Development of SNP markers for the identification of apple flesh color based on RNA-Seq data
2017
Kim, S.H., National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Republic of Korea | Park, S.J., National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Republic of Korea | Cho, K.H., National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Republic of Korea | Lee, H.C., National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Republic of Korea | Lee, J.W., National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Republic of Korea | Choi, I.M., National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Republic of Korea
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.
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