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Citation for Study 16453

Citation title: "Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins".

Study name: "Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins".

This study is part of submission 16453 (Status: Published).

Citation

Menda N., Strickler S.R., Edwards J.D., Bombarely A., Dunham D.M., Martin G.B., Mejia L., Hutton S.F., Havey M.J., Maxwell D.P., & Mueller L.A. 2014. Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins. BMC Plant Biology, .

Authors

• Menda N. (submitter) 607-254-3569
• Strickler S.R.
• Edwards J.D.
• Bombarely A.
• Dunham D.M.
• Martin G.B.
• Mejia L.
• Hutton S.F.
• Havey M.J.
• Maxwell D.P.
• Mueller L.A.

Abstract

Background Decades of intensive tomato breeding using wild-species germplasm have resulted in the genomes of domesticated germplasm (Solanum lycopersicum) being intertwined with introgressions from their wild relatives. Comparative analysis of genomes among cultivated tomatoes and wild species that have contributed genetic variation can help identify desirable genes, such as those conferring disease resistance. The ability to identify introgression position, borders, and contents can reveal ancestral origins and facilitate harnessing of wild variation in crop breeding. Results Here we present the whole-genome sequences of two tomato inbreds, Gh13 and BTI-87, both carrying the begomovirus resistance locus Ty-3 introgressed from wild tomato species. Introgressions of different sizes on chromosome 6 of Gh13 and BTI-87, both corresponding to the Ty-3 region, were identified as from a source close to the wild species S. chilense. Other introgressions were identified throughout the genomes of the inbreds and showed major differences in the breeding pedigrees of the two lines. Interestingly, additional large introgressions from the close tomato relative S. pimpinellifolium were identified in both lines. Some of the polymorphic regions were attributed to introgressions in the reference Heinz 1706 genome, indicating wild genome sequences in the reference tomato genome. Conclusions The methods developed in this work can be used to delineate genome introgressions, and subsequently contribute to development of molecular markers to aid phenotypic selection, fine mapping and discovery of candidate genes for important phenotypes, and for identification of novel variation for tomato improvement. These universal methods can easily be applied to other crop plants.

Keywords

Solanum lycopersicum, Solanum pimpinellifolium, Solanum chilense, genomic introgressions, genome sequencing, disease resistance, single nucleotide polymorphism, wild species, domestication, phylogenetics

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S16453
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref23725,
  	 author = {Naama  Menda and Susan R Strickler and Jeremy D Edwards and Aureliano  Bombarely and Diane M Dunham and Gregory B Martin and Luis  Mejia and Samuel F Hutton and Michael J Havey and Douglas P Maxwell and Lukas A Mueller},
  	 title = {Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins},
  	 year = {2014},
  	 keywords = {Solanum lycopersicum, Solanum pimpinellifolium, Solanum chilense, genomic introgressions, genome sequencing, disease resistance, single nucleotide polymorphism, wild species, domestication, phylogenetics},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {BMC Plant Biology},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Background
  Decades of intensive tomato breeding using wild-species germplasm have resulted in the genomes of domesticated germplasm (Solanum lycopersicum) being intertwined with introgressions from their wild relatives. Comparative analysis of genomes among cultivated tomatoes and wild species that have contributed genetic variation can help identify desirable genes, such as those conferring disease resistance. The ability to identify introgression position, borders, and contents can reveal ancestral origins and facilitate harnessing of wild variation in crop breeding.
  Results
  Here we present the whole-genome sequences of two tomato inbreds, Gh13 and BTI-87, both carrying the begomovirus resistance locus Ty-3 introgressed from wild tomato species. Introgressions of different sizes on chromosome 6 of Gh13 and BTI-87, both corresponding to the Ty-3 region, were identified as from a source close to the wild species S. chilense. Other introgressions were identified throughout the genomes of the inbreds and showed major differences in the breeding pedigrees of the two lines. Interestingly, additional large introgressions from the close tomato relative S. pimpinellifolium were identified in both lines. Some of the polymorphic regions were attributed to introgressions in the reference Heinz 1706 genome, indicating wild genome sequences in the reference tomato genome.
  Conclusions
  The methods developed in this work can be used to delineate genome introgressions, and subsequently contribute to development of molecular markers to aid phenotypic selection, fine mapping and discovery of candidate genes for important phenotypes, and for identification of novel variation for tomato improvement. These universal methods can easily be applied to other crop plants.
  }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 23725
  AU  - Menda,Naama 
  AU  - Strickler,Susan R
  AU  - Edwards,Jeremy D
  AU  - Bombarely,Aureliano 
  AU  - Dunham,Diane M
  AU  - Martin,Gregory B
  AU  - Mejia,Luis 
  AU  - Hutton,Samuel F
  AU  - Havey,Michael J
  AU  - Maxwell,Douglas P
  AU  - Mueller,Lukas A
  T1  - Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins
  PY  - 2014
  KW  - Solanum lycopersicum
  KW  - Solanum pimpinellifolium
  KW  - Solanum chilense
  KW  - genomic introgressions
  KW  - genome sequencing
  KW  - disease resistance
  KW  - single nucleotide polymorphism
  KW  - wild species
  KW  - domestication
  KW  - phylogenetics
  UR  - http://dx.doi.org/
  N2  - Background
  Decades of intensive tomato breeding using wild-species germplasm have resulted in the genomes of domesticated germplasm (Solanum lycopersicum) being intertwined with introgressions from their wild relatives. Comparative analysis of genomes among cultivated tomatoes and wild species that have contributed genetic variation can help identify desirable genes, such as those conferring disease resistance. The ability to identify introgression position, borders, and contents can reveal ancestral origins and facilitate harnessing of wild variation in crop breeding.
  Results
  Here we present the whole-genome sequences of two tomato inbreds, Gh13 and BTI-87, both carrying the begomovirus resistance locus Ty-3 introgressed from wild tomato species. Introgressions of different sizes on chromosome 6 of Gh13 and BTI-87, both corresponding to the Ty-3 region, were identified as from a source close to the wild species S. chilense. Other introgressions were identified throughout the genomes of the inbreds and showed major differences in the breeding pedigrees of the two lines. Interestingly, additional large introgressions from the close tomato relative S. pimpinellifolium were identified in both lines. Some of the polymorphic regions were attributed to introgressions in the reference Heinz 1706 genome, indicating wild genome sequences in the reference tomato genome.
  Conclusions
  The methods developed in this work can be used to delineate genome introgressions, and subsequently contribute to development of molecular markers to aid phenotypic selection, fine mapping and discovery of candidate genes for important phenotypes, and for identification of novel variation for tomato improvement. These universal methods can easily be applied to other crop plants.
  
  L3  - 
  JF  - BMC Plant Biology
  VL  - 
  IS  - 
  ER  -