CiteULike

Delicious

Connotea

Citation for Study 21562

Citation title: "Transposable elements generate population-specific insertional patterns and allelic variation in protein-coding genes of wild emmer wheat (Triticum turgidum ssp. dicoccoides)".

Study name: "Transposable elements generate population-specific insertional patterns and allelic variation in protein-coding genes of wild emmer wheat (Triticum turgidum ssp. dicoccoides)".

This study is part of submission 21562 (Status: Published).

Citation

Domb K., Keidar D., Yaakov B., Khasdan V., & Kashkush K. 2017. Transposable elements generate population-specific insertional patterns and allelic variation in protein-coding genes of wild emmer wheat (Triticum turgidum ssp. dicoccoides). BMC Plant Biology, .

Authors

• Domb K.
• Keidar D.
• Yaakov B. (submitter) 972544727025
• Khasdan V.
• Kashkush K.

Abstract

Background: Natural populations of the tetraploid wild emmer wheat (genome AABB) were previously shown to demonstrate eco-geographically structured genetic and epigenetic diversity. Transposable elements (TEs) might make up a significant part of the genetic and epigenetic structure between individuals and populations because they comprise over 80% of the wild emmer wheat genome. In this study, we performed detailed analyses to assess the dynamics of transposable elements in 50 accessions of wild emmer wheat collected from 5 geographically isolated sites. The analyses included: the copy number variation of TEs among accessions in the five populations, population-unique insertional patterns, and the genetic and epigenetic impact of population-unique/specific TE insertions on protein-coding genes. Results: We assessed the copy numbers of 12 TE families using real-time quantitative PCR, and found significant copy number variation (CNV) in the 50 wild emmer wheat accessions, in a population-specific manner. In some cases the CNV difference reached up to 6-fold. However, the CNV was TE-specific, namely some TE families showed higher copy numbers in one or more populations, and other TE families showed lower copy numbers in the same population(s). Furthermore, we assessed the insertional patterns of 6 TE families using transposon display (TD), and observed significant population-specific insertional patterns. The polymorphism levels of TE-insertional patterns reached 92% among all wild emmer wheat accessions, in some cases. In addition, we observed population-specific/unique TE insertions, some of which were located within or close to protein-coding genes, creating allelic variations in a population-specific manner. We also showed that those genes are differentially expressed in wild emmer wheat. Conclusions: For the first time, this study shows that TEs proliferate in wild emmer wheat in a population-specific manner, creating new alleles of protein-coding genes, which contribute to the divergent evolution of homeologous genes from the A and B subgenomes.

Keywords

Copy number variation, Dicoccoides, Emmer wheat, Genetic variation, Transposable elements, TE dynamics

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S21562
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref27613,
  	 author = {Katherine  Domb and Danielle  Keidar and Beery  Yaakov and Vadim  Khasdan and Khalil  Kashkush},
  	 title = {Transposable elements generate population-specific insertional patterns and allelic variation in protein-coding genes of wild emmer wheat (Triticum turgidum ssp. dicoccoides)},
  	 year = {2017},
  	 keywords = {Copy number variation, Dicoccoides, Emmer wheat, Genetic variation, Transposable elements, TE dynamics},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {BMC Plant Biology},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Background: Natural populations of the tetraploid wild emmer wheat (genome AABB) were previously shown to demonstrate eco-geographically structured genetic and epigenetic diversity. Transposable elements (TEs) might make up a significant part of the genetic and epigenetic structure between individuals and populations because they comprise over 80% of the wild emmer wheat genome. In this study, we performed detailed analyses to assess the dynamics of transposable elements in 50 accessions of wild emmer wheat collected from 5 geographically isolated sites. The analyses included: the copy number variation of TEs among accessions in the five populations, population-unique insertional patterns, and the genetic and epigenetic impact of population-unique/specific TE insertions on protein-coding genes.  
  Results: We assessed the copy numbers of 12 TE families using real-time quantitative PCR, and found significant copy number variation (CNV) in the 50 wild emmer wheat accessions, in a population-specific manner. In some cases the CNV difference reached up to 6-fold. However, the CNV was TE-specific, namely some TE families showed higher copy numbers in one or more populations, and other TE families showed lower copy numbers in the same population(s). 
  Furthermore, we assessed the insertional patterns of 6 TE families using transposon display (TD), and observed significant population-specific insertional patterns. The polymorphism levels of TE-insertional patterns reached 92% among all wild emmer wheat accessions, in some cases. In addition, we observed population-specific/unique TE insertions, some of which were located within or close to protein-coding genes, creating allelic variations in a population-specific manner. We also showed that those genes are differentially expressed in wild emmer wheat.
  Conclusions: For the first time, this study shows that TEs proliferate in wild emmer wheat in a population-specific manner, creating new alleles of protein-coding genes, which contribute to the divergent evolution of homeologous genes from the A and B subgenomes.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 27613
  AU  - Domb,Katherine 
  AU  - Keidar,Danielle 
  AU  - Yaakov,Beery 
  AU  - Khasdan,Vadim 
  AU  - Kashkush,Khalil 
  T1  - Transposable elements generate population-specific insertional patterns and allelic variation in protein-coding genes of wild emmer wheat (Triticum turgidum ssp. dicoccoides)
  PY  - 2017
  KW  - Copy number variation
  KW  - Dicoccoides
  KW  - Emmer wheat
  KW  - Genetic variation
  KW  - Transposable elements
  KW  - TE dynamics
  UR  - http://dx.doi.org/
  N2  - Background: Natural populations of the tetraploid wild emmer wheat (genome AABB) were previously shown to demonstrate eco-geographically structured genetic and epigenetic diversity. Transposable elements (TEs) might make up a significant part of the genetic and epigenetic structure between individuals and populations because they comprise over 80% of the wild emmer wheat genome. In this study, we performed detailed analyses to assess the dynamics of transposable elements in 50 accessions of wild emmer wheat collected from 5 geographically isolated sites. The analyses included: the copy number variation of TEs among accessions in the five populations, population-unique insertional patterns, and the genetic and epigenetic impact of population-unique/specific TE insertions on protein-coding genes.  
  Results: We assessed the copy numbers of 12 TE families using real-time quantitative PCR, and found significant copy number variation (CNV) in the 50 wild emmer wheat accessions, in a population-specific manner. In some cases the CNV difference reached up to 6-fold. However, the CNV was TE-specific, namely some TE families showed higher copy numbers in one or more populations, and other TE families showed lower copy numbers in the same population(s). 
  Furthermore, we assessed the insertional patterns of 6 TE families using transposon display (TD), and observed significant population-specific insertional patterns. The polymorphism levels of TE-insertional patterns reached 92% among all wild emmer wheat accessions, in some cases. In addition, we observed population-specific/unique TE insertions, some of which were located within or close to protein-coding genes, creating allelic variations in a population-specific manner. We also showed that those genes are differentially expressed in wild emmer wheat.
  Conclusions: For the first time, this study shows that TEs proliferate in wild emmer wheat in a population-specific manner, creating new alleles of protein-coding genes, which contribute to the divergent evolution of homeologous genes from the A and B subgenomes.
  L3  - 
  JF  - BMC Plant Biology
  VL  - 
  IS  - 
  ER  -