Timothy Sexton

Pectin Methylesterase Genes Influence Solid Wood Properties of Eucalyptus pilularis

This association study of Eucalyptus pilularis populations provides empirical evidence for the role of Pectin Methylesterase (PME) in influencing solid wood characteristics of Eucalyptus. PME6 was primarily associated with the shrinkage and collapse of drying timber, which are phenotypic traits consistent with the role of pectin as a hydrophilic polysaccharide. PME7 was primarily associated with cellulose and pulp yield traits and had an inverse correlation with lignin content. Selection of specific alleles in these genes may be important for improving trees as sources of high-quality wood products. A heterozygote advantage was postulated for the PME7 loci and, in combination with haplotype blocks, may explain the absence of a homozygous class at all single-nucleotide polymorphisms investigated in this gene.

Application of large-scale sequencing to marker discovery in plants

Advances in DNA sequencing provide tools for efficient large-scale discovery of markers for use in plants. Discovery options include large-scale amplicon sequencing, transcriptome sequencing, gene-enriched genome sequencing and whole genome sequencing. Examples of each of these approaches and their potential to generate molecular markers for specific applications have been described. Sequencing the whole genome of parents identifies all the polymorphisms available for analysis in their progeny. Sequencing PCR amplicons of sets of candidate genes from DNA bulks can be used to define the available variation in these genes that might be exploited in a population or germplasm collection. Sequencing of the transcriptomes of genotypes varying for the trait of interest may identify genes with patterns of expression that could explain the phenotypic variation. Sequencing genomic DNA enriched for genes by hybridization with probes for all or some of the known genes simplifies sequencing and analysis of differences in gene sequences between large numbers of genotypes and genes especially when working with complex genomes. Examples of application of the above-mentioned techniques have been described.

Genetic association studies in Eucalyptus pilularis Smith (blackbutt)

Summary Breeding for wood quality is limited by the long generation times and the delay before wood quality can be measured reliably. Association studies allow links between phenotype and genotype to be made, and are a prelude to accelerated domestication of trees by molecular breeding approaches. This study uses association genetics to identify DNA polymorphisms that correlate with solid wood properties of Eucalyptus pilularis Smith (blackbutt). We undertook extensive phenotyping of dimensional stability, growth and structural wood properties on a nine-year-old progeny trial established by Forests NSW at Hannam Vale, near Port Macquarie in NSW. A subset of 372 phenotyped individuals representing 284 families collected from 37 provenances was used as the association population for genotypic assessment. Fifty-two out of 127 novel DNA polymorphisms were surveyed within four candidate genes, CCR, CAD, MYB1 and MYB2. Several putative associations between wood quality traits and selected DNA polymorphisms are reported, along with the likely mechanism of action on wood quality. Association studies such as this will facilitate non-destructive DNA tests for heritable wood properties that can be used to enrich breeding populations at any developmental stage with desirable alleles.

SNP discovery and association mapping in Eucalyptus pilularis (blackbutt)

Background This research explores the universality of genetic variation in genes controlling wood formation across the genus Eucalyptus. Breeding and deploying Eucalypts for improved wood quality is constrained by the delay before wood traits can be measured reliably. Marker assisted selection (MAS) offers aw ay to make earlier selection of wood properties, by selecting Single Nucleotide Polymorphisms (SNPs) in the DNA which can predict specific phenotypic traits (genotype-phenotype links). SNPs shared between species (trans-specific SNPs) may have broad application to multiple species. When the species are more distantly related, ancient SNPs shared between subgenera (trans-subgeneric SNPs) are likely to be of adaptive importance and persist in separate lineages due to balancing selection [1]. Sample and methods