Not AvailableTwo major nuclear genes, Rf3 and Rf4, are
known to be associated with fertility restoration of
wild-abortive cytoplasmic male sterility (WA-CMS)
in rice. In the present study, through a comparative
sequence analysis of the reported putative candidate
genes, viz. PPR9-782-(M,I) and PPR762 (for Rf4) and
SF21 (for Rf3), among restorer and maintainer lines of
rice, we identified significant polymorphism between
the two lines and developed a set of PCR-based
codominant markers, which could distinguish maintainers
from restorers. Among the five markers
developed targeting the polymorphisms in PPR9-
782-(M,I), the marker RMS-PPR9-1 was observed to
show clear polymorphism between the restorer
(n = 120) and maintainer lines (n = 44) analyzed.
Another codominant marker, named RMS-PPR762
targeting PPR762, displayed a lower efficiency in
identification of restorers and maintainers, indicating
that PPR9-782-(M,I) is indeed the candidate gene for
Rf4. With respect to Rf3, a codominant marker, named
RMS-SF21-5 developed targeting SF21, displayed
significantly lower efficiency in identification of
restorers and non-restorers as compared to the Rf4-
specific markers. Validation of these markers in a F2
mapping population segregating for fertility restoration
indicated that Rf4 has a major influence on
fertility restoration and Rf3 is a minor gene. Further,
the functional marker RMS-PPR9-1 was observed to
be very useful in identification of impurities in a seed
lot of the popular hybrid, DRRH3. Interestingly, when
RMS-PPR9-1 and RMS-SF21-5 were considered in
conjunction with analysis, near-complete, marker–
trait co-segregation was observed, indicating that
deployment of the candidate gene-specific markers
both Rf4 and Rf3, together, can be helpful in accurate
identification of fertility restorer lines and can facilitate
targeted transfer of the two restorer genes into
elite varieties through marker-assisted breeding.Not Availabl