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.
Highlights
Tomatoes come in a multitude of shapes and flavors despite a narrow genetic pool
We show that TE insertions polymorphisms (TIPs) tend to have large transcriptional effects when located within or near genes and long-read Nanopore transcriptomics reveals that intronic transposable elements (TEs) insertions can generate multiple transcript isoforms with potential phenotypic consequences
The vast majority of these annotations correspond to ancestral TE copies that have degenerated to different degrees and potentially lost their ability to transpose[24]
Summary
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. 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 These findings highlight the unique role of TE mobilization in tomato diversification, with important implications for breeding. While genomics-enabled genetics has revolutionized our ability to identify loci underlying domestication and improvement traits in virtually any crop[4,5,6], our understanding of the genetic basis of crop diversity is still limited This situation stems in part from the fact that, with few notable exceptions[7,8,9,10,11], most genome-wide association studies (GWAS) consider only single-nucleotide polymorphisms (SNPs) and short indels[12,13], when structural variants, which include gene presence/absence variants and typically segregate at low frequency, account for the largest amount of DNA sequence differences between individuals and cultivars[3,10,11,14]. Our approaches and findings provide a framework to study the implication of TIPs to crop diversity
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