Originally published as Genetics Published Articles Ahead of Print on November 16, 2006.

Genetics, Vol. 175, 399-409, January 2007, Copyright © 2007
doi:10.1534/genetics.106.061127

Association Genetics in Pinus taeda L. I. Wood Property Traits

Santiago C. González-Martínez^*,, Nicholas C. Wheeler^,1, Elhan Ersoz^*, C. Dana Nelson and David B. Neale^*,**,2

^* Department of Plant Sciences, University of California, Davis, California 95616, Department of Forest Systems and Resources, Forest Research Institute, CIFOR-INIA, 28040 Madrid, Spain, Weyerhaeuser, Weyerhaeuser Technical Center, Tacoma, Washington 98477, Southern Institute of Forest Genetics, USDA Forest Service, Saucier, Mississippi 39574 and ^** Institute of Forest Genetics, Pacific Southwest Research Station, USDA Forest Service, Davis, California 95616

² Corresponding author: Department of Plant Sciences, University of California, 1 Shields Ave., Davis, CA 95616.
E-mail: dbneale{at}ucdavis.edu

Genetic association is a powerful method for dissecting complex adaptive traits due to (i) fine-scale mapping resulting from historical recombination, (ii) wide coverage of phenotypic and genotypic variation within a single experiment, and (iii) the simultaneous discovery of loci and alleles. In this article, genetic association among single nucleotide polymorphisms (58 SNPs) from 20 wood- and drought-related candidate genes and an array of wood property traits with evolutionary and commercial importance, namely, earlywood and latewood specific gravity, percentage of latewood, earlywood microfibril angle, and wood chemistry (lignin and cellulose content), was tested using mixed linear models (MLMs) that account for relatedness among individuals by using a pairwise kinship matrix. Population structure, a common systematic bias in association studies, was assessed using 22 nuclear microsatellites. Different phenotype:genotype associations were found, some of them confirming previous evidence from collocation of QTL and genes in linkage maps (for example, 4cl and percentage of latewood) and two that involve nonsynonymous polymorphisms (cad SNP M28 with earlywood specific gravity and 4cl SNP M7 with percentage of latewood). The strongest genetic association found in this study was between allelic variation in -tubulin, a gene involved in the formation of cortical microtubules, and earlywood microfibril angle. Intragenic LD decays rapidly in conifers; thus SNPs showing genetic association are likely to be located in close proximity to the causative polymorphisms. This first multigene association genetic study in forest trees has shown the feasibility of candidate gene strategies for dissecting complex adaptive traits, provided that genes belonging to key pathways and appropriate statistical tools are used. This approach is of particular utility in species such as conifers, where genomewide strategies are limited by their large genomes.

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