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Development of SNP markers for the identification of apple flesh color based on RNA-Seq data
J Plant Biotechnol 2017;44:372-378
Published online December 31, 2017
© 2017 The Korean Society for Plant Biotechnology.

Se Hee Kim1・Seo Jun Park1・Kang Hee Cho1・Han Chan Lee1・Jung Woo Lee2・In Myung Choi1

1Fruit Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea
2Ginseng Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong 27709, Korea
Correspondence to: S. H. Kim (⊠)
Fruit Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea
e-mail: ezsehee@korea.kr
Received October 21, 2017; Revised November 1, 2017; Accepted November 1, 2017.
cc 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
For comparison of the transcription profiles in apple (Malus domestica L.) cultivars differing in flesh color expression, two cDNA libraries were constructed. Differences in gene expression between red flesh apple cultivar, ‘Redfield’ and white flesh apple cultivar, ‘Granny Smith’ were investigated by next-generation sequencing (NGS). Expressed sequence tag (EST) of clones from the red flesh apple cultivar and white flesh apple cultivar were selected for nucleotide sequence determination and homology searches. High resolution melting (HRM) technique measures temperature induced strand separation of short PCR amplicons, and is able to detect variation as small as one base difference between red flesh apple cultivars and white flesh apple cultivars. We applied high resolution melting (HRM) analysis to discover single nucleotide polymorphisms (SNP) based on the predicted SNP information derived from the apple EST database. All 103 pairs of SNPs were discriminated, and the HRM profiles of amplicons were established. Putative SNPs were screened from the apple EST contigs by HRM analysis displayed specific difference between 10 red flesh apple cultivars and 11 white flesh apple cultivars. In this study, we report an efficient method to develop SNP markers from an EST database with HRM analysis in apple. These SNP markers could be useful for apple marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in apple cultivars.
Keywords : Anthocyanin, Gene expression, Transcription factor, Breeding, Cultivars


December 2017, 44 (4)
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