Characterizing the SSR Markers for Black Rice Using the Illumina Sequencing Platform. Preprints2020, 2020030119. https://doi.org/10.20944/preprints202003.0119.v1
Kumar, D.; Das, P.K.; Singha, C.; Sarmah, B.K. Mining and Characterizing the SSR Markers for Black Rice Using the Illumina Sequencing Platform. Preprints 2020, 2020030119. https://doi.org/10.20944/preprints202003.0119.v1
Kumar, D.; Das, P.K.; Singha, C.; Sarmah, B.K. Mining and Characterizing the SSR Markers for Black Rice Using the Illumina Sequencing Platform. Preprints2020, 2020030119. https://doi.org/10.20944/preprints202003.0119.v1
APA Style
Kumar, D., Das, P.K., Singha, C., & Sarmah, B.K. (2020). Mining and Characterizing the SSR Markers for Black Rice Using the Illumina Sequencing Platform. Preprints. https://doi.org/10.20944/preprints202003.0119.v1
Chicago/Turabian Style
Kumar, D., Chandra Singha and Bidyut Kumar Sarmah. 2020 "Mining and Characterizing the SSR Markers for Black Rice Using the Illumina Sequencing Platform" Preprints. https://doi.org/10.20944/preprints202003.0119.v1
Abstract
Study in black rice has gain prominence in recent times due to its high nutritive value, curative effect, and anti-oxidant properties. However, its poor agronomic traits, including low yield necessitates the incorporation of the colour-grain trait into elite varieties through plant breeding techniques. SSR markers play an important role in plant identification and breeding. Here, the generation of reference-based transcriptome, annotation of transcriptome datasets, and a large set of simple sequence repeat (SSR) markers derived from Black rice have been described. In all 28664 SSRs were predicted in 34978 (48.59%) expressed transcripts. However, 7068 (20.20%) transcripts were found to have more than one SSR. The identified SSRs were dominated by tri-nucleotide and tetra-nucleotide repeats representing about 54.11% and 33.31% respectively, of total SSRs. Validation of selected markers associated with anthocyanin trait performed across different black rice accessions established the reliability of the process used for mining SSR markers. The SSR markers identified in this study could be used to select varieties with desired traits, and to investigate the genetic mechanism underlying anthocyanin accumulation in the pericarps of black rice. Furthermore, the findings from this study may prove beneficial in future genetic diversity studies, primer development, and selective breeding programs.
Keywords
black rice; transcriptome sequencing; genic SSRs; genetic diversity
Subject
Biology and Life Sciences, Biology and Biotechnology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
