Mapping AFLP markers associated with subspecific differentiation of Oryza sativa (rice) and an investigation of segregation distortion

AFLP marker data were generated for a doubled haploid rice mapping populati on developed from a cross between IR64 (indica) and Azucena (japonica) vari eties, as well as for a diverse set of rice germplasm. A total of 151 AFLP markers were incorporated into an existing restriction fragment length poly morphism framework map and compared with a published map. Markers associate d with the indica-japonica subspecific differentiation in Asian rice were a lso mapped and were found to be distributed throughout the genome. Sources of mapping errors were examined and the possibility of such errors being ca used by co-migration of bands and segregation distortion was explored. In t he case of markers that show distorted segregation, it was concluded that o ne-third of these may be affected by gametophytic/sterility genes and a fut her one-third may arise because of association with the indica-japonica dif ferentiation.