title: Nucleotide diversity and linkage disequilibrium in cold-hardiness- and wood quality-related candidate genes in Douglas fir.
abstract: 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.
authors.affiliation: Institute of Forest Genetics, Pacific Southwest Research Station, US Department of Agriculture Forest Service, Davis, CA 95616, USA.
authors.forename: Konstantin V
authors.initials: KV
authors.lastname: Krutovsky
authors.forename: David B
authors.initials: DB
authors.lastname: Neale
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D001483:Base Sequence; D003080:Cold Temperature; D017343:Genes, Plant / Q000235:genetics*; D014644:Genetic Variation; D006239:Haplotypes / Q000235:genetics; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D009922:Oregon; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D028224:Pseudotsuga / Q000235:genetics*; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA; D014861:Washington