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The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor
Year:
2019
Source of publication :
Nature Genetics
Authors :
גונדה, איתי
;
.
Volume :
51
Co-Authors:

Gao, L., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States;  Sun, H., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States; Ma, Q., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States; Bao, K., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States; Tieman, D.M., Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL, United States; Burzynski-Chang, E.A., Department of Food Science, Cornell University, Ithaca, NY, United States; Fish, T.L., US Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States; Stromberg, K.A., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States; Sacks, G.L., Department of Food Science, Cornell University, Ithaca, NY, United States; Thannhauser, T.W., US Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States; Foolad, M.R., Department of Plant Science, The Pennsylvania State University, University Park, PA, United States; Diez, M.J., Institute for the Conservation and Improvement of Agricultural Biodiversity, Polytechnic University of Valencia, Valencia, Spain; Blanca, J., Institute for the Conservation and Improvement of Agricultural Biodiversity, Polytechnic University of Valencia, Valencia, Spain; Canizares, J., Institute for the Conservation and Improvement of Agricultural Biodiversity, Polytechnic University of Valencia, Valencia, Spain; Xu, Y., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States; van der Knaap, E., Department of Horticulture, University of Georgia, Athens, GA, United States; Huang, S., Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; Klee, H.J., Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL, United States; Giovannoni, J.J., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States, US Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States; Fei, Z., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States, US Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States

Facilitators :
From page:
1044
To page:
1051
(
Total pages:
8
)
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.

Note:
Related Files :
Fruit Flavor
tomato
עוד תגיות
תוכן קשור
More details
DOI :
10.1038/s41588-019-0410-2
Article number:
0
Affiliations:
Database:
סקופוס
Publication Type:
מאמר
;
.
Language:
אנגלית
Editors' remarks:
ID:
41038
Last updated date:
02/03/2022 17:27
Creation date:
28/05/2019 11:26
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Scientific Publication
The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor
51

Gao, L., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States;  Sun, H., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States; Ma, Q., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States; Bao, K., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States; Tieman, D.M., Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL, United States; Burzynski-Chang, E.A., Department of Food Science, Cornell University, Ithaca, NY, United States; Fish, T.L., US Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States; Stromberg, K.A., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States; Sacks, G.L., Department of Food Science, Cornell University, Ithaca, NY, United States; Thannhauser, T.W., US Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States; Foolad, M.R., Department of Plant Science, The Pennsylvania State University, University Park, PA, United States; Diez, M.J., Institute for the Conservation and Improvement of Agricultural Biodiversity, Polytechnic University of Valencia, Valencia, Spain; Blanca, J., Institute for the Conservation and Improvement of Agricultural Biodiversity, Polytechnic University of Valencia, Valencia, Spain; Canizares, J., Institute for the Conservation and Improvement of Agricultural Biodiversity, Polytechnic University of Valencia, Valencia, Spain; Xu, Y., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States; van der Knaap, E., Department of Horticulture, University of Georgia, Athens, GA, United States; Huang, S., Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; Klee, H.J., Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL, United States; Giovannoni, J.J., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States, US Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States; Fei, Z., Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, United States, US Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States

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

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.

Scientific Publication
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