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.

Modelling environmental variation in Young's modulus for Pinus radiata and implications for determination of critical buckling height.

BACKGROUND AND AIMS: Although density-specific stiffness, E/rho, (where E is Young's modulus and rho is wood density) is often assumed constant by the elastic similarity model, and in determination of critical buckling height (H(crit)), few studies have tested this assumption within species. Here this assumption is tested for Pinus radiata growing across an environmental gradient, and theory is combined with data to develop a model of Young's modulus. METHODS: Analyses use an extensive series of environmental plots covering the range of climatic and edaphic conditions over which P. radiata is grown in New Zealand. Reduced major axis regression was used to determine scaling exponents between log-log plots of H(crit) vs. groundline diameter (D), and E/rho vs. D. Path analysis was used to identify significant direct and indirect (through stem slenderness) edaphic and climatic influences on E. KEY RESULTS: Density-specific stiffness exhibited 3-fold variation. As E/rho scaled positively with D, the exponent of 0.95 between H(crit) and D exceeded the assumed value of 0.67 under constant E/rho. The final path analysis model included mean air temperature in early autumn (T(aut)) and slenderness as significant (P < 0.05) positive direct influences on E. Tree leaf area index and T(aut) were indirectly associated with E through their significant (P < 0.05) positive direct relationship with stem slenderness. Young's modulus was most sensitive to T(aut), followed by stem slenderness then leaf area index, and the final model explained 76 % of the variance in E. CONCLUSIONS: The findings suggest that within species E/rho variation may influence H(crit) and the scaling exponent between D and H(crit) so important in assumptions regarding allometric relationships. The model presented may provide a useful means of determining variation in E, E/rho and H(crit) across environmental gradients.