Abstract
Chestnut species have large ecological, cultural and economic importance. Developing genetic markers for these species is of interest for conservation, breeding or evolutionary studies. We designed 192 primer pairs targeting microsatellites detected in the Castanea mollissima reference genome and tested them on C. sativa and C. crenata. We PCR amplified 3 × 50 microsatellites in 106 chestnut trees. Microhaplotype calling accounting for all polymorphisms resulted in a total of 98 high confidence polymorphic markers. Mean number of haplotypes per marker was 9.05 with respectively 71%, 12% and 16% of the variation corresponding to microsatellite variation in repeats number, SNP within the repeat motif and SNP or INDEL in the flanking sequence. Overall, the simple protocol described here generated a powerful multilocus genetic dataset for chestnut genetic investigations.
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Acknowledgements
BL was financially supported by the Region Nouvelle-Aquitaine (Grant Number 2018-1R20204 project DIGIE “chestnut DIeback: vulnerability and GenetIc determinism of ink disEase resistance). Genotyping by sequencing was conducted at the Genome Transcriptome Facility of Bordeaux (Grants from ANR-10-EQPX-16).
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Laurent, B., Larue, C., Chancerel, E. et al. Microhaplotype genotyping-by-sequencing of 98 highly polymorphic markers in three chestnut tree species. Conservation Genet Resour 12, 567–580 (2020). https://doi.org/10.1007/s12686-020-01157-5
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DOI: https://doi.org/10.1007/s12686-020-01157-5