Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing

The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs) and insertions/ deletions (InDels) were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family– based QTL and association analysis in Eucalyptus.

Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping

A set of over 8000 Diversity Arrays Technology (DArT) markers was tested for its utility in high-resolution population and phylogenetic studies across a range of Eucalyptus taxa. Small-scale population studies of Eucalyptus camaldulensis, Eucalyptus cladocalyx, Eucalyptus globulus, Eucalyptus grandis, Eucalyptus nitens, Eucalyptus pilularis and Eucalyptus urophylla demonstrated the potential of genome-wide genotyping with DArT markers to differentiate species, to identify interspecific hybrids and to resolve biogeographic disjunctions within species. The population genetic studies resolved geographically partitioned clusters in E. camaldulensis, E. cladocalyx, E. globulus and E. urophylla that were congruent with previous molecular studies. A phylogenetic study of 94 eucalypt species provided results that were largely congruent with traditional taxonomy and ITS-based phylogenies, but provided more resolution within major clades than had been obtained previously. Ascertainment bias (the bias introduced in a phylogeny from using markers developed in a small sample of the taxa that are being studied) was not detected. DArT offers an unprecedented level of resolution for population genetic, phylogenetic and evolutionary studies across the full range of Eucalyptus species.

Characterization of polymorphic microsatellite DNA markers in Hakea oldfieldii Benth. (Proteaceae)

A genomic library was constructed and 13 polymorphic microsatellite markers were developed for Hakea oldfieldii, a woody shrub endemic to southwest Western Australia. Polymorphism was investigated for these markers in 28 individuals from a single population located in restricted habitat at the base of the Whicher Range south of Busselton. Expected heterozygosity ranged from 0.279 to 0.770 and averaged 0.633. Observed heterozygosity ranged from 0.321 to 0.786 and averaged 0.598. The number of alleles per locus ranged from 2.0 to 6.0 and averaged 4.5. These markers will be used to assay genetic diversity and pollen dispersal in this species.

Extensive pollen dispersal in a bird-pollinated shrub,Calothamnus quadrifidus, in a fragmented landscape

Pollen dispersal was investigated in six populations of Calothamnus quadrifidus, a bird-pollinated shrub in the fragmented agricultural region of southern Western Australia. Paternity analysis using six microsatellite loci identified a pollen source within populations for 67% of seedlings, and the remainder were assumed to have arisen from pollen sources outside the populations. Outcrossing was variable, ranging from 5% to 82%, and long-distance pollen dispersal was observed in all populations with up to 43% of pollen sourced from outside the populations over distances of up to 5 km. This extensive pollen immigration was positively associated with population size but not isolation. Comparison of two populations of similar size but different density showed greater internal pollination and less selfing in the denser population, suggesting an influence of density on pollinator behaviour. The study revealed extensive long-distance pollen dispersal for C. quadrifidus within this fragmented agricultural landscape and highlighted the interaction between reserve populations and isolated road verge remnants in maintaining genetic connectivity at the landscape scale.

Identification of quantitative trait loci influencing foliar concentrations of terpenes and formylated phloroglucinol compounds in Eucalyptus nitens

Leaves of eucalypt species contain a variety of plant secondary metabolites, including terpenoids and formylated phloroglucinol compounds (FPCs). Both terpene and FPC concentrations are quantitative traits that can show large variation within a population and have been shown to be heritable. The molecular genetic basis of this variation is currently unknown. Progeny from a field trial of a three-generation mapping pedigree of Eucalyptus nitens were assayed for terpenes and FPCs. Quantitative trait loci (QTL) analyses were conducted using a map constructed from 296 markers to locate regions of the genome influencing foliar concentrations of these plant secondary compounds. A large number of significant QTL for 14 traits were located across nine linkage groups, with significant clustering of QTL on linkage groups 7, 8 and 9. As expected, QTL for biosynthetically related compounds commonly colocated, but QTL for unrelated monterpenes and FPCs also mapped closely together. Colocation of these QTL with mapped candidate genes from the various biosynthetic pathways, and subsequent use of these genes in association mapping, will assist in determining the causes of variation in plant secondary metabolites in eucalypts.

Polymorphisms in cinnamoyl CoA reductase (CCR) are associated with variation in microfibril angle in Eucalyptus spp

Linkage disequilibrium (LD) mapping using natural populations results in higher resolution of marker-trait associations compared to family-based quantitative trait locus (QTL) studies. Depending on the extent of LD, it is possible to identify alleles within candidate genes associated with a trait. Analysis of a natural mutant in Arabidopsis has shown that mutations in cinnamoyl CoA reductase (CCR), a key lignin gene, affect physical properties of the secondary cell wall such as stiffness and strength. Using this gene, we tested whether LD mapping could identify alleles associated with microfibril angle (MFA), a wood quality trait affecting stiffness and strength of wood. We identified 25 common single-nucleotide polymorphism (SNP) markers in the CCR gene in Eucalyptus nitens. Using single-marker and haplotype analyses in 290 trees from a E. nitens natural population, two haplotypes significantly associated with MFA were found. These results were confirmed in two full-sib families of E. nitens and Eucalyptus globulus. In an effort to understand the functional significance of the SNP markers, we sequenced the cDNA clones and identified an alternatively spliced variant from the significant haplotype region. This study demonstrates that LD mapping can be used to identify alleles associated with wood quality traits in natural populations of trees.

Nuclear RFLP variation in Eucalyptus camaldulensis Dehnh. from northern Australia

Eucalyptus camaldulensis Dehnh. is the most widely planted eucalypt in the tropics. Natural populations are riparian and sampling strategies for breeding programmes have assumed that gene flow among drainage basins is limited. RFLP variation, within and among 31 populations from river systems across northern Australia, was analysed to test this hypothesis. To allow comparisons within and between river systems, trees were sampled from up to three populations per river system. Allele frequencies were correlated with longitude for more than half the 33 RFLP loci surveyed. Genetic identity was greatest between populations in closest geographic proximity, irrespective of river system, suggesting that sampling strategies for breeding programmes should be based on geographic distance rather than river system. The level of genetic variation was similar throughout the geographic range examined (mean H(E) = 0.49). However, there was evidence of a barrier to gene flow between populations in the east and west of the species range. The RFLP data support morphological evidence of hybridisation between E. camaldulensis and E. tereticornis Sm. in several populations in northeast Queensland and the genetic divergence of E. camaldulensis subsp. simulata Brooker and Kleinig.

Genetic differentiation between mallee and tree forms in the Eucalyptus loxophleba complex

The Eucalyptus loxophleba complex comprises two tree taxa (E. loxophleba ssp. loxophleba and ssp. supralaevis), two mallee taxa (E. loxophleba ssp. lissophloia and ssp. gratiae), and three rare mallee species, of which one, E. blaxellii, is included in this study. The genetic diversity and phylogenetic relationships between the taxa, particularly in relation to habit, were assessed using anonymous nuclear RFLP loci. The level of diversity in the taxa was high and similar to that detected in other eucalypt species. The populations showed low differentiation at both the subspecies and the species levels. Phylogenetic relationships showed some genetic separation between the tree and mallee habit but no separation of the two taxa within the tree habit or within the mallee habit. The genetic analysis does not support the recognition of E. gratiae as a separate species. The geographically restricted E. blaxellii showed similar levels of diversity to populations of the other widespread taxa of E. loxophleba.