Journal of Applied Genetics

, Volume 48, Issue 2, pp 107–113

IRAP and REMAP assessments of genetic similarity in rice

  • Castelo J. S. Branco
  • Eduardo A. Vieira
  • Gaspar Malone
  • Mauricio M. Kopp
  • Emilia Malone
  • Albina Bernardes
  • Claudete C. Mistura
  • Fernando I. F. Carvalho
  • Costa A. Oliveira
Original Article

DOI: 10.1007/BF03194667

Cite this article as:
Branco, C.J.S., Vieira, E.A., Malone, G. et al. J Appl Genet (2007) 48: 107. doi:10.1007/BF03194667

Abstract

Rice is a model genome for cereal research, providing important information about genome structure and evolution. Retrotransposons are common components of grass genomes, showing activity at transcription, translation and integration levels. Their abundance and ability to transpose make them good potential markers. In this study, we used 2 multilocus PCR-based techniques that detect retrotransposon integration events in the genome: IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism). Markers derived fromTos17, a copia-like endogenous retrotransposon of rice, were used to identify genetic similarity among 51 rice cultivars (Oryza sativa L.). Genetic similarity analysis was performed by means of the Dice coefficient, and dendrograms were developed by using the average linkage distance method. A cophenetic correlation coefficient was also calculated. The clustering techniques revealed a good adjustment between matrices, with correlation coefficients of 0.74 and 0.80, or lower (0.21) but still significant, between IRAP and REMAP-based techniques. Consistent clusters were found for Japanese genotypes, while a subgroup clustered the irrigated Brazilian genotypes.

Keywords

Oryza sativa L.retrotransposonsTos 17

Copyright information

© Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2007

Authors and Affiliations

  • Castelo J. S. Branco
    • 1
  • Eduardo A. Vieira
    • 2
  • Gaspar Malone
    • 1
  • Mauricio M. Kopp
    • 1
  • Emilia Malone
    • 1
  • Albina Bernardes
    • 1
  • Claudete C. Mistura
    • 1
  • Fernando I. F. Carvalho
    • 1
  • Costa A. Oliveira
    • 1
  1. 1.Eliseu Maciel School of AgronomyFederal University of PelotasPelotasRS-Brazil
  2. 2.Embrapa CerradosBrazil
  3. 3.Bennetzen lab, Department of GeneticsUniversity of GeorgiaAthensUSA