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Originally published as Genetics Published Articles Ahead of Print on September 12, 2005.
Genetics, Vol. 171, 2029-2041, December 2005, Copyright © 2005
doi:10.1534/genetics.105.044420
Nucleotide Diversity and Linkage Disequilibrium in Cold-Hardiness- and Wood Quality-Related Candidate Genes in Douglas Fir
Konstantin V. Krutovsky*,1 and
David B. Neale
,2
* Institute of Forest Genetics, Pacific Southwest Research Station, U.S. Department of Agriculture Forest Service, Davis, California 95616 and Department of Plant Sciences, University of California, Davis, California 95616
2 Corresponding author: Institute of Forest Genetics, Pacific Southwest Research Station, USDA Forest Service, Department of Plant Sciences, University of California, 1 Shields Ave., Davis, CA 95616.
E-mail: dbneale{at}ucdavis.edu
Nuclear sequence variation and linkage disequilibrium (LD) were studied in 15 cold-hardiness- and 3 wood quality-related candidate genes in Douglas fir [Pseudotsuga menziesii (Mirb.) Franco]. This set of genes was selected on the basis of its function in other plants and collocation with cold-hardiness-related quantitative trait loci (QTL). The single-nucleotide polymorphism (SNP) discovery panel represented 24 different trees from six regions in Washington and Oregon plus parents of a segregating population used in the QTL study. The frequency of SNPs was one SNP per 46 bp across coding and noncoding regions on average. Haplotype and nucleotide diversities were also moderately high with Hd = 0.827 ± 0.043 and 
= 0.00655 ± 0.00082 on average, respectively. The nonsynonymous (replacement) nucleotide substitutions were almost five times less frequent than synonymous ones and substitutions in noncoding regions. LD decayed relatively slowly but steadily within genes. Haploblock analysis was used to define haplotype tag SNPs (htSNPs). These data will help to select SNPs for association mapping, which is already in progress.
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