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Article

Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods

Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064 Bydgoszcz, Poland
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Academic Editor: Tadeusz Malewski
Forests 2021, 12(2), 222; https://doi.org/10.3390/f12020222
Received: 26 January 2021 / Revised: 9 February 2021 / Accepted: 11 February 2021 / Published: 15 February 2021
(This article belongs to the Special Issue Forest Genomics and Transcriptomics)
Next-generation sequencing of reduced representation genomic libraries (RRL) is capable of providing large numbers of genetic markers for population genetic studies at relatively low costs. However, one major concern of these types of markers is the precision of genotyping, which is related to the common problem of missing data, which appears to be particularly important in association and genomic selection studies. We evaluated three RRL approaches (GBS, RADseq, ddRAD) and different SNP identification methods (de novo or based on a reference genome) to find the best solutions for future population genomics studies in two economically and ecologically important broadleaved tree species, namely F. sylvatica and Q. robur. We found that the use of ddRAD method coupled with SNP calling based on reference genomes provided the largest numbers of markers (28 k and 36 k for beech and oak, respectively), given standard filtering criteria. Using technical replicates of samples, we demonstrated that more than 80% of SNP loci should be considered as reliable markers in GBS and ddRAD, but not in RADseq data. According to the reference genomes’ annotations, more than 30% of the identified ddRAD loci appeared to be related to genes. Our findings provide a solid support for using ddRAD-based SNPs for future population genomics studies in beech and oak. View Full-Text
Keywords: restriction-site associated DNA sequencing; SNP genotyping; technical replicates; population genomics; European beech; pedunculate oak restriction-site associated DNA sequencing; SNP genotyping; technical replicates; population genomics; European beech; pedunculate oak
MDPI and ACS Style

Ulaszewski, B.; Meger, J.; Burczyk, J. Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods. Forests 2021, 12, 222. https://doi.org/10.3390/f12020222

AMA Style

Ulaszewski B, Meger J, Burczyk J. Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods. Forests. 2021; 12(2):222. https://doi.org/10.3390/f12020222

Chicago/Turabian Style

Ulaszewski, Bartosz, Joanna Meger, and Jaroslaw Burczyk. 2021. "Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods" Forests 12, no. 2: 222. https://doi.org/10.3390/f12020222

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