Details

Autor(en) / Beteiligte

• Castanera, Raúl
• Vendrell‐Mir, Pol
• Bardil, Amélie
• Carpentier, Marie‐Christine
• Panaud, Olivier
• Casacuberta, Josep M.

Titel

Amplification dynamics of miniature inverted‐repeat transposable elements and their impact on rice trait variability

Ist Teil von

• The Plant journal : for cell and molecular biology, 2021-07, Vol.107 (1), p.118-135

Ort / Verlag

Oxford: Blackwell Publishing Ltd

Erscheinungsjahr

2021

Quelle

Wiley Online Library - AutoHoldings Journals

Beschreibungen/Notizen

• Summary Transposable elements (TEs) are a rich source of genetic variability. Among TEs, miniature inverted‐repeat TEs (MITEs) are of particular interest as they are present in high copy numbers in plant genomes and are closely associated with genes. MITEs are deletion derivatives of class II transposons, and can be mobilized by the transposases encoded by the latter through a typical cut‐and‐paste mechanism. However, MITEs are typically present at much higher copy numbers than class II transposons. We present here an analysis of 103 109 transposon insertion polymorphisms (TIPs) in 738 Oryza sativa genomes representing the main rice population groups. We show that an important fraction of MITE insertions has been fixed in rice concomitantly with its domestication. However, another fraction of MITE insertions is present at low frequencies. We performed MITE TIP‐genome‐wide association studies (TIP‐GWAS) to study the impact of these elements on agronomically important traits and found that these elements uncover more trait associations than single nucleotide polymorphisms (SNPs) on important phenotypes such as grain width. Finally, using SNP‐GWAS and TIP‐GWAS we provide evidence of the replicative amplification of MITEs. Significance Statement We performed genome‐wide association studies using miniature inverted‐repeat transposable element insertions as genotype information and found that they uncover more associations with agronomically important traits than single nucleotide polymorphisms. These analyses also provide evidence of the replicative amplification of miniature inverted‐repeat transposable elements.