Microsatellite resources of Eucalyptus: current status and future perspectives

Identification and genetic diversity analysis of hybrid offspring of azalea based on EST-SSR markers

Azalea is a world famous flower with high economic and ornamental value. The breeding of new azalea varieties is mainly done by cross breeding. However, there is a risk that cross breeding may cause errors in the hybrid offspring due to contamination by exogenous pollen. Therefore, the identification of hybrid offspring is an important part of azalea breeding. In this study, the parents of three hybrid combinations and their 88 F1 hybrid offspring were selected to screen 15 pairs of EST-SSR primers to identify the authenticity of azalea hybrid offspring. The results showed that the authenticity of 88 azalea F1 hybrid progenies could be determined by at least four primer pairs. Genetic diversity analysis of azalea hybrid progeny revealed that the number of alleles and polymorphic information content of the progeny increased to different degrees, and the more distant the genetic distance between parents, the richer the polymorphic information. It is suggested that EST-SSR molecular marker can be applied for the early identification and genetic diversity analysis of the progeny of azalea hybrids. This method is of positive significance for improving the breeding efficiency of new varieties and exploring the genetic background of azalea.

The Genetics and Ecology of Post-Fire Eucalyptus globulus Recruitment in an Isolated Stand in Central Portugal

Eucalyptus globulus Labill. is a widespread forest tree species, reported as naturalized across the introduced range, often showing abundant natural regeneration after wildfires. This paper studies a post-fire cohort of seedlings derived from a small, isolated E. globulus stand in central Portugal. The aim is to better understand the genetic dynamics and dispersal mechanisms of naturally established E. globulus populations in the introduced range. The seedling density at 55 m from adult trees was 12,000 ha−1, the farthest seedling being registered at 101 m. Post-fire expansion occurred in a southward direction, in accordance with predominant wind. Seedlings had significantly lower levels of genetic diversity (Ae = 5.8.; He = 0.8) than adult trees (Ae = 6.5; He = 0.8). Crossings were strongly unbalanced, with only eight trees contributing to the sampled seedlings, and one single tree contributing to 52% of these seedlings. Moreover, the co-ancestry amongst seedlings more than doubled (from θ = 0.03 to 0.076), and the population status number was around one third of the value registered for the adult population (from Ns = 16.2 to 6.6). Despite its isolation, external pollen was detected in the stand, and appears to have travelled at least 700 m, contributing to 22% of the offspring. Overall, the seedling cohort is much less diverse than the parent trees, with expected lower resilience and persistence to environmental stresses.

Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation

Eucalyptus is one of the major plantation species with wide variety of industrial uses. Polymorphic and informative simple sequence repeats (SSRs) have broad range of applications in genetic analysis. In this study, two individuals of Eucalyptus tereticornis (ET217 and ET86), one individual each from E. camaldulensis (EC17) and E. grandis (EG9) were subjected to whole genome resequencing. Low coverage (10×) genome sequencing was used to find polymorphic SSRs between the individuals. Average number of SSR loci identified was 95,513 and the density of SSRs per Mb was from 157.39 in EG9 to 155.08 in EC17. Among all the SSRs detected, the most abundant repeat motifs were di-nucleotide (59.6%–62.5%), followed by tri- (23.7%–27.2%), tetra- (5.2%–5.6%), penta- (5.0%–5.3%), and hexa-nucleotide (2.7%–2.9%). The predominant SSR motif units were AG/CT and AAG/TTC. Computational genome analysis predicted the SSR length variations between the individuals and identified the gene functions of SSR containing sequences. Selected subset of polymorphic markers was validated in a full-sib family of eucalypts. Additionally, genome-wide characterization of single nucleotide polymorphisms, InDels and transcriptional regulators were carried out. These variations will find their utility in genome-wide association studies as well as understanding of molecular mechanisms involved in key economic traits. The genomic resources generated in this study would provide an impetus to integrate genomics in marker-trait associations and breeding of tropical eucalypts.

Use of Eucalyptus DNA profiling in a case of illegal logging

Eucalyptus is grown world-wide for paper pulp, solid wood, and other industries. Theft or illegal cutting of the trees causes hardship to owners of plantations and countries whose economies rely on the sale and export of eucalyptus products. Unfortunately, many of these crimes go unpunished due to lack of forensic evidence. Over 1200 short tandem repeat (STR) markers have been identified in the genomes of genus Eucalyptus and related species. However, their importance and utility in aiding forensic investigations of wood theft have not been explored. This study evaluated nine STRs for diversity and applied them to a case involving suspected wood theft. As expected, three dinucleotide STR markers showed greater variability but resulted in harder to interpret profiles. Four STR tetranucleotide markers evaluated in this study were found to contain additional repeat structures (dinucleotide or trinucleotide) that enhanced their variability but resulted in profiles with peaks at multiple stutter positions and heterozygote peak imbalance. The most promising STR markers were EGM37 and EMBRA 1374. Though less variable, they yielded robust and reproducible DNA profiles. All nine STR markers were applied to a case involving suspected wood theft. Samples were collected from seized wood and from remaining stumps in a plantation. No DNA match was found, thus eliminating the evidence samples as having originated from the forest. Dendrochronology analysis also resulted in an exclusion. This case study represents the first report using STR markers in any eucalyptus species to provide DNA evidence in a case of suspected wood theft.

Genome survey and development of 18 microsatellite markers to assess genetic diversity in Spondias tuberosa Arruda Câmara (Anacardiaceae) and cross-amplification in congeneric species

Spondias tuberosa Arr. Cam belongs to the Anacardiaceae family, an economically important family of plants whose fruits are consumed by humans and animals. The aim of this study was to develop microsatellite markers using sequences from high-throughput sequencing and a magnetic bead enrichment method. The sequences were used to obtain contigs with a minimum of 500 nucleotides using Ray software and the mining of the simple sequence repeats (SSR) was performed with Phobos software, while the primers were designed by Primer3. We developed 18 polymorphic nuclear microsatellite markers and successfully cross-amplified them to three Spondias species. In S. tuberosa, the alleles ranged from 2 to 5 for each locus and Hardy-Weinberg equilibrium was found for 16 loci, with an expected and observed heterozygosity at 0.095-0.755 and 0.1-0.75, respectively. Cross-transferability was obtained for all loci in S. bahiensis, S. dulcis and S. purpurea. We concluded that the microsatellite markers developed in this study are useful in genetic population and conservation studies, as well as for investigating the hybrid origins of Spondias species.