Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

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. (July 2020) Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell, 182 (1). 145-161.e23. ISSN 0092-8674 (Print)0092-8674

URL: https://pubmed.ncbi.nlm.nih.gov/32553272/
DOI: 10.1016/j.cell.2020.05.021

Abstract

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-to-phenotype relationships and their widespread importance and utility in crop improvement.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
organism description > plant behavior
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > alleles
organism description > plant behavior > crop yield improvement
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > genome annotation
CSHL Authors:
Communities: CSHL labs > Gillis Lab
CSHL labs > Lippman lab
CSHL labs > McCombie lab
CSHL labs > Schatz lab
School of Biological Sciences > Publications
CSHL Cancer Center Program
CSHL Cancer Center Program > Cancer Genetics and Genomics Program
CSHL Cancer Center Shared Resources
Depositing User: Matthew Dunn
Date: 9 July 2020
Date Deposited: 30 Nov 2020 20:11
Last Modified: 13 Feb 2024 19:48
PMCID: PMC7354227
Related URLs:
URI: https://repository.cshl.edu/id/eprint/39748

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