Genetic Resources and Crop Evolution

, Volume 64, Issue 2, pp 405–418 | Cite as

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

Research Article


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 indicajaponica 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.


indicajaponica Insertion-deletion markers Oryza Subspecies-specific markers Wild rice 



This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center, No. PJ01102401), Rural Development Administration, Republic of Korea and support from the Global Rice Science Partnership (GRiSP) to the International Rice Research Institute. The authors thank Christine Jade Dilla-Ermita, Joie Ramos and Eleazar Manalaysay for providing technical support.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Human and animal rights

This research does not involve human participants or animals.

Supplementary material

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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  1. 1.Plant Breeding, Genetics and BiotechnologyInternational Rice Research InstituteManilaPhilippines
  2. 2.Division of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
  3. 3.Division of Agriculture, College of Plant ScienceJilin UniversityChangchunChina
  4. 4.Department of Soil and Crop SciencesTexas A&M UniversityCollege StationUSA

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