Evaluation of changes in the expression profile of candidate genes in apple rootstockss with a different degree of frost tolerance .
Sylwia Keller-Przybyłkowicz
sylwia.keller@inhort.plZakład Hodowli Roślin Ogrodniczych, Instytut Ogrodnictwa, ul. Konstytucji 3 Maja 1/3, 96‒100 Skierniewice (Poland)
http://orcid.org/0000-0002-3473-9706
Mariusz Lewandowski
Zakład Hodowli Roślin Ogrodniczych, Instytut Ogrodnictwa, ul. Konstytucji 3 Maja 1/3, 96‒100 Skierniewice (Poland)
http://orcid.org/0000-0002-4852-5514
Abstract
The aim of presented study was to identify putative candidate genes associated with apple rootstock winter hardiness. The assessment of changes in expression profile of isolated differentially expressed genes, was performed using two subsequent experiments: RNAseq (based on New Generation Sequencing, NGS) and qRT-PCR (Real Time transcript amplification). In terms of traits of interests two apple rootstocks P 66 (frost tolerant) and M.9 (frost sensitive) were evaluated. As a result of the RNA sequence readings (de novo sequencing, Illumina Solid system), approximately 167 million reads of unique sequences were identified. Finally, fifteen functionally annotated expressed tags, representing different expression profile, were chosen. Selected putative genes coding: structural and integral proteins of cell membranes and cellular vacuoles, transcription factors, proteins regulating intercellular and intracellular transport, C-O and C-N bonds hydrolyzes, and proteins binding macro- and microelements.
In order to verify the type of regulation of the transcriptome sequences obtained in NGS technology, qRT-PCR tests were carried out for the same samples layout. Three of studied sequences, represented identical type of regulation in both RNA-seq and qRT-PCR experiments. The selected genes seems to represent potential candidate sequences (functional molecular markers), enabling the early selection of frost-tolerant apple rootstocks.
Supporting Agencies
Keywords:
expression profile, gene annotation, Malus domestica Borkh., new generation sequencing (NGS), quantitative transcript level (qRT-PCR)References
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Authors
Sylwia Keller-Przybyłkowiczsylwia.keller@inhort.pl
Zakład Hodowli Roślin Ogrodniczych, Instytut Ogrodnictwa, ul. Konstytucji 3 Maja 1/3, 96‒100 Skierniewice Poland
http://orcid.org/0000-0002-3473-9706
Authors
Mariusz LewandowskiZakład Hodowli Roślin Ogrodniczych, Instytut Ogrodnictwa, ul. Konstytucji 3 Maja 1/3, 96‒100 Skierniewice Poland
http://orcid.org/0000-0002-4852-5514
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