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Gene Expression Analysis and Polymorphism Discovery to Investigate Drought Responsive System in Tropical Maize
Plant Breed. Biotech. 2018;6:354-362
Published online December 1, 2018
© 2018 Korean Society of Breeding Science.

Kitae Song1, Hyo Chul Kim1, Kyung-Hee Kim1, Jun-Cheol Moon2, Jae Yoon Kim3, Sang-Kyu Lee4, Byung-Moo Lee1*

1Department of Life Science, Dongguk University-Seoul, Seoul 10326, Korea
2Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea
3Department of Plant Resources, Kongju National University, Yesan 32439, Korea
4Asia-Seed Company, Limited, Seoul 05855, Korea
Correspondence to: Byung-Moo Lee, bmlee@dongguk.edu, Tel: +82-31-961-5130, Fax: +82-31-961-5107
Received August 28, 2018; Revised September 21, 2018; Accepted September 22, 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
Maize has high food and industrial value, whereas has difficulties in research because of their complex and huge size genome. Nested association mapping (NAM) was constructed to better understand maize genetics. However, most studies were conducted using the reference genome B73, and only a few studies were conducted on tropical maize. Ki3, one of the founder lines of the NAM population, is a tropical maize. We analyzed the genetic characteristics of Ki3 by using RNA sequencing and bioinformatics tools for various genetic studies. As results, a total of 30,526 genes were expressed, and expression profile were constructed. A total of 1,558 genes were differentially expressed in response to drought stress, and 513 contigs of them come from de novo assemblies. In addition, high-density polymorphisms including 464,930 single nucleotide polymorphisms (SNPs), 21,872 multiple nucleotide polymorphisms (MNPs) and 93,313 insertions and deletions (InDels) were found compared to reference genome. Among them, 15.0 % of polymorphisms (87,838) were passed non-synonymous test which could alter amino acid sequences. The variants have 66,550 SNPs, 5,853 MNPs, and 14,801 InDels, also proportion of homozygous type was higher than heterozygous. These variants were found in a total of 15,643 genes. Of these genes, 637 genes were found as differentially expressed genes (DEGs) under drought stress. Our results provide a genome-wide analysis of differentially expressed genes and information of variants on expressed genes of tropical maize under drought stress. Further characterization of these changes in genetic regulation and genetic traits will be of great value for improvement of maize genetics.
Keywords : Maize, Polymorphisms, Drought, Expression profiling


December 2018, 6 (4)
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