Genomic analyses provide insights into the history of tomato breeding

Nat Genet. 2014 Nov;46(11):1220-6. doi: 10.1038/ng.3117. Epub 2014 Oct 12.

Abstract

The histories of crop domestication and breeding are recorded in genomes. Although tomato is a model species for plant biology and breeding, the nature of human selection that altered its genome remains largely unknown. Here we report a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions. We provide evidence that domestication and improvement focused on two independent sets of quantitative trait loci (QTLs), resulting in modern tomato fruit ∼100 times larger than its ancestor. Furthermore, we discovered a major genomic signature for modern processing tomatoes, identified the causative variants that confer pink fruit color and precisely visualized the linkage drag associated with wild introgressions. This study outlines the accomplishments as well as the costs of historical selection and provides molecular insights toward further improvement.

Publication types

  • Historical Article
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • Breeding / history*
  • Breeding / methods
  • Chromosome Mapping
  • Cluster Analysis
  • Genetics, Population
  • Genome, Plant / genetics*
  • History, Ancient
  • Likelihood Functions
  • Linkage Disequilibrium
  • Lycopersicon esculentum / genetics*
  • Lycopersicon esculentum / history
  • Models, Genetic
  • Molecular Sequence Data
  • Phylogeny*
  • Pigmentation / genetics
  • Polymorphism, Single Nucleotide / genetics
  • Quantitative Trait Loci / genetics*
  • Selection, Genetic / genetics*
  • Sequence Analysis, DNA

Associated data

  • SRA/SRP045767