Abstract
Eucalyptus is the premier paper pulp, short rotation plantation species grown all over the world. Genetic improvement programs integrating molecular marker tools are in progress in many parts of the globe to increase the productivity. Whole genome sequence and expressed sequence tags (ESTs) of the eucalypts paved way for introduction of molecular genetics and breeding in this genus. Different molecular characterization approaches have been used simultaneously in eucalypts, however, microsatellites or simple sequence repeats (SSRs) with their prolific characteristics could occupy a special niche in Eucalyptus genetic improvement. Further, highly informative SSRs were used for the clonal identity, genetic fidelity and in certification of breeder’s rights. Eucalyptus genetic linkage maps generated with microsatellite loci were used successfully to identify quantitative trait loci (QTLs) for various economically important traits. Progressively more numbers of microsatellites are being linked to genes associated with adaptive and functional variations, therefore making their utility broader in genetic applications. Availability of common SSR markers across the species provides an opportunity to validate the expression of QTLs across variable genetic backgrounds and accurately compare the position of QTLs in other species. Recent evidences suggest that the presence of SSRs in micro RNAs of plant species play a role in the quantitative trait expression. Similar studies in eucalypts may provide new insights into the genetic architecture of transcript-level variations and post transcriptional gene regulation. This review on eucalypts microsatellites, highlights the availability and characteristics of genomic and eSSRs and their potential in genetic analysis of natural and breeding populations and also discusses the future prospects in population genetics and marker assisted selection.Electronic supplementary materialThe online version of this article (doi:10.1186/s40529-014-0073-3) contains supplementary material, which is available to authorized users.
Highlights
Eucalyptus is the world’s leading industrial plantation species due to its fast growth, wider adaptability and multipurpose utility
In recent times, tremendous data on genomic SSRs (gSSRs) and eSSRs are made available through generation sequencing (NGS) methods (Zalapa et al 2012; Kudapa et al 2014) which can readily be used in population genetics and breeding applications
A small breeding arboretum of E. globulus in Australia was analyzed with four highly polymorphic simple sequence repeats (SSRs) revealed 47.9% outcrosssing rate and 17.6% contamination rate (Rao et al 2008). These results indicate that microsatellites are the best tools for predicting the seed orchard performance and revealing the importance of strategies to arrest outside pollen like flowering asynchrony and isolation distance of adjacent populations
Summary
Eucalyptus is the world’s leading industrial plantation species due to its fast growth, wider adaptability and multipurpose utility. Transcriptome resources were generated from various tissues including xylem, phloem, root, shoot, leaf and reproductive tissues from species such as E. grandis, E. gunnii, E. globulus, E. camaldulensis and E. tereticornis (Mizrachi et al 2010; http://web.up.ac.za/eucagen/; http://eucgenie.org/; Healey et al 2014) All these transcriptome resources have promoted the development of SSR markers in silico and many of which were used for diverse purposes across eucalypt species (Ceresini et al 2005; Rabello et al 2005; Yasodha et al 2008; Rengel et al 2009; He et al 2012; Zhou et al 2014). Many of the SSR loci isolated from E. grandis and E. urophylla were cross amplified in different species like E. globulus, E. nitens, E. pilularis, E. urophylla, E. pyrocarpa, E. camaldulensis and E. tereticornis (Bundock et al 2000; Glaubitz et al 2001; Steane et al 2001; Agrama et al 2002; Ottewell et al 2005; Arumugasundaram et al 2011; Subashini et al 2013). E. camaldulensis, E. victrix, E. marginata Bradbury et al 2013a; Wheeler et al 2013
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