Application of subspecies-specific marker system identified from Oryza sativa to Oryza glaberrima accessions and Oryza sativa ◊ Oryza glaberrima F 1 interspecific progenies

Interspecific hybrids (F1's) between Asian rice (Oryza sativa 2n=24 AA) and African rice (Oryza glaberrima 2n=24 AA) are almost completely sterile. This hybrid sterility barrier is mainly caused by an arrest of pollen development at the microspore stage. Intersubspecific F1 hybrid sterility is mainly caused by cryptic chromosomal aberrations and allelic interaction between indica and japonica. To identify O. glaberrima specific loci, 67 subspecies-specific (SS) sequenced-tagged site (STS) marker were used to evaluate 30 O. glaberrima accessions, which could be classified into sub eleven groups. SPI (subspecies-prototype index) of O. glaberrima accessions ranged from 51.67 to 60.00, suggesting intermediate subspecific type based on whole-genome. Some informative markers for classifying O. glaberrima accessions, called reference markers, S01054, S01160, S02085, S02140, S03041, and S08107, showed indica allele, which might have contributed to genomic diversification of O. glaberrima. Ten (14.9%) SS markers generated glaberrima-specific allele, implying loci adjacent with these markers could be a key for interspecific hybrid sterility. Only 40 (59.7%) SS markers might be useful in O. glaberrima analysis, as other markers did not amplify heterozygous allele in F1 of O. sativa ◊ O. glaberrima.