title: Patterns of DNA sequence variation at candidate gene loci in black poplar (Populus nigra L.) as revealed by single nucleotide polymorphisms.
abstract: Black poplar (Populus nigra L.) is an economically and ecologically important tree species and an ideal organism for studies of genetic variation. In the present work, we use a candidate gene approach to infer the patterns of DNA variation in natural populations of this species. A total of 312 single nucleotide polymorphisms (SNPs) are found among 8,056 bp sequenced from nine drought-adaptation and photosynthesis-related gene loci. The median SNP frequency is one site per 26 bp. The average nucleotide diversity is calculated to be theta(W) = 0.01074 and pi(T) = 0.00702, higher values than those observed in P. tremula, P. trichocarpa and most conifer species. Tests of neutrality for each gene reveal a general excess of low-frequency mutations, a greater number of haplotypes than expected and an excess of high-frequency derived variants in P. nigra, which is consistent with previous findings that genetic hitchhiking has occurred in this species. Linkage disequilibrium is low, decaying rapidly from 0.45 to 0.20 or less within a distance of 300 bp, although the declines of r(2) are variable among different loci. This is similar to the rate of decay reported in most other tree species. Our dataset is expected to enhance understanding of how evolutionary forces shape genetic variation, and it will contribute to molecular breeding in black poplar.
authors.affiliation: Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, 100091 WanShouShan, Beijing, The People's Republic of China.
authors.forename: Yanguang
authors.initials: Y
authors.lastname: Chu
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Su
authors.forename: Qinjun
authors.initials: Q
authors.lastname: Huang
authors.forename: Xianghua
authors.initials: X
authors.lastname: Zhang
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D001483:Base Sequence; D055864:Droughts; D005060:Europe; D014644:Genetic Variation; D006239:Haplotypes / Q000235:genetics; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010788:Photosynthesis / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D032107:Populus / Q000235:genetics*; D017422:Sequence Analysis, DNA