Abstract
The genera Castanea (chestnuts), Fagus (beechs) and Quercus (oaks) are the only genera of the family Fagaceae distributed throughout the temperate forests of the northern hemisphere (Kremer et al. 2007). Comprising more than 900 species and nine genera (Manos et al. 2001), this family is considered highly complex at the phylogenetic level. However, its taxonomic classification is presently being widely revised due to the availability of new molecular data. Inter-simple sequence repeats (ISSRs) have been used in different Fagaceae species for genetic diversity analyses, DNA fingerprinting and estimation of interspecific and intraspecific relationships (Goulao et al. 2001; Carvalho et al. 2009; Coutinho et al. 2014). ISSRs could be used alone or in combination with other markers such as the simple sequence repeats (SSRs) (Lopez-Aljorna et al. 2007). Recent technological progresses made in single-locus markers reduced the importance of multi-locus markers. SSRs are the marker system of choice for genetic diversity evaluation in species with reduced polymorphism, otherwise, both SSRs and ISSRs could be used for the same (Lopez-Aljorna et al. 2007; Gomes et al. 2008; Kumar and Sharma 2011; Jia et al. 2011; Noormohammadi et al. 2013). Many expressed sequence tags (EST) were developed for Fagaceae species such as Quercus petraea, Q. robur, C. sativa and F. sylvatica (NCBI dbEST, http://www.ncbi.nlm.nih.gov/dbest/index. html). The ESTs are useful for comparative mapping studies but their transferability is dependent on the occurrence of point mutations in the primer annealing sites, and could lead to some uncertainty in phylogenetic inferences. On the other hand, ISSRs are ubiquitous, simple, affordable and produce a large number of polymorphic fragments (increasing their resolving power and polymorphic information content), thus being suitable for genetic diversity assessment of distant and closely related species and for the estimation of phylogenies.
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