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Tree Genetics & Genomes

, 13:127 | Cite as

Assessment of gene copy number variation of Scots pine thaumatin-like protein gene using real-time PCR based methods

  • Vilnis ŠķiparsEmail author
  • Elza Rauda
  • Ilze Snepste
  • Baiba Krivmane
  • Dainis Rungis
Original Article
Part of the following topical collections:
  1. Genome Biology

Abstract

The importance and impact of gene copy number variations (CNVs) as a source of polymorphism in the human and other genomes is being increasingly recognized. Less information is available about CNVs in forest tree species, mainly due to the relative lack of genomic resources. In this study, several methods—quantitative polymerase chain reaction, comparative high-resolution melting curve analysis (C-HRM), and digital polymerase chain reaction (dPCR)—were used to investigate CNV of the Scots pine thaumatin-like protein gene (PsTLP). The obtained results were supported by transcriptome analysis of a single Pinus sylvestris individual and publically available pine genome sequences. Although estimations of gene copy number (CN) varied, depending on the region of the PsTLP gene investigated and the endogenous control utilized, our results revealed the existence of copy number variations of the PsTLP gene between Scots pine individuals. Of 23 individuals analyzed, two had an increased calculated relative CN regardless of the analyzed gene region and endogenous control used, while several samples had increased copy numbers of regions of the PsTLP gene. C-HRM results were highly correlated with qPCR data (R 2 TLP3′  = 0.88; R 2 TLPc  = 0.92), but interpretation of gene CN from C-HRM results proved to be difficult. The results from selected samples analyzed by digital PCR also were highly correlated with qPCR results (R 2 = 0.90).

Keywords

Copy number variation Pinus sylvestris L. qPCR Comparative high resolution melting curve analysis Thaumatin-like protein Heterobasidion annosum 

Notes

Acknowledgments

This study was funded by the Latvian Council of Science project “Investigation of molecular defense mechanisms in Scots pine (Pinus sylvestris L.)” (No. 284/2012). We would like to thank Carl Gunnar Fossdal and Adam Vivian-Smith from Norwegian Institute of Bioeconomy Research for digital PCR.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Data archiving statement

DNA sequences are available in NCBI, and their accession numbers are mentioned in text of the manuscript. The haplotype sequences obtained from the transcriptome have been attached as supplementary text file 1 in FASTA format.

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Genetic Resource CentreLatvian State Forest Research Institute “Silava”SalaspilsLatvia

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