Abstract
To better study and manage chestnut trees and species, we identified nuclear single nucleotide polymorphism (SNP) markers using restriction-associated DNA sequencing. Out of 343 loci tested, 68 SNP markers were selected that withhold stringent quality criteria such as quasi-systematic amplification across species and Mendelian segregation in both purebred and hybrid individuals. They provide sufficient power for species, hybrids and backcross characterization as well as for clonal identification, as shown by a comparison with single sequenced repeat (SSR) loci.
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All data are available on Data INRAE: Larue C (2021) Development of SNP markers for the identification of chestnut species, hybrids and varieties. Portail Data INRAE, V2, UNF:6:eJQwJJ12X/74swiSKl9V2A== [fileUNF]. https://doi.org/10.15454/XEMDLD
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Acknowledgements
We thank J. Schoeters for developing MISMATCHFINDER software, C. Lalanne for DNA isolation protocol development and L. Dubois, C. Boury and C. Mouden for SNP identification and genotyping. We thank INRAE experimental unit Vigne Bordeaux (UEVB) in Villenave d’Ornon, and INRAE experimental unit Forêt Pierroton (UEFP) for their continuous support for chestnut orchards management.
Funding
This paper is part of the PhD of CL. The work was supported by ANRt funding under CIFRE PhD program to CL. Financial support to Invenio for this project was provided by the Conseil Régional d’Aquitaine for CL PhD work, as part of the REGINA project, and for BL work (Grant Number 2018-1R20204 project DIGIE “chestnut dieback: vulnerability and genetic determinism of ink disease resistance”). SNP development and genotyping were performed at the Genome Transcriptome Facility of Bordeaux (Grants from the Conseil Régional d’Aquitaine No. 20030304002FA and 20040305003FA, from the European Union FEDER No. 2003227 and from Investissements d’Avenir ANR-10-EQPX-16-01).
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CL: Conceptualization, investigation, resources, formal analysis, writing—original draft. EG: Conceptualization, methodology, formal analysis, writing—review & editing. BL: Formal analysis, writing—review & editing. TB: Conceptualization, funding acquisition, writing—review & editing. CR: Conceptualization, funding acquisition, writing—review & editing. MM: Investigation, resources, writing—review & editing. AD: Investigation, resources, writing—review & editing. RJP: Conceptualization, funding acquisition, supervision, writing—review & editing.
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Larue, C., Guichoux, E., Laurent, B. et al. Development of highly validated SNP markers for genetic analyses of chestnut species. Conservation Genet Resour 13, 383–388 (2021). https://doi.org/10.1007/s12686-021-01220-9
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DOI: https://doi.org/10.1007/s12686-021-01220-9