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

Abstract

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.

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Acknowledgements

The authors acknowledge Santiago C. González-Martínez from INRA, Bordeaux (France) for providing unpublished SNP data, and Amir Sherman and Ada Rozen for assistance with TaqMan technique. We also would like to thank the David-Schwartz lab members for technical assistance. We would like to thank the editors and three anonymous referees for providing useful comments and suggestions that substantially improved the article.

Funding

This research was supported by research grant IS-4929-16FR from BARD, The United States-Israel Binational Agricultural Research and Development Fund, and by research grant 10-03-408-19 from KKL – JNF, Keren Kayemeth LeIsrael - Jewish National Fund.

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Correspondence to Rakefet David-Schwartz.

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Data archiving statement

Data of this project have been deposited with links to BioProject accession number PRJNA658090 in The National Center for Biotechnology Information (NCBI). The raw data from the Illumina sequencing have been deposited in NCBI Sequence Read Archive (SRA) under accession numbers SRR13189310, SRR13189309, SRR13189308, SRR13189307, SRR13189306, and SRR13189305, for pools A–F, respectively.

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Houminer, N., Doron-Faigenboim, A., Shklar, G. et al. Transcriptome-based single-nucleotide polymorphism markers between Pinus brutia and Pinus halepensis and the analysis of their hybrids. Tree Genetics & Genomes 17, 14 (2021). https://doi.org/10.1007/s11295-021-01496-w

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Keywords

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