Originally published as Genetics Published Articles Ahead of Print on December 30, 2005.

Genetics, Vol. 172, 1915-1926, March 2006, Copyright © 2006
doi:10.1534/genetics.105.047126

DNA Sequence Variation and Selection of Tag Single-Nucleotide Polymorphisms at Candidate Genes for Drought-Stress Response in Pinus taeda L.

Santiago C. González-Martínez^*,, Elhan Ersoz^*, Garth R. Brown^*, Nicholas C. Wheeler^,1 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 Company, Weyerhaeuser Technical Center, Tacoma, Washington 98477 and Institute of Forest Genetics, USDA Forest Service, Davis, California 95616

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

Genetic association studies are rapidly becoming the experimental approach of choice to dissect complex traits, including tolerance to drought stress, which is the most common cause of mortality and yield losses in forest trees. Optimization of association mapping requires knowledge of the patterns of nucleotide diversity and linkage disequilibrium and the selection of suitable polymorphisms for genotyping. Moreover, standard neutrality tests applied to DNA sequence variation data can be used to select candidate genes or amino acid sites that are putatively under selection for association mapping. In this article, we study the pattern of polymorphism of 18 candidate genes for drought-stress response in Pinus taeda L., an important tree crop. Data analyses based on a set of 21 putatively neutral nuclear microsatellites did not show population genetic structure or genomewide departures from neutrality. Candidate genes had moderate average nucleotide diversity at silent sites (_sil = 0.00853), varying 100-fold among single genes. The level of within-gene LD was low, with an average pairwise r² of 0.30, decaying rapidly from 0.50 to 0.20 at 800 bp. No apparent LD among genes was found. A selective sweep may have occurred at the early-response-to-drought-3 (erd3) gene, although population expansion can also explain our results and evidence for selection was not conclusive. One other gene, ccoaomt-1, a methylating enzyme involved in lignification, showed dimorphism (i.e., two highly divergent haplotype lineages at equal frequency), which is commonly associated with the long-term action of balancing selection. Finally, a set of haplotype-tagging SNPs (htSNPs) was selected. Using htSNPs, a reduction of genotyping effort of 30–40%, while sampling most common allelic variants, can be gained in our ongoing association studies for drought tolerance in pine.

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