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Development of InDel markers to identify Capsicum disease resistance using whole genome resequencing
J Plant Biotechnol 2018;45:228-235
Published online September 30, 2018
© 2018 The Korean Society for Plant Biotechnology.

Sandeep Karna, Yul-Kyun Ahn

BK21 PLUS Life Science, School of Dentistry, Seoul National University, 101 Daehak-Ro, Jongno-Gu, Seoul 03080, Korea
Correspondence to: e-mail:
Received December 14, 2017; Revised April 9, 2018; Accepted April 9, 2018.
cc This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
In this study, two pepper varieties, PRH1 (powdery mildew resistance line) and Saengryeg (powdery mildew resistance line), were resequenced using next generation sequencing technology in order to develop InDel markers. The genome-wide discovery of InDel variation was performed by comparing the whole-genome resequencing data of two pepper varieties to the Capsicum annuum cv. CM334 reference genome. A total of 334,236 and 318,256 InDels were identified in PRH1 and Saengryeg, respectively. The greatest number of homozygous InDels were discovered on chromosome 1 in PRH1 (24,954) and on chromosome 10 (29,552) in Saengryeg. Among these homozygous InDels, 19,094 and 4,885 InDels were distributed in the genic regions of PRH1 and Saengryeg, respectively, and 198,570 and 183,468 InDels were distributed in the intergenic regions. We have identified 197,821 polymorphic InDels between PRH1 and Saengryeg. A total of 11,697 primers sets were generated, resulting in the discovery of four polymorphic InDel markers. These new markers will be utilized in order to identify disease resistance genotypes in breeding populations. Therefore, our results will make a one-step advancement in whole genome resequencing and add genetic resource datasets in pepper breeding research.
Keywords : chromosome, InDel markers, next generation sequencing, Capsicum disease

September 2018, 45 (3)
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