QTL analysis for growth and wood properties across multiple pedigrees and sites in Eucalyptus globulus

Eucalyptus globulus is the most widely planted species for pulpwood production in temperate regions of the world and there are breeding programs in numerous countries. There is interest in molecular approaches to breeding, particularly marker assisted selection of wood properties. QTL analysis has an important role in identifying positional candidate genes responsible for variation in wood properties. This is one approach to targeting genes which may harbour functional allelic variants (SNPs). The objective of this study was to detect and validate QTL across multiple sites and pedigrees, in order to identify genomic regions and genes affecting growth and wood properties with wide applicability in the species. We also aimed to determine the proportion of QTL which were stable in their expression across sites of contrasting productivity. Such information will be important to exploit the full potential of the impending Eucalyptus genome sequences. [Oral Presentation

Genomic patterns of species diversity and divergence in Eucalyptus

We examined genome-wide patterns of DNA sequence diversity and divergence among six species of the important tree genus Eucalyptus and investigated their relationship with genomic architecture. Using c. 90 range-wide individuals of each Eucalyptus species (E. grandis, E. urophylla, E. globulus, E. nitens, E. dunnii and E. camaldulensis), genetic diversity and divergence were estimated from 2840 polymorphic diversity arrays technology markers covering the 11 chromosomes. Species differentiating markers (SDMs) identified in each of 15 pairwise species comparisons, along with species diversity (HHW) and divergence (FST), were projected onto the E. grandis reference genome. Across all species comparisons, SDMs totalled 1.1–5.3% of markers and were widely distributed throughout the genome. Marker divergence (FST and SDMs) and diversity differed among and within chromosomes. Patterns of diversity and divergence were broadly conserved across species and significantly associated with genomic features, including the proximity of markers to genes, the relative number of clusters of tandem duplications, and gene density within or among chromosomes. These results suggest that genomic architecture influences patterns of species diversity and divergence in the genus. This influence is evident across the six species, encompassing diverse phylogenetic lineages, geography and ecology.Australian Research Council (DP110101621, DP0986491, DP130104220 and DP140102552), Sappi and Mondi, the Technology and Human Resources for Industry Programme (THRIP, UID 80118), the National Research Foundation (NRF, UID 71255 and 86936) and the Department of Science and Technology (DST) of South Africa.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1469-81372016-06-30hb201

Climate-adjusted provenancing: A strategy for climate-resilient ecological restoration

Investments in ecological restoration are estimated at $US 2 trillion per annum worldwide and are increasing rapidly (Cunningham, 2008; Williams et al., 2014). These investments are occurring in an environment of accelerated climate change that is projected to continue into the next century, yet they currently take little account of such change. This has significant implications for the long-term success of restoration plantings across millions of hectares, with germplasm used in current restoration efforts potentially poorly-adapted to future climates. New approaches that optimize the climate-resilience of these restoration efforts are thus essential (Breed et al., 2013; Williams et al., 2014; Havens et al., 2015)..

An investigation into the ecological requirements and niche partitioning of Pterostylidinae (Orchidaceae) species

The in situ management of many orchid species is problematic because individual species' ecology and habitat requirements are poorly understood. Here, the requirements of nine Pterostylis species are investigated for the first time. Individual species' abundances were recorded from 35 sites and correlated with known environmental and climatic variables using canonical correspondence analysis to determine which variables may explain species distribution. Altitude, aspect, drainage, precipitation, radiation, temperature and moisture index were identified as important variables that influence distribution patterns. The positioning of several members of the Pterostylis longifolia species complex in ordination space was poorly resolved, as was the relationship between Pterostylis pedoglossa and Pterostylis parviflora. Distinct ecological partitioning was evident among the remaining three species. This study has identified important environmental variables that can be assessed in the field and assist in the detection of suitable habitat for orchid translocations

What does population structure analysis reveal about the Pterostylis longifolia complex (Orchidaceae)?

