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

Vilnis Šķipars (Coresponding Author), Elza Rauda, Ilze Snepste, Baiba Krivmane, Dainis Rungis

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)


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 (R2 TLP3′ = 0.88; R2 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 (R2 = 0.90).

Original languageEnglish
Article number127
Number of pages13
JournalTree Genetics and Genomes
Issue number6
Publication statusPublished - 1 Dec 2017
Externally publishedYes


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

Field of Science*

  • 1.6 Biological sciences
  • 4.1 Agriculture, Forestry, and Fisheries

Publication Type*

  • 1.1. Scientific article indexed in Web of Science and/or Scopus database


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