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The impact of transposable elements on tomato diversity.

Abstract：

:Tomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leverage whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity. We identify 6,906 TE insertions polymorphisms (TIPs), which result from the mobilization of 337 distinct TE families. Most TIPs are low frequency variants and TIPs are disproportionately located within or adjacent to genes involved in environmental responses. In addition, genic TE insertions tend to have strong transcriptional effects and they can notably lead to the generation of multiple transcript isoforms. Using genome-wide association studies (GWAS), we identify at least 40 TIPs robustly associated with extreme variation in major agronomic traits or secondary metabolites and in most cases, no SNP tags the TE insertion allele. Collectively, these findings highlight the unique role of TE mobilization in tomato diversification, with important implications for breeding.

journal_name

Nat Commun

journal_title

Nature communications

authors

Domínguez M,Dugas E,Benchouaia M,Leduque B,Jiménez-Gómez JM,Colot V,Quadrana L

doi

10.1038/s41467-020-17874-2

subject

Has Abstract

pub_date

2020-08-13 00:00:00

pages

4058

issue

1

issn

2041-1723

pii

10.1038/s41467-020-17874-2

journal_volume

11

pub_type

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