A Selected Set of EST-Derived Microsatellites, Polymorphic and Transferable across 6 Species of Eucalyptus (original) (raw)
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Cross-species amplification of Eucalyptus microsatellite loci
Molecular Ecology Resources, 2008
This study examined the interspecific amplification of nuclear microsatellite loci developed mainly for eucalypts in the subgenus Symphyomyrtus across five species within the second most speciose subgenus, subgenus Eucalyptus. A set of eight to 10 loci, depending on taxon, have been identified that are highly variable and easily scored. The successful transfer of microsatellite loci to these eucalypt species sidesteps the expensive and time-consuming development of species-specific microsatellite libraries. This primer set will enable the examination and cross-species comparison of the genetic resources of commercially and ecologically important members of the subgenus Eucalyptus.
Conservation and Genetic Diversity of Microsatellite loci in the Genus Eucalyptus
Australian Journal of Botany, 1996
Four microsatellite loci have been characterised in Eucalyptus nitens Maiden and in six other eucalypt species. The dinucleotide repeats were identified by screening a Sau3AI genomic DNA library from E. nitens with (CA)n and (GA)n oligonucleotide probes and sequencing the positive clones. Genetic analysis of 20 unrelated individuals from five populations of E. nitens showed all loci to be highly polymorphic with an average of 9.5 alleles per locus and an average heterozygosity of 0.575. Analysis of four individuals from each of six species from three subgenera showed complete conservation of microsatellite loci between species within the same subgenus, Symphyomyrtus, and conservation of 50% of loci across species between the two main subgenera, Symphyomyrtus and Monocalyptus. None of the primers amplified microsatellite loci in Eucalyptus maculata from the subgenus Corymbia. All microsatellite loci that were detected were polymorphic. Highly polymorphic microsatellite loci that are ...
BMC plant biology, 2006
Eucalypts are the most widely planted hardwood trees in the world occupying globally more than 18 million hectares as an important source of carbon neutral renewable energy and raw material for pulp, paper and solid wood. Quantitative Trait Loci (QTLs) in Eucalyptus have been localized on pedigree-specific RAPD or AFLP maps seriously limiting the value of such QTL mapping efforts for molecular breeding. The availability of a genus-wide genetic map with transferable microsatellite markers has become a must for the effective advancement of genomic undertakings. This report describes the development of a novel set of 230 EMBRA microsatellites, the construction of the first comprehensive microsatellite-based consensus linkage map for Eucalyptus and the consolidation of existing linkage information for other microsatellites and candidate genes mapped in other species of the genus. The consensus map covers approximately 90% of the recombining genome of Eucalyptus, involves 234 mapped EMBR...
Microsatellite resources of Eucalyptus: current status and future perspectives
Botanical Studies, 2014
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.
Scientia Forestalis
Polymorphic and transferable microsatellite loci among five Eucalyptus species (Eucalytpus grandis, Eucalytpus urophylla, Eucalytpus tereticornis, Eucalytpus saligna and Eucalytpus brassiana) were developed in order to use them in further studies of population structure, conservation, forest management and breeding programs of the genus. Four new microsatellite loci were isolated from the database Eucalyptus Sequencing Project Consortium (FORESTs). Allele numbers ranged from two to ten, the observed heterozygosity (Ho) ranged from 0 to 1 and the expected heterozygosity (He) ranged from 0.255 to 0.792. Microsatellite loci described demonstrated a great variation and reliable findings that could support other future studies focusing breeding programs and related areas.
Silvae Genetica
Microsatellite markers remain the most broadly used molecular marker in eucalypt genetics. A major advantage of microsatellite markers is that they often transfer readily between related taxa circumventing the need to develop new markers de novo in each species. Markers have been developed for a number of species of major economic importance, mainly from the Subgenus Symphyomyrtus, but these may also be available for use in species of lesser economic importance from other subgenera. Here we report on the sourcing of microsatellite markers for E. pilularis (Subgenus Eucalyptus (Formerly Monocalyptus)) from species outside the subgenus. Ninety-seven precent (60 out of 62) of loci that amplified in the source taxon (E. grandis) also amplified in the target taxon E. pilularis. By characterising them on a diversity panel (n=24) and a pedigree, a subset of 41 loci were distilled out that could be scored reliably and were polymorphic (Mean unbiased heterozygosity= 0.81). Predictions of eff...
Theoretical and Applied Genetics, 1998
We report on the development, genetic characterization and linkage mapping of a battery of SSR (simple sequence repeat) loci in Eucalyptus grandis and E. urophylla. This study reveals the abundance of SSRs in Eucalyptus, the very high information content of these markers for mapping and individual identification, and demonstrates the feasibility of constructing a comprehensive microsatellite-based linkage map for Eucalyptus. Primer sequence for a set of 20 highly informative EMBRA (Eucalyptus microsatellites from Brazil) loci are made available together with their map position and estimates of the expected heterozygosity and allele size range in these two species. Using genomic library enrichment and anchored-PCR screening prior to sequencing, the efficiency of SSR marker locus development was 63% from sequencing data to operationally useful SSR loci. Absolute transportability between the two species and very high levels of allelic variability and expected heterozygosity (H) were seen at all SSR loci surveyed. The number of alleles per locus ranged from 9 to 26 with an average of 16.
Molecular Genetics and Genomics, 2002
A novel set of 50 highly polymorphic microsatellite markers were developed and mapped on existing RAPD framework maps of Eucalyptus grandis and E. urophylla. Together with the twenty previously developed microsatellite markers, these were used to align the existing maps for the two most commercially important Eucalyptus species in the tropics. Sixty-three microsatellite markers were placed on the E. grandis map in 11 linkage groups, and 53 on the E. urophylla map distributed in 10 linkage groups. Approximately 66% of the microsatellite markers segregated in a fully informative fashion, allowing the establishment of colinear syntenic linkage groups between the two maps. The 50 new microsatellite markers were highly informative, with an average of 14 alleles per locus, and average expected heterozygosity between 0.82 and 0.87. Furthermore, within the subgenus Symphyomyrtus, to which the vast majority of commercially important Eucalyptus species belong, these markers display on average 90% transportability. This set of 70 mapped microsatellite markers represents a significant step toward the development of a genus-wide reference linkage map for Eucalyptus. These highly multiallelic and transportable markers constitute a powerful tool for QTL discovery and validation, and can be used in directed searches for QTL allele variation across Eucalyptus pedigrees.
Conservation Genetics Resources, 2009
Eucalyptus camaldulensis Dehnh is an Australian tree species which occurs in various climatic and environmental conditions and show large genetic diversity. Twenty five microsatellite markers were developed from a CT 8 -GT 8 enriched genomic library of E. camaldulensis. The number of alleles ranged from 4 to 13 (average of 8). The polymorphism information content (PIC) and the discriminating power (D) of each primer ranged from 0.37 to 0.88 (average of 0.72) and 0.48 to 0.99 (average of 0.84), respectively. The observed and expected heterozygosities ranged from 0.28 to 0.84 and 0.25 to 0.90, respectively. Four loci showed statistically significant from Hardy-Weinberg equilibrium after Bonferroni correction (P, (5%) \ 0.0038). All polymorphic markers were tested for cross-amplification in 25 different Eucalyptus species. Those microsatellite loci will be useful to investigate questions of genetic diversity and structure, gene flow, mating system and ex situ genetic conservation of E. camaldulensis.