Dillon SK, Nolan MF, Li W, Matter P, Wu HX, Southerton SG
Allelic variation in cell wall candidate genes affects solid wood properties in natural populations and land races of radiata pine
Genetics: 2010 185:1477-1487

Forest trees are ideally suited to association mapping due totheir high levels of diversity and low genomic linkage disequilibrium.Using an association mapping approach, single-nucleotide polymorphism(SNP) markers influencing quantitative variation in wood qualitywere identified in a natural population of Pinus radiata. Of149 sites examined, 10 demonstrated significant associations(P < 0.05, q < 0.1) with one or more traits after accountingfor population structure and experimentwise error. Without accountingfor marker interactions, phenotypic variation attributed toindividual SNPs ranged from 2 to 6.5%. Undesirable negativecorrelations between wood quality and growth were not observed,indicating potential to break negative correlations by selectingfor individual SNPs in breeding programs. Markers that yieldedsignificant associations were reexamined in an Australian landrace. SNPs from three genes (PAL1, PCBER, and SUSY) yieldedsignificant associations. Importantly, associations with twoof these genes validated associations with density previouslyobserved in the discovery population. In both cases, decreasedwood density was associated with the minor allele, suggestingthat these SNPs may be under weak negative purifying selectionfor density in the natural populations. These results demonstratethe utility of LD mapping to detect associations, even whenthe power to detect SNPs with small effect is anticipated tobe low.

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