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doi:10.1534/genetics.105.047126
A more recent version of this article appeared on March 1, 2006.
REGULAR RESEARCH PAPERS |
DNA Sequence Variation and Selection of Tag SNPs at Candidate Genes for Drought-Stress Response in Pinus taeda L
Santiago C Gonzalez-Martinez 1, Elhan Ersoz 1, Garth R Brown 1, Nicholas C Wheeler 2 and David B Neale 1*
1 University of California at Davis
2 Weyerhaeuser Company
* To whom correspondence should be addressed. E-mail: dbneale{at}ucdavis.edu.
Submitted on June 21, 2005
Revised on August 17, 2005
Accepted on 18 December 2005
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 paper, 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 genome-wide 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 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 about 30-40%, while sampling most common allelic variants, can be gained in our ongoing association studies for drought-tolerance in pine.
Key Words: association studies, conifers, drought response, neutrality tests, nucleotide diversity
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