A large deletion within intron 20 sequence of single-copy PolA1 gene as a useful marker for the speciation in Oryza AA-genome species.

Oryza AA-genome complex comprises five wild species, O. rufipogon , O. barthii , O. longistaminata , O. glumaepatula , and O. meridionalis . Evolutionary relationships among these five wild species have remained contentious and inconclusive. We found that intron 20 of PolA1 , a single-copy nuclear gene, was short (S-type: 141-142 bp) in O. rufipogon , O. barthii , and O. glumaepatula , while long (L-type: ca. 1.5 kb) introns were apparent in O. longistaminata and O. meridionalis . Because Oryza species containing BB, CC, EE, FF, and GG genome showed L-type introns, the S-type intron was probably derived from the L-type intron by the deletion of a 1.4 kb fragment through intramolecular homologous recombination between two tandem TTTTGC repeats. Excluding the large deletion sequence, intron 20 sequence of O. barthii was identical to that of O. longistaminata . As more than 3,470 accessions of O. rufipogon and O. sativa also contained the same intron 20 sequence with O. longistaminata except for single T-nucleotide deletion, which was shared with O. glumaepatuala , the deletion of the T-nucleotide probably occurred in the L-type intron 20 of O. logistaminata . Deletions of a large 1.4 kb fragment and single T-nucleotide within the intron 20 of PolA1 gene were considered as useful DNA markers to study the evolutionary relationships among Oryza AA-genome species.