Data from: The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

DOI

Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in TomLoxC promoter selected against during domestication. QTL mapping and analysis of transgenic plants reveal a novel role for TomLoxC in apocarotenoid production, which contributes to desirable tomato flavor. In orange-stage fruit, accessions harboring both the rare and common TomLoxC alleles (heterozygotes) have higher TomLoxC expression than those homozygous for either, and are resurgent in modern tomatoes. The tomato pan-genome adds depth and completeness to the reference genome, and is useful for future biological discovery and breeding.

Identifier
DOI http://dx.doi.org/doi:10.5061/dryad.m463f7k
Metadata Access https://easy.dans.knaw.nl/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=oai:easy.dans.knaw.nl:easy-dataset:127169
Provenance
Creator Tieman, Denise M.;Canizares, Joaquin;Ma, Qiyue;Gao, Lei;Klee, Harry J.;Sacks, Gavin L.;Sun, Honghe;Fei, Zhangjun;van der Knaap, Esther;Fish, Tara L.;Thannhauser, Theodore W.;Huang, Sanwen;Foolad, Majid R.;Gonda, Itay;Burzynski-Chang, Elizabeth A.;Xu, Yimin;Bao, Kan;Giovannoni, James J.;Diez, Maria Jose;Stromberg, Kaitlin A.
Publisher Data Archiving and Networked Services (DANS)
Publication Year 2019
Rights info:eu-repo/semantics/openAccess
Representation
Resource Type Dataset
Coverage
Discipline Medicine
Temporal Point 2019-05-14T11:59:59Z