Genome Scan to Detect Genetic Structure and Adaptive Genes of Natural Populations of Cryptomeria japonica

We investigated 29 natural populations of Cryptomeria japonica using 148 cleaved amplified polymorphic sequence markers to elucidate their genetic structure and identify candidate adaptive genes of this species. In accordance with the inferred evolutionary history of the species during and after the...

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Vydáno v:Genetics (Austin) Ročník 176; číslo 4; s. 2393 - 2403
Hlavní autoři: Tsumura, Yoshihiko, Kado, Tomoyuki, Takahashi, Tomokazu, Tani, Naoki, Ujino-Ihara, Tokuko, Iwata, Hiroyoshi
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States Genetics Soc America 01.08.2007
Genetics Society of America
Copyright © 2007 by the Genetics Society of America
Témata:
Adaptation, Physiological
Adaptation, Physiological - genetics
Amplified Fragment Length Polymorphism Analysis
chromosome mapping
Cryptomeria
Cryptomeria - genetics
Cryptomeria - physiology
Cryptomeria japonica
Deoxyribonucleic acid
DNA
DNA, Plant
DNA, Plant - genetics
Evolution, Molecular
Forests
Gene expression
genes
Genes, Plant
Genetic diversity
Genetic Markers
Genetic structure
Genetic Variation
genetics
Genetics, Population
Genomics
heterozygosity
Investigations
Japan
loci
Models, Genetic
Natural populations
Numbers
Phylogeny
physiology
plant genetics
population genetics
Studies
Trees
Japan
ISSN:0016-6731, 1943-2631, 1943-2631
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Shrnutí:We investigated 29 natural populations of Cryptomeria japonica using 148 cleaved amplified polymorphic sequence markers to elucidate their genetic structure and identify candidate adaptive genes of this species. In accordance with the inferred evolutionary history of the species during and after the last glacial episode, the genetic diversity was higher in western populations than in northern populations. The results of phylogenetic and genetic structure analyses suggest that populations of the two main varieties of the species have clearly diverged from each other and that two of the examined loci are strongly associated with the differentiation between the two varieties. Using a coalescent simulation based on FST and He values, we detected five genes that had higher, and two that had lower, values than the respective 99% confidence intervals (C.I.s) that are theoretically expected intervals under a neutral infinite-island model. We also detected 13 outlier loci using a coalescent simulation based on the assumption that the 2 varieties originated from the splitting of an ancestral population. Four of these loci were detected by both methods, two of which were detected in a genetic structure analysis as loci associated with differentiation between the two varieties of the species, and are strong candidates for genes that have been subject to selection.
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Corresponding author: Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan. E-mail: ytsumu@ffpri.affrc.go.jp
Communicating editor: O. Savolainen
ISSN:0016-6731
1943-2631
1943-2631
DOI:10.1534/genetics.107.072652