Geoff Downes

Identification of a Cis-Acting Regulatory Polymorphism in a Eucalypt COBRA-Like Gene Affecting Cellulose Content

Populations with low linkage disequilibrium (LD) offer unique opportunities to study functional variants influencing quantitative traits. We exploited the low LD in forest trees to identify functional polymorphisms in a Eucalyptus nitens COBRA-like gene (EniCOBL4A), whose Arabidopsis homolog has been implicated in cellulose deposition. Linkage analysis in a full-sib family revealed that EniCOBL4A is the most strongly associated marker in a quantitative trait locus (QTL) region for cellulose content. Analysis of LD by genotyping 11 common single-nucleotide polymorphisms (SNPs) and a simple sequence repeat (SSR) in an association population revealed that LD declines within the length of the gene. Using association studies we fine mapped the effect of the gene to SNP7, a synonymous SNP in exon 5, which occurs between two small haplotype blocks. We observed patterns of allelic expression imbalance (AEI) and differential binding of nuclear proteins to the SNP7 region that indicate that SNP7 is a cis-acting regulatory polymorphism affecting allelic expression. We also observed AEI in SNP7 heterozygotes in a full-sib family that is linked to heritable allele-specific methylation near SNP7. This study demonstrates the potential to reveal functional polymorphisms underlying quantitative traits in low LD populations.

The effect of growth strain and other defects on the sawn timber quality of 10-year-old Eucalyptus globulus Labill

Summary Fifty-nine trees were sampled from three provenances of Eucalyptus globulus Labili, in 10-year-old plantations at two separate sites. The butt logs were selected as the study sawlogs. Growth strain was measured at three heights along the log length and three circumferential positions at each height. The logs were sawn and graded before and after seasoning to appearance grade. The impact of each grade-limiting defect on the result was examined. Particular attention was given to the effect of growth strain on the percentage of sawn boards that exceeded the permissible distortion limits of Australian standard AS2796.1 as feedstock. The logs were from young, small-diameter, unpruned trees knots and pith were the primary grade-limiting defects. Average growth strain of the sawlogs and the tree diameter at breast height in combination accounted for 42% of the total variation in the percentage of excessively distorted boards. Density had no direct causal effect on this percentage, but had an indirect effect through its significant correlation with growth strain.

A multi-site, multi-species near infrared calibration for the prediction of cellulose content in eucalypt woodmeal.

Calibrations between spectra derived from near infrared (NIR) spectroscopy and chemical analyses can be used to predict cellulose content in samples of ground eucalypt woodmeal. Past calibrations have used small sample sets (<100 samples) often representing a single stand or region and only one species, making their application to wider populations of samples problematic. A robust, nondestructive prediction capability for eucalypt wood cellulose that works across stands, regions and species would find many applications in tree breeding and resource assessment. Here, we describe the development and test the performance of a large (> 1000 samples) multi-site and species NIR calibration for predicting cellulose content of eucalypt woodmeal obtained from increment cores, wood chips and stem cross-sections. Most of the samples came from Eucalyptus globulus and E. nitens. The calibration was tested against four independent sample sets and explained between 65% and 84% of the variance in each set. A higher proportion of variance was explained in those sample sets that had a wider range of cellulose content. Standard errors of prediction were between 0.5% and 1.5% cellulose for the four independent sample sets. The test samples were added to the large calibration and a new calibration with 1260 samples was constructed. Principal components analysis suggests additional wood samples with more diverse chemistries are required to enable the calibration to capture more fully the chemical variation present in the genus.