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 the TomLoxC promoter selected against during domestication. Quantitative trait locus mapping and analysis of transgenic plants reveal a 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.
%0 Journal Article
%1 gao2019tomato
%A Gao, L
%A Gonda, I
%A Sun, H
%A Ma, Q
%A Bao, K
%A Tieman, D M
%A Burzynski-Chang, E A
%A Fish, T L
%A Stromberg, K A
%A Sacks, G L
%A Thannhauser, T W
%A Foolad, M R
%A Diez, M J
%A Blanca, J
%A Canizares, J
%A Xu, Y
%A van der Knaap, E
%A Huang, S
%A Klee, H J
%A Giovannoni, J J
%A Fei, Z
%D 2019
%J Nat Genet
%K pangenome species_complex tomato
%N 6
%P 1044-1051
%R 10.1038/s41588-019-0410-2
%T The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor
%U https://www.ncbi.nlm.nih.gov/pubmed/31086351
%V 51
%X 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 the TomLoxC promoter selected against during domestication. Quantitative trait locus mapping and analysis of transgenic plants reveal a 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.
@article{gao2019tomato,
abstract = {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 the TomLoxC promoter selected against during domestication. Quantitative trait locus mapping and analysis of transgenic plants reveal a 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.},
added-at = {2019-07-03T23:37:46.000+0200},
author = {Gao, L and Gonda, I and Sun, H and Ma, Q and Bao, K and Tieman, D M and Burzynski-Chang, E A and Fish, T L and Stromberg, K A and Sacks, G L and Thannhauser, T W and Foolad, M R and Diez, M J and Blanca, J and Canizares, J and Xu, Y and van der Knaap, E and Huang, S and Klee, H J and Giovannoni, J J and Fei, Z},
biburl = {https://www.bibsonomy.org/bibtex/2d9abaf4a56281845ff94ce4b80dc5ad5/peter.ralph},
doi = {10.1038/s41588-019-0410-2},
interhash = {36aaafebd1aa626d419d6915792a4ef6},
intrahash = {d9abaf4a56281845ff94ce4b80dc5ad5},
journal = {Nat Genet},
keywords = {pangenome species_complex tomato},
month = {06},
number = 6,
pages = {1044-1051},
pmid = {31086351},
timestamp = {2019-07-03T23:37:46.000+0200},
title = {The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor},
url = {https://www.ncbi.nlm.nih.gov/pubmed/31086351},
volume = 51,
year = 2019
}