Tomato domestication: Slowing down the clock

Abstract

Sci. Data 2, 150072 (2015) Crop improvement by selective breeding requires genetically diverse populations, but this selection tends to reduce such diversity. A detailed knowledge of the genome-level diversity available to breeders can help resolve this paradox. To this end, Thomas Schmutzer, Birgit Samans and colleagues have undertaken a comprehensive genome resequencing of a panel of 52 Brassica napus accessions and in the process identified 4.3 million high-confidence, genome-wide single nucleotide polymorphisms (SNPs). Brassica napus-commonly known as oilseed rape or canola-is a major source of vegetable oil for food and biofuel. It is a tetraploid species created by the hybridization of B. rapa and B. oleracea around 7,500 years ago. To obtain the widest possible genetic range, Schmutzer et al. sequenced 32 crop varieties, including two elite modern lines and 20 'synthetic' B. napus accessions. These synthetic lines were created by de novo hybridization of B. rapa and B. oleracea, giving access to a greater diversity of the parental species than is present in cultivated B. napus. Using next-generation sequencing, reads to an average depth of between 12 x and 15x were obtained and aligned against a B. napus reference genome. These individual genome sequences and the associated SNPs will provide a foundation for screening and selection by crop breeders and a resource for exploring the genetics of polyploidy evolution.