Literature DB >> 22209904

Extended linkage disequilibrium in noncoding regions in a conifer, Cryptomeria japonica.

Etsuko Moritsuka1, Yosuke Hisataka, Miho Tamura, Kentaro Uchiyama, Atsushi Watanabe, Yoshihiko Tsumura, Hidenori Tachida.   

Abstract

We measured linkage disequilibrium in mostly noncoding regions of Cryptomeria japonica, a conifer belonging to Cupressaceae. Linkage disequilibrium was extensive and did not decay even at a distance of 100 kb. The average estimate of the population recombination rate per base pair was 1.55 × 10(-5) and was <1/70 of that in the coding regions. We discuss the impact of low recombination rates in a large part of the genome on association studies.

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Year:  2011        PMID： 22209904      PMCID： PMC3296249          DOI： 10.1534/genetics.111.136697

Source DB:  PubMed          Journal:  Genetics        ISSN： 0016-6731            Impact factor:   4.562


  33 in total

1.  Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers.

Authors:  S M Chaw; C L Parkinson; Y Cheng; T M Vincent; J D Palmer
Journal:  Proc Natl Acad Sci U S A       Date:  2000-04-11       Impact factor: 11.205

2.  Relationships within Cupressaceae sensu lato: a combined morphological and molecular approach.

Authors:  P A Gadek; D L Alpers; M M Heslewood; C J Quinn
Journal:  Am J Bot       Date:  2000-07       Impact factor: 3.844

Review 3.  Structure of linkage disequilibrium in plants.

Authors:  Sherry A Flint-Garcia; Jeffry M Thornsberry; Edward S Buckler
Journal:  Annu Rev Plant Biol       Date:  2003       Impact factor: 26.379

Review 4.  Association genetics of complex traits in conifers.

Authors:  David B Neale; Outi Savolainen
Journal:  Trends Plant Sci       Date:  2004-07       Impact factor: 18.313

5.  Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae).

Authors:  Andrew J Eckert; Andrew D Bower; Santiago C González-Martínez; Jill L Wegrzyn; Graham Coop; David B Neale
Journal:  Mol Ecol       Date:  2010-08-13       Impact factor: 6.185

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

Authors:  Konstantin V Krutovsky; David B Neale
Journal:  Genetics       Date:  2005-09-12       Impact factor: 4.562

Review 7.  Forest tree genomics: growing resources and applications.

Authors:  David B Neale; Antoine Kremer
Journal:  Nat Rev Genet       Date:  2011-02       Impact factor: 53.242

8.  Multilocus patterns of nucleotide diversity and divergence reveal positive selection at candidate genes related to cold hardiness in coastal Douglas Fir (Pseudotsuga menziesii var. menziesii).

Authors:  Andrew J Eckert; Jill L Wegrzyn; Barnaly Pande; Kathleen D Jermstad; Jennifer M Lee; John D Liechty; Brandon R Tearse; Konstantin V Krutovsky; David B Neale
Journal:  Genetics       Date:  2009-07-13       Impact factor: 4.562

9.  Nucleotide diversity and linkage disequilibrium in loblolly pine.

Authors:  Garth R Brown; Geoffrey P Gill; Robert J Kuntz; Charles H Langley; David B Neale
Journal:  Proc Natl Acad Sci U S A       Date:  2004-10-11       Impact factor: 11.205

10.  Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.

Authors:  Susanna Atwell; Yu S Huang; Bjarni J Vilhjálmsson; Glenda Willems; Matthew Horton; Yan Li; Dazhe Meng; Alexander Platt; Aaron M Tarone; Tina T Hu; Rong Jiang; N Wayan Muliyati; Xu Zhang; Muhammad Ali Amer; Ivan Baxter; Benjamin Brachi; Joanne Chory; Caroline Dean; Marilyne Debieu; Juliette de Meaux; Joseph R Ecker; Nathalie Faure; Joel M Kniskern; Jonathan D G Jones; Todd Michael; Adnane Nemri; Fabrice Roux; David E Salt; Chunlao Tang; Marco Todesco; M Brian Traw; Detlef Weigel; Paul Marjoram; Justin O Borevitz; Joy Bergelson; Magnus Nordborg
Journal:  Nature       Date:  2010-03-24       Impact factor: 49.962
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  12 in total

