@article{fdi:010048406,
  title = {{D}iversity of the {T}y-1 copia retrotransposon {T}os17 in rice ({O}ryza sativa {L}.) and the {AA} genome of the {O}ryza genus},
  author = {{P}etit, {J}. and {B}ourgeois, {E}. and {S}tenger, {W}. and {B}es, {M}. and {D}roc, {G}. and {M}eynard, {D}. and {C}ourtois, {B}. and {G}hesqui{\`e}re, {A}lain and {S}abot, {F}ran{\c{c}}ois and {P}anaud, {O}. and {G}uiderdoni, {E}.},
  editor = {},
  language = {{ENG}},
  abstract = {{R}etrotransposons are mobile genetic elements, ubiquitous in {E}ukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. {W}e investigate here the diversity of the {T}y1-copia retrotransposon {T}os17 in the cultivated rice of {A}sian origin ({O}ryza sativa {L}.) and related {AA} genome species of the {O}ryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the element in the lineages. {I}n that aim, we used a combination of {S}outhern hybridization with a reverse transcriptase ({RT}) probe and an adapter-{PCR} mediated amplification, which allowed the sequencing of the genomic regions flanking {T}os17 insertions. {T}his analysis was carried out in a collection of 47 {A}-genome {O}ryza species accessions and 202 accessions of a core collection of {O}ryza sativa {L}. representative of the diversity of the species. {O}ur {S}outhern hybridization results show that {T}os17 is present in all the accessions of the {A}-genome {O}ryza species, except for the {S}outh {A}merican species {O}. glumaepatula and the {A}frican species {O}. glaberrima and {O}. breviligulata. {I}n {O}. sativa, the number of putative copies of {T}os17 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. {A}dapter {PCR} amplification and sequencing of flanking regions of {T}os17 insertions in {A}-genome species other than {O}. sativa, followed by anchoring on the {N}ipponbare genome sequence, revealed 13 insertion sites of {T}os17 in the surveyed {O}. rufipogon and {O}. longistaminata accessions, including one shared by both species. {I}n {O}. sativa, the same approach revealed 25 insertions in the 6 varietal groups. {F}our insertion sites located on chromosomes 1, 2, 10, and 11 were found orthologous in {O}. rufipogon and {O}. sativa. {T}he chromosome 1 insertion was also shared between {O}. rufipogon and {O}. longistaminata. {T}he presence of {T}os17 at three insertion sites was confirmed by retrotransposon-based insertion polymorphism ({RBIP}) in a sample of {O}. sativa accessions. {T}he first insertion, located on chromosome 3 was only found in two japonica accessions from the {B}hutan region while the second insertion, located on chromosome 10 was specific to the varietal groups 1, 2, and 5. {T}he third insertion located on chromosome 7 corresponds to the only insertion shown active in rice so far, notably in cv. {N}ipponbare, where it has been extensively used for insertion mutagenesis. {T}his copy was only found in a few varieties of the japonica group 6 and in one group 5 accession. {T}aken together, these results confirm that {T}os17 was probably present in the ancestor of {A}-genome species and that some copies of the element remained active in some {O}ryza lineages-notably in {O}. rufipogon and {O}. longistaminata-as well as in the indica and japonica {O}. sativa {L}. lineages.},
  keywords = {{D}iversity ; {O}ryza sativa {L}. ; {AA} genome ; {T}os17 ; {R}etrotransposon},
  booktitle = {},
  journal = {{M}olecular {G}enetics and {G}enomics},
  volume = {282},
  numero = {6},
  pages = {633--652},
  ISSN = {1617-4615},
  year = {2009},
  DOI = {10.1007/s00438-009-0493-z},
  URL = {https://www.documentation.ird.fr/hor/fdi:010048406},
}