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.
Highlights
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
High heritabilities have been observed for solid wood traits including density, cellulose microfibril angle (MFA), and modulus of elasticy (MOE) (Baltunis et al 2007) and for carbohydrate composition, pulp yield, fiber length, and perimeter (Evans et al 1997; Kibblewhite 1999); and genetic
Summary
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. 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. To date there have been few functional studies in forest trees revealing genes directly affecting wood quality (MacKay et al 1997; Tsai et al 1998; Valerio et al 2003; Lu et al 2004; Spokevicius et al 2007), largely due to inherent features of forest trees including their long generation times, large size, and lack of inbred or pure lines (Oh et al 2003)
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