Nucleotide Diversity and Linkage Disequilibrium in Cold-Hardiness- and Wood Quality-Related Candidate Genes in Douglas Fir

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-hardin...

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Bibliographic Details
Published in:Genetics (Austin) 2005-12, Vol.171 (4), p.2029-2041
Main Authors: Krutovsky, Konstantin V, Neale, David B
Format: Article
Language:English
Subjects:
Adaptation, Physiological - genetics
Base Sequence
Cold Temperature
Design
Genes
Genes, Plant - genetics
Genetic Variation
Genetics
Genomics
Haplotypes - genetics
Investigations
Linkage Disequilibrium
Molecular Sequence Data
Oregon
Plant populations
Polymorphism, Single Nucleotide - genetics
Pseudotsuga - genetics
Pseudotsuga menziesii
Quantitative Trait Loci
Samples
Sequence Analysis, DNA
Washington
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Summary: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 H(d) = 0.827 +/- 0.043 and pi = 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.
ISSN:0016-6731
1943-2631
1943-2631
DOI:10.1534/genetics.105.044420