Nucleotide diversity and linkage disequilibrium in cold-hardiness- and wood quality-related candidate genes in Douglas fir

被引：124

作者：

Krutovsky, KV ^{[1
]}

Neale, DB ^{[1
]}

机构：

[1] Univ Calif Davis, Inst Forest Genet, Pacific SW Res Stn, USDA Forest Serv,Dept Plant Sci, Davis, CA 95616 USA

来源：

GENETICS | 2005年 / 171卷 / 04期

关键词：

D O I：

10.1534/genetics.105.044420

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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 by 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.

引用

页码：2029 / 2041

页数：13

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