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Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato
Open accessAbstract
SUMMARY Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV-genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher-order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-tophenotype relationships and their widespread importance and utility in crop improvement.
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Cited by
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Self-citationPan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations
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How the pan-genome is changing crop genomics and improvement
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Metadata
- Authors
- Alonge, M., Wang, X., Benoit, M., Soyk, S., Pereira, L., Zhang, L., Suresh, H., Ramakrishnan, S., Maumus, F., Ciren, D., Levy, Y., Harel, T. H., Shalev-Schlosser, G., Amsellem, Z., Razifard, H., Caicedo, A. L., Tieman, D. M., Klee, H., Kirsche, M., Aganezov, S., Ranallo-Benavidez, T. R., Lemmon, Z. H., Kim, J., Robitaille, G., Kramer, M., Goodwin, S., McCombie, W. R., Hutton, S., Van Eck, J., Gillis, J., Eshed, Y., Sedlazeck, F. J., van der Knaap, E., Schatz, M. C., & Lippman, Z. B.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2020-07
- Volume
- 182
- Issue
- 1
- Pages
- 145-161.e23
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W3036928921
- Cited by
- 819
- References
- 95
- FWCI
- 67.89
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Alonge, M., Wang, X., Benoit, M., Soyk, S., Pereira, L., Zhang, L., Suresh, H., Ramakrishnan, S., Maumus, F., Ciren, D., Levy, Y., Harel, T. H., Shalev-Schlosser, G., Amsellem, Z., Razifard, H., Caicedo, A. L., Tieman, D. M., Klee, H., Kirsche, M., . . . Lippman, Z. B. (2020). Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell. https://doi.org/10.1016/j.cell.2020.05.021
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