A Small Set of Nuclear Markers for Reliable Differentiation of the Two Closely Related Oak Species Quercus Robur and Q. Petraea

Abstract

Quercus robur and Q. petraea are, in addition to Fagus sylvatica, the main economically used deciduous tree species in Europe. Identification of these two species is crucial because they differ in their ecological demands. Because of a changing climate, foresters must know more than ever which species will perform better under given environmental conditions. The search for differentiating molecular markers between these two species has already lasted for decades. Until now, differentiation has only been possible in approaches with a combination of several molecular markers and a subsequent statistical analysis to calculate the probability of being one or the other species. Here, we used MiSeq Illumina data from pools of Q. robur and Q. petraea specimens and identified nuclear SNPs and small InDels versus the Q. robur reference genome. Selected sequence variants with 100% allele frequency difference between the two pools were further validated in an extended set of Q. robur and Q. petraea specimens, and then the number of markers was deliberately reduced to the smallest possible set for species differentiation. A combination of six markers from four nuclear regions is enough to identify Q. robur, Q. petraea or hybrids between these two species quite well and represents a marker set that is cost-efficient and useable in every laboratory.

Whole-genome screening for near-diagnostic genetic markers for four western European white oak species identification

“…In response to this challenge, molecular tools have been continuously improved, and a number of species marker kits have been developed and applied during the last decade (Guichoux et al 2011;Neophytou 2014;Reutimann et al 2020;Degen et al 2021;Schroeder and Kersten 2023). These methods have set new milestones for the delimitation of oak species, but their validity has been constrained by some biological and technical limitations.…”

“…Earlier surveys (Scotti-Saintagne et al 2004;Reutimann et al 2020;Lesur et al 2018) in European white oaks indicated that such ideal cases rarely exist. However, some markers exhibit species frequency profiles close to the ideal case (so-called near-diagnostic SNPs, for example, an allele with a frequency larger than 0.9 in the target species, and alternate allele frequency larger than 0.9 in all other species) (Schroeder and Kersten 2023). Only a few of such markers would then be enough to assign trees to the correct species using appropriate analytical approaches.…”

Whole-genome screening for near-diagnostic genetic markers for white oak species identification in Europe

“…Earlier surveys (Scotti-Saintagne et al , 2004; Reutimann et al , 2020; Lesur et al , 2018) in European white oaks indicated that such ideal cases rarely exist. However, some markers exhibit species frequency profiles close to the ideal case (so-called near-diagnostic SNPs; for example an allele with a frequency larger than 0.9 in the target species, and alternate allele frequency larger than 0.9 in all other species) (Schroeder and Kersten, 2023). Only a few of such markers would then be enough to correctly assign trees to the correct species using appropriate analytical approaches.…”