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Nat Genet. 2019 Jun;51(6):1044-1051. doi: 10.1038/s41588-019-0410-2. Epub 2019 May 13.

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor.

Author information

1
Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA.
2
Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel.
3
Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL, USA.
4
Department of Food Science, Cornell University, Ithaca, NY, USA.
5
US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA.
6
Department of Plant Science, The Pennsylvania State University, University Park, PA, USA.
7
Institute for the Conservation and Improvement of Agricultural Biodiversity, Polytechnic University of Valencia, Valencia, Spain.
8
Department of Horticulture, University of Georgia, Athens, GA, USA.
9
Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
10
Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA. jjg33@cornell.edu.
11
US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA. jjg33@cornell.edu.
12
Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA. zf25@cornell.edu.
13
US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA. zf25@cornell.edu.

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.

PMID:
31086351
DOI:
10.1038/s41588-019-0410-2
[Indexed for MEDLINE]

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