The impact of transposable elements on the structure, evolution and function of the rice genome

Akakpo, Roland; Carpentier, Marie-Christine; Hsing, Y. I.; Panaud, Olivier

doi:10.1111/nph.16356

Cited by 64 publications

(64 citation statements)

References 53 publications

(59 reference statements)

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“…Likewise, we found that most TE insertions in tomato are low-frequency variants rarely tagged by SNPs. Thus, our findings reinforce the notions that TIPs and SNPs contribute distinct phenotypic variants, and that TIPs identified in GWAS as leading variants are likely causal [7][8][9][10] , which opens up the way for their use for future breeding.…”

Section: Discussionsupporting

confidence: 83%

“…Here, we show that TIPs, which to date have been ignored from population genomic studies in tomato, are an important diversifying force to consider, as has been proposed for other plant species 27,33,34,[50][51][52][53][54][55] . For instance, GWAS in rice for grain length and width using respectively structural variants and TIPs uncovered associations that could not be detected using SNP data 8,9 . Moreover, in the case of grain width, the associated TIP is very rare and in low LD with nearby SNPs.…”

Section: Discussionmentioning

confidence: 99%

“…Nonetheless, 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 . Furthermore, the majority of structural variants result from the mobilization of transposable elements (TEs), which by themselves are potentially an important source of large-effect alleles 15 .…”

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confidence: 99%

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The impact of transposable elements on tomato diversity

et al. 2020

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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.

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Section: Discussionsupporting

confidence: 83%

Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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The impact of transposable elements on tomato diversity

et al. 2020

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“…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, account for the largest amount of DNA sequence differences between individuals and cultivars 3,10,11,14 . Furthermore, the majority of structural variants result from the mobilization of transposable elements (TEs), which by themselves are potentially an important source of large effect alleles 15 .…”

Section: Abstract (156 Words)mentioning

confidence: 99%

The impact of transposable elements on tomato diversity

Domínguez

Dugas

Benchouaia

et al. 2020

Preprint

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Tomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leveraged whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity. We identified 6,906 TE insertions polymorphisms (TIPs), which result from the mobilization of 337 distinct TE families. Most TIPs are low frequency variants and disproportionately located within or adjacent to genes involved in environmental response. In addition, we show that genic TE insertions tend to have strong transcriptional effects and can notably lead to the generation of multiple transcript isoforms. We also uncovered through genome-wide association studies (GWAS) ~180 TIPs associated with extreme variations in major agronomic traits or secondary metabolites. Importantly, these TIPs tend to affect loci that are distinct from those tagged by SNPs. Collectively, our findings suggest a unique and important role for TE mobilization in tomato diversification, with important implications for future breeding.

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“…Transposable elements (TEs) are ubiquitous in the genomes of eukaryotes, and their relocalization within genomes serves to generate genomic plasticity by inducing various types of genic and intergenic mutations that can increase allelic diversity [ 14 , 15 , 16 ]. After being discovered first by McClintock in the 1940s, TEs were initially considered junk or selfish DNA [ 17 , 18 ].…”

Section: Introductionmentioning

confidence: 99%

Epigenetic Variation Induced by Gamma Rays, DNA Methyltransferase Inhibitors, and Their Combination in Rice

Lee

Park

Kwon

et al. 2020

Plants

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DNA methylation plays important roles in the regulation of gene expression and maintenance of genome stability in many organisms, including plants. In this study, we treated rice with gamma rays (GRs) and DNA methyltransferase inhibitors (DNMTis) to induce variations in DNA methylation and evaluated epigenetic diversity using methylation-sensitive amplified polymorphism (MSAP) and transposon methylation display (TMD) marker systems. Comparative and integrated analyses of the data revealed that both GRs and DNMTis alone have epimutagenic effects and that combined treatment enhanced these effects. Calculation of methylation rates based on band scoring suggested that both GRs and DNMTis induce epigenetic diversity by demethylation in a dose-dependent manner, and combined treatment can induce variations more synergistically. The difference in the changes in full and hemi-methylation rates between MSAP and TMD is presumed to be caused by the different genomic contexts of the loci amplified in the two marker systems. Principal coordinate, phylogenic, and population structure analyses commonly yielded two clusters of individuals divided by DNMTi treatment. The clustering pattern was more apparent in TMD, indicating that DNMTis have a stronger effect on hypermethylated repetitive regions. These findings provide a foundation for understanding epigenetic variations induced by GRs and DNMTis and for epigenetic mutation breeding.

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The impact of transposable elements on the structure, evolution and function of the rice genome

Cited by 64 publications

References 53 publications

The impact of transposable elements on tomato diversity

The impact of transposable elements on tomato diversity

The impact of transposable elements on tomato diversity

Epigenetic Variation Induced by Gamma Rays, DNA Methyltransferase Inhibitors, and Their Combination in Rice

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