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Genomic Variations of Rice Regenerants from Tissue Culture Revealed by Whole Genome Re-Sequencing
Plant Breed. Biotech. 2018;6:426-433
Published online December 1, 2018
© 2018 Korean Society of Breeding Science.

Yang Qin, Kong-Sik Shin, Hee-Jong Woo*, Myung-Ho Lim*

National Academy of Agricultural Science, Rural Development Administration (RDA), Jeonju 54874, Korea
Correspondence to: Hee-Jong Woo, woo001@korea.kr, Tel: +82-63-238-2128, Fax: +82-63-238-3811
Myung-Ho Lim, mlim312@korea.kr, Tel: +82-63-238-4708, Fax: +82-63-238-4704
Received October 17, 2018; Revised November 5, 2018; Accepted November 5, 2018.
This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Plant tissue culture is a technique that has invariably been used for various purposes such as obtaining transgenic plants for crop improvement or functional analysis of genes. However, this process can be associated with a variety of genetic and epigenetic instabilities in regenerated plants, termed as somaclonal variation. In this study, we investigated mutation spectrum, chromosomal distributions of nucleotide substitution types of single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) by whole genome re-sequencing between Dongjin and Nipponbare along with regenerated plants of Dongjin from different induction periods. Results indicated that molecular spectrum of mutations in regenerated rice against Dongjin genome ranged from 9.14 × 10−5 to 1.37 × 10−4 during one- to three-month callus inductions, while natural mutation rate between Dongjin and Nipponbare genomes was 6.97 × 10−4. Non-random chromosome distribution of SNP and InDel was observed in both regenerants and Dongjin genomes, with the highest densities on chromosome 11. The transition to transversion ratio was 2.25 in common SNPs of regenerants against Dongjin genome with the highest C/T transition frequency, which was similar to that of Dongjin against Nipponbare genome.
Keywords : Rice, Tissue culture, Genomic variations, Whole genome re-sequencing


December 2018, 6 (4)
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