Allelic variation in cell wall candidate genes affecting solid wood properties in natural populations and land races of Pinus radiata

Abstract

Forest trees are ideally suited to association mapping due to their high levels of diversity and low genomic linkage disequilibrium. Using an association mapping approach, single-nucleotide polymorphism (SNP) markers influencing quantitative variation in wood quality were identified in a natural population of Pinus radiata. Of 149 sites examined, 10 demonstrated significant associations (P < 0.05, q < 0.1) with one or more traits after accounting for population structure and experimentwise error. Without accounting for marker interactions, phenotypic variation attributed to individual SNPs ranged from 2 to 6.5%. Undesirable negative correlations between wood quality and growth were not observed, indicating potential to break negative correlations by selecting for individual SNPs in breeding programs. Markers that yielded significant associations were reexamined in an Australian land race. SNPs from three genes (PAL1, PCBER, and SUSY) yielded significant associations. Importantly, associations with two of these genes validated associations with density previously observed in the discovery population. In both cases, decreased wood density was associated with the minor allele, suggesting that these SNPs may be under weak negative purifying selection for density in the natural populations. These results demonstrate the utility of LD mapping to detect associations, even when the power to detect SNPs with small effect is anticipated to be low.

Figure 1.—

(a) P-value density histograms for associations tested in the discovery population (a) and the validation population (b) under the general linear model, with adjustment for structure and multiple testing (solid line). P-values for the general linear model without adjustment for structure are provided for comparison (shaded line). Modal bins were observed in both populations at 0 < P < 0.05, demonstrating a skew in P-values near zero. The dashed line is the density histogram expected if all SNPs were null.

Figure 2.—

Percentage of significant associations (P < 0.05) per gene region and SNP type. Differences in the proportion of significant associations for silent and nonsynonymous sites were significant (P < 0.01) (Z = 2.6) for the binomial test.

Figure 3.—

Mean and standard error for trait values categorized by genotype for two SNPs in the discovery population (left) and the validation population (right). In each case associations with density were detected in both populations. Gene action observed for SNP 60 was additive in all cases. In the case of SNP 64 the gene model was dominant in the validation population; however, the effect of the GG homozygote “flipped” between populations.