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

Abstract

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.

A novel synthesis of two decades of microsatellite studies on European beech reveals decreasing genetic diversity from glacial refugia

“… Correlation scatter plots (linear regression as blue line with confidence interval as gray area) between longitude and the raw and scaled He dataset from Ulaszewski et al, 2021 . Populations were splitted into north (blue) versus south group (yellow), west (blue) versus east (yellow) group, and two random groups.…”

“…In addition, a previously unpublished nuclear microsatellite dataset was included, because of its wide and even geographic coverage of the distribution range (see description of sampling in Ulaszewski et al 2021 ). Briefly, trees from two provenance trials, situated in Siemianice (Barzdajn and Rzeznik 2002 ) and in Choczewo (Chmura and Rozkowski 2002 ), were sampled with 10–20 individuals per seed source population, representing a total of 85 different populations across Europe (see Dryad dataset for this paper).…”

“…Therefore, He may significantly depend on both locus identity and geographic location. In order to test the utility of the scaling approach for correcting these types of bias, we used the novel, range-wide nuclear microsatellite dataset described above and in Ulaszewski et al 2021 , to perform two re-sampling studies.…”

Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing

“…Second- and third-generation sequencing platforms, such as Illumina’s various platforms, 454 pyrosequencing (Roche), SOLID (Invitrogen) and Ion Torrent (Invitrogen), have the ability to obtain results from many sequences, which can be used to discover new molecular markers in a viable way and at low cost [ 77 , 78 ]. These techniques have been used on a large scale for the discovery of SNPs in representative sets of individuals of various species of plants, such as rice [ 79 ], wheat [ 80 ] and different trees [ 81 , 82 ]. The discovery of SNP markers has made important contributions to advancements in various fields of study, such as genomics, transcriptomics and population genetics, such as for mapping QTLs.…”

Genomic signatures of natural selection at phenology-related genes in a widely distributed tree species Fagus sylvatica L

“…Other approaches have also been tested. Although genomic scans became attractive tools for studying genomic diversity in trees [ 38 , 39 ], their applicability to the study of genomic signatures of adaptation has been debatable [ 8 , 40 , 41 ]. Instead, SNP arrays, exome, or whole-genome sequencing have been more suitable tools with which to conduct detailed identification [ 7 , 42 , 43 ].…”