Transcriptome-based single-nucleotide polymorphism markers between Pinus brutia and Pinus halepensis and the analysis of their hybrids

Naomi Houminer, Adi Doron-Faigenboim, Galina Shklar, Amanda R. De La Torre, David Neale, Leonid Korol, Mor Ashkenazi, Yosi Moshe, Joseph Riov, Yagil Osem, Rakefet David-Schwartz

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Natural hybridization occurs in sites where Pinus halepensis Mill. and Pinus brutia Ten. overlap geographically. Studies have shown that these hybrids demonstrate vigorous growth. Currently, there is no efficient method for hybrid identification. In the present study, a transcriptome database that was established from P. halepensis and P. brutia provided 111,388 potential SNP markers for hybrid identification. We selected 295 SNPs that were verified in silico using the Integrative Genomics Viewer (IGV) program. Forty-three SNPs were confirmed in vitro using several methods, including CAPS, HRM, TaqMan, KASP, and direct sequencing. Seven SNPs that were used for genotyping P. brutia trees in three planted sites along the climatic gradient of Israel demonstrated hybrid incidences of 2.5, 6.3, and 9.4%. The trunk volume of the hybrids in these sites was 2.9, 2.4, and 1.2 times larger than that of their P. brutia neighboring trees. Differences among the sites in the hybrid vigorous growth extent might have resulted from several factors, including genetic source, stand age, thinning history, and site conditions. However, the overall vigorous growth of the hybrids that was more pronounced in the arid site highlights the potential of interspecific hybridization as a means for improving the drought resistance of forest trees. This work provides a reliable SNP database for the identification of P. brutia × P. halepensis hybrids for the potential utilization of these hybrids to confront changes in climate.

Original languageEnglish (US)
Article number14
JournalTree Genetics and Genomes
Issue number2
StatePublished - Apr 2021


  • Climate change
  • DNA markers
  • Hybrid vigor
  • Pine hybrids

ASJC Scopus subject areas

  • Forestry
  • Molecular Biology
  • Genetics
  • Horticulture


Dive into the research topics of 'Transcriptome-based single-nucleotide polymorphism markers between Pinus brutia and Pinus halepensis and the analysis of their hybrids'. Together they form a unique fingerprint.

Cite this