1.  The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae).

Authors:  Andrew J Eckert; Jill L Wegrzyn; John D Liechty; Jennifer M Lee; W Patrick Cumbie; John M Davis; Barry Goldfarb; Carol A Loopstra; Sreenath R Palle; Tania Quesada; Charles H Langley; David B Neale
Journal:  Genetics       Date:  2013-10-11       Impact factor: 4.562

2.  Genome scanning for detecting adaptive genes along environmental gradients in the Japanese conifer, Cryptomeria japonica.

Authors:  Y Tsumura; K Uchiyama; Y Moriguchi; S Ueno; T Ihara-Ujino
Journal:  Heredity (Edinb)       Date:  2012-08-29       Impact factor: 3.821

3.  Genetic differentiation and evolutionary adaptation in Cryptomeria japonica.

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Journal:  G3 (Bethesda)       Date:  2014-10-14       Impact factor: 3.154

4.  Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness.

Authors:  Jérôme Bartholomé; Marco Cam Bink; Joost van Heerwaarden; Emilie Chancerel; Christophe Boury; Isabelle Lesur; Fikret Isik; Laurent Bouffier; Christophe Plomion
Journal:  PLoS One       Date:  2016-11-02       Impact factor: 3.240

5.  Identification of novel putative causative genes and genetic marker for male sterility in Japanese cedar (Cryptomeria japonica D.Don).

Authors:  Kentaro Mishima; Tomonori Hirao; Miyoko Tsubomura; Miho Tamura; Manabu Kurita; Mine Nose; So Hanaoka; Makoto Takahashi; Atsushi Watanabe
Journal:  BMC Genomics       Date:  2018-04-23       Impact factor: 3.969

6.  Distribution of long-range linkage disequilibrium and Tajima's D values in Scandinavian populations of Norway Spruce (Picea abies).

Authors:  Hanna Larsson; Thomas Källman; Niclas Gyllenstrand; Martin Lascoux
Journal:  G3 (Bethesda)       Date:  2013-05-20       Impact factor: 3.154

7.  Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms.

Authors:  Jun Chen; Severin Uebbing; Niclas Gyllenstrand; Ulf Lagercrantz; Martin Lascoux; Thomas Källman
Journal:  BMC Genomics       Date:  2012-11-02       Impact factor: 3.969

8.  Demonstration of genome-wide association studies for identifying markers for wood property and male strobili traits in Cryptomeria japonica.

Authors:  Kentaro Uchiyama; Hiroyoshi Iwata; Yoshinari Moriguchi; Tokuko Ujino-Ihara; Saneyoshi Ueno; Yuriko Taguchi; Miyoko Tsubomura; Kentaro Mishima; Taiichi Iki; Atsushi Watanabe; Norihiro Futamura; Kenji Shinohara; Yoshihiko Tsumura
Journal:  PLoS One       Date:  2013-11-19       Impact factor: 3.240

9.  Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine.

Authors:  Christophe Plomion; Emilie Chancerel; Jeffrey Endelman; Jean-Baptiste Lamy; Eric Mandrou; Isabelle Lesur; François Ehrenmann; Fikret Isik; Marco C A M Bink; Joost van Heerwaarden; Laurent Bouffier
Journal:  BMC Genomics       Date:  2014-03-01       Impact factor: 3.969

10.  A Picea abies linkage map based on SNP markers identifies QTLs for four aspects of resistance to Heterobasidion parviporum infection.

Authors:  Mårten Lind; Thomas Källman; Jun Chen; Xiao-Fei Ma; Jean Bousquet; Michele Morgante; Giusi Zaina; Bo Karlsson; Malin Elfstrand; Martin Lascoux; Jan Stenlid
Journal:  PLoS One       Date:  2014-07-18       Impact factor: 3.240
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