Characterization of indica–japonica subspecies-specific InDel loci in wild relatives of rice (Oryza sativa L. subsp. indica Kato and subsp. japonica Kato)

Insertion/deletion (InDel) polymorphisms are generally irreversible and, thus, are useful for evaluating the genetic relationships within the genus Oryza. Moreover, subspecies-specific (SS) InDel markers linked to conserved genomic regions specific to the indica and japonica subspecies of Oryza sativa can provide insight into the genetic relationships between cultivated and wild rice. The evolutionary relationship among Oryza species in respect to their indica and japonica alleles was investigated using 67 selected indica–japonica InDel SS-STS primers across 290 accessions, including 61 Asian cultivated rice (O. sativa) cultivars, 27 African cultivated rice (O. glaberrima) accessions, and 202 accessions of wild Orzya species. The average SS allele frequency of the various Oryza species, from AA-genome to BB ~ EE, and FF ~ HHKK showed an increased proportion of non-O. sativa and null alleles in the more distantly related wild species. Most of the wild species, except the more distant EE, GG, HHJJ, and HHKK genome accessions, consisted of relatively more indica than japonica alleles of SS markers. To validate the SS-STS study, PCR products of nine markers were sequenced across 24–33 accessions. Sequencing results revealed that Oryza species share indica or japonica-like conserved InDel regions even across the different genomes. The presence of some japonica alleles beyond the AA genome at some SS InDel loci also suggests that japonica-specific alleles occurred early in the history of the Oryza genus. The O. sativa sub-species specific markers thus provide further insight into the evolutionary pathway in the genus Oryza and the process of differentiation between indica and japonica.