Amplification dynamics of miniature inverted-repeat transposable elements and their impact on rice trait variability
Castanera, Raúl (Centre de Recerca en Agrigenòmica)
Vendrell-Mir, Pol (Centre de Recerca en Agrigenòmica)
Bardil, Amélie (Centre de Recerca en Agrigenòmica)
Carpentier, Marie-Christine (Université de Perpignan. Laboratoire Génome et Développement des Plantes)
Panaud, Olivier (Université de Perpignan. Laboratoire Génome et Développement des Plantes)
Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)

Data:	2021
Resum:	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.
Ajuts:	Ministerio de Economía y Competitividad AGL2016-78992-R Ministerio de Ciencia e Innovación PID2019-106374RB-I00
Drets:	Tots els drets reservats.
Llengua:	Anglès
Document:	Article ; recerca ; Versió acceptada per publicar
Publicat a:	The Plant journal, Vol. 107, Issue 1 (July 2021) , p. 118-135, ISSN 1365-313X

DOI: 10.1111/tpj.15277

Postprint 46 p, 19.9 MB

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