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Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus

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Abstract

Retrotransposons are mobile genetic elements, ubiquitous in Eukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. We investigate here the diversity of the Ty1-copia retrotransposon Tos17 in the cultivated rice of Asian origin (Oryza sativa L.) and related AA genome species of the Oryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the element in the lineages. In that aim, we used a combination of Southern hybridization with a reverse transcriptase (RT) probe and an adapter-PCR mediated amplification, which allowed the sequencing of the genomic regions flanking Tos17 insertions. This analysis was carried out in a collection of 47 A-genome Oryza species accessions and 202 accessions of a core collection of Oryza sativa L. representative of the diversity of the species. Our Southern hybridization results show that Tos17 is present in all the accessions of the A-genome Oryza species, except for the South American species O. glumaepatula and the African species O. glaberrima and O. breviligulata. In O. sativa, the number of putative copies of Tos17 per accession ranged from 1 to 11 and multivariate analysis based on presence/absence of putative copies yielded a varietal clustering which is consistent with the isozyme classification of rice. Adapter PCR amplification and sequencing of flanking regions of Tos17 insertions in A-genome species other than O. sativa, followed by anchoring on the Nipponbare genome sequence, revealed 13 insertion sites of Tos17 in the surveyed O. rufipogon and O. longistaminata accessions, including one shared by both species. In O. sativa, the same approach revealed 25 insertions in the 6 varietal groups. Four insertion sites located on chromosomes 1, 2, 10, and 11 were found orthologous in O. rufipogon and O. sativa. The chromosome 1 insertion was also shared between O. rufipogon and O. longistaminata. The presence of Tos17 at three insertion sites was confirmed by retrotransposon-based insertion polymorphism (RBIP) in a sample of O. sativa accessions. The first insertion, located on chromosome 3 was only found in two japonica accessions from the Bhutan region while the second insertion, located on chromosome 10 was specific to the varietal groups 1, 2, and 5. The third insertion located on chromosome 7 corresponds to the only insertion shown active in rice so far, notably in cv. Nipponbare, where it has been extensively used for insertion mutagenesis. This copy was only found in a few varieties of the japonica group 6 and in one group 5 accession. Taken together, these results confirm that Tos17 was probably present in the ancestor of A-genome species and that some copies of the element remained active in some Oryza lineages—notably in O. rufipogon and O. longistaminata—as well as in the indica and japonica O. sativa L. lineages.

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Acknowledgments

EB has benefited of a post doctoral grant from the French Genomics Initiative Génoplante. The authors warmly thank Dr M. Yano from NIAS for providing us with seeds of the Nipponbare/Kasalath BCIL population and of their parents.

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Authors and Affiliations

  1. CIRAD, UMR DAP, TAA96/03, 2477 Avenue Agropolis, 34398, Montpellier Cedex 5, France

    Julie Petit, Emmanuelle Bourgeois, Martine Bès, Gaétan Droc, Donaldo Meynard, Brigitte Courtois & Emmanuel Guiderdoni

  2. Université de Perpignan-CNRS, UMR GDP, 52, Avenue Paul Alduy, 66860, Perpignan, France

    Wilfried Stenger & Olivier Panaud

  3. IRD, UMR GDP, 911, Avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France

    Alain Ghesquière & François Sabot

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  1. Julie Petit
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  2. Emmanuelle Bourgeois
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Correspondence to Emmanuel Guiderdoni.

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Communicated by M.-A. Grandbastien.

J. Petit and E. Bourgeois equally contributed to this work.

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438_2009_493_MOESM1_ESM.ppt

Figure 1: Location of Tos17 copies of Nipponbare, Kasalath, IR64 and Azucena and of QTLs related to germinal (He et al. 1998; Yamagishi et al. 1998) and somatic (Taguchi-Shiobara et al. 1997; Takeuchi et al. 2000)tissue culture abilities represented in the IR64/Azucena mapping framework (Huang et al. 1997), Figure 2: Southern hybridization of XbaI digests of DNA isolated from plants regenerated from 4 month-old, seed-embryo derived calli of cvs. Azucena (A) Nipponbare (B) and Kasalath (C) containing 4, 2 and 3 native copies of the retrotransposon Tos 17 respectively. Arrows point position of endogenous copies of Tos17 in the 3 cultivars. A reverse transcriptase probe of Tos17 was used for hybridization, Figure 3: Adapter PCR mediated amplification of regions flanking the 3’ LTR of Tos17 in Ssp1 and EcoRV digests of genomic DNA of O.sativa and O. rufipogon accessions. Supplementary material 1 (PPT 9094 kb)

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Petit, J., Bourgeois, E., Stenger, W. et al. Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus. Mol Genet Genomics 282, 633–652 (2009). https://doi.org/10.1007/s00438-009-0493-z

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