Morphologically similar groups of species are common and pose significant challenges for taxonomists. Differences in approaches to classifying unique species can result in some species being overlooked, whereas others are wrongly conserved. The genetic diversity and population structure of the Pterostylis longifolia complex (Orchidaceae) in Tasmania was investigated to determine if four species, and potential hybrids, could be distinguished through genomic AFLP and chloroplast restriction-fragment-length polymorphism (RFLP) markers. Analysis of molecular variance (AMOVA) results indicated that little genetic variation was present among taxa, whereas PCoA analyses revealed genetic variation at a regional scale irrespective of taxa. Population genetic structure analyses identified three clusters that correspond to regional genetic and single taxon-specific phenotypic variation. The results from this study suggest that "longifolia" species have persisted throughout the last glacial maximum in Tasmania and that the complex may be best treated as a single taxon with several morphotypes. These results could have serious evolutionary and conservation implications as taxonomic changes could result in the instatement of a single, widespread taxon in which rarer morphotypes are not protected

The occurrence and conservation status of Tasmanian Pterostylis (Orchidaceae)

Orchids belong to one of the largest plant families present in Tasmania and yet they remain poorly researched. In Tasmania, Pterostylis R.Br. comprises about 37 terrestrial species, commonly called greenhoods. Little is understood about Tasmanian Pterostylis ecology and a recent assessment of species' abundances and distributions have not been conducted. Over a two year period known Pterostylis locations within mainland Tasmania, King Island and Flinders Island were visited for the purpose of collecting detailed data for species abundance, distribution and flowering. Several species within the genus Pterostylis are facing significant threats, and recommendations to prevent the decline of these species are provided

Linkage maps of Eucalyptus globulus using RAPD and microsatellite markers

The construction of linkage maps based on RAPD markers using F1 intraprovenance cross in Eucalyptus globulus subsp. globulus is reported. Twenty-one microsatellite loci originating from E. globulus and four other Eucalyptus species were added to the RAPD maps. Linkages between microsatellites previous reported for E. grandis/E. urophylla were found to be conserved in E. globulus allowing confident assignment of homology for several linkage groups between maps of these species. Homology was also identifiable between most linkage groups of the two E. globulus parents based on microsatellites and RAPD loci segregating from both parents. At a LOD score threshold of 4.9 the male parent has 13 linkage groups covering 1013 cM with 101 framework markers ordered at LOD 3.0. The female parent has 11 linkage groups covering 701cM with 97 framework markers. On the female map there were more regions of segregation distortion than expected and genetic mechanisms to explain distorted segregation are discussed. Several linkages that arise between pairs of E. globulus linkage groups as the LOD score is reduced are supported by interspecific homologies identified using microsatellite loci

A molecular phylogeny of the subtribe Pterostylidinae (Orchidaceae): resolving the taxonomic confusion

In the past decade, two major classification schemes of the subtribe Pterostylidinae have resulted in taxonomic confusion because a single well known genus was split into a large number of new genera and subgenera, many of which are difficult to discriminate accurately. These classifications have not been accepted widely among systematists because of poor phylogenetic support for several genera. Analyses of the internal transcribed spacer (ITS) region of nuclear rDNA in a large number of species and samples facilitate further clarification of the relationships within the Pterostylidinae. The phylogenetic trees were reconstructed using parsimony and Bayesian methods. These phylogenetic trees indicate that subtribe Pterostylidinae is monophyletic, and support the concept of a single genus, Pterostylis R.Br. sensu lato within the Pterostylidinae. Two clades representing subgenera correlate with the morphology of the lateral sepals, whereas several of the previously erected genera consistently have poor support. The proposed subgenera are divided further into 10 sections. Several closely related taxa with identical ITS sequences require further scrutiny by population-level molecular techniques to determine their taxonomic status

Parental and consensus linkage maps of \u3cem\u3eEucalyptus globulus\u3c/em\u3e using AFLP and microsatellite markers

Parental and consensus maps were constructed in an F2 inter-provenance cross of Eucalyptus globulus, using amplified fragment length polymorphism (AFLP) and microsatellite (or simple sequence repeats [SSR]) markers. The female map had 12 linkage groups and 118 markers, comprising 33 SSR and 85 AFLP loci. The male map had 14 linkage groups and 130 markers comprising 36 SSR and 94 AFLP loci. The integrated map featured 10 linkage groups and 165 markers, including 33 SSR and 132 AFLP loci, a small 11th group was identified in the male parent. Moderate segregation distortion was detected, concentrated in gender specific groups. The strongest distortion was detected in the female parent for which causal mechanisms are discussed. The inclusion of SSR markers previously mapped in several different eucalypt species within the subgenus Symphyomyrtus (E. globulus, E. camaldulensis, and predominantly E. grandis and E. urophylla), allowed comparison of linkage groups across species and demonstrated that linkage orders previously reported in E. globulus, E. grandis and E. urophylla were largely conserved