Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins

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• 作者：Naama Menda (1)
  Susan R Strickler (1)
  Jeremy D Edwards (1)
  Aureliano Bombarely (1)
  Diane M Dunham (1)
  Gregory B Martin (1) (2)
  Luis Mejia (3)
  Samuel F Hutton (4)
  Michael J Havey (5)
  Douglas P Maxwell (6)
  Lukas A Mueller (1)
  
  1. Boyce Thompson Institute for Plant Research ; 533 Tower Rd ; Ithaca ; NY ; 14853 ; USA
  2. Department of Plant Pathology and Plant-Microbe Biology ; Cornell University ; Ithaca ; NY ; 14853 ; USA
  3. Facultad de Agronom铆a ; Universidad de San Carlos de Guatemala ; Guatemala City ; 01012 ; Guatemala
  4. University of Florida ; Gulf Coast Research and Education Center ; 14625 CR 672 ; Wimauma ; FL ; 33598 ; USA
  5. USDA-ARS Department of Horticulture ; University of Wisconsin ; 1575 Linden Drive ; Madison ; WI ; 53706 ; USA
  6. Department of Plant Pathology ; University of Wisconsin-Madison ; Madison ; WI ; 53706 ; USA
  
• 关键词：Solanum lycopersicum ; Solanum pimpinellifolium ; Solanum chilense ; Genomic introgressions ; Genome sequencing ; Disease resistance ; Single nucleotide polymorphism ; Wild species ; Domestication ; Phylogenetics
• 刊名：BMC Plant Biology
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：14
• 期：1
• 全文大小：2,803 KB
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• 刊物主题：Plant Sciences; Agriculture; Tree Biology;
• 出版者：BioMed Central
• ISSN：1471-2229

文摘

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.