Stem rot (Sclerotium oryzae) is an important
disease constraint in Californian rice production. Measurement
of resistance is laborious, and the low heritability
of the trait limits the effectiveness of selection in
breeding programs. Molecular markers linked to the trait
would therefore provide a superior selection screen to
assist in transferring resistance into improved cultivars.
The genetics of resistance to stem rot was studied in the
germplasm line 87-Y-550 (PI566666), which inherited
its resistance from the wild species Oryza rufipogon.
Four crosses of 87-Y-550 with susceptible lines were
made and recombinant inbred lines of only the most-resistant
and most-susceptible progeny within each cross
were advanced for late-generation testing. Approximately
900 AFLP (amplified fragment length polymorphism)
primer combinations were applied to resistant and susceptible
bulks within each cross. One AFLP marker
showed significant association with stem rot resistance
and accounted for approximately 45.0% of the phenotypic
variation in 59 progenies. This marker was mapped on
rice chromosome 2 between the RFLP markers RZ166
and RG139 by using F2-reference population information.
The accuracy of AFLP marker mapping was validated
by size and sequence comparison of AFLP bands
from 87-Y-550 and the reference population. With the
strategy of selective genotyping combined with a parental
survey, two microsatellite markers, RM232 and
RM251, on chromosome 3 were also found associated
with stem rot resistance and accounted for 41.1% and 37.9% of the phenotypic variation, respectively. The
multiple linear regression model included TAA/GTA167
on chromosome 2 and RM232 on chromosome 3 and cumulatively
explained 49.3% of total variation. The molecular
markers linked to stem rot resistance should facilitate
selection for this recalcitrant trait in rice breeding
programs by eliminating the need for early generation
screening.