Not AvailableWA-CMS system based rice hybrids are
widely adopted in many rice growing countries,
including India. Even though it is well known that the
trait is controlled by mitochondria, the genes underpinning
the trait remain enigmatic. In the present
study, a complete genome-wide comparative
sequence analysis was performed using draft mitochondrial
genomes of WA-CMS and male fertile lines
in a step-wise manner, progressively covering
5–10 kb every time through BLASTN tool. The
sequence polymorphisms identified in different mitochondrial
regions were targeted to develop two
different sets of dominant PCR-based markers, one
consisting of six markers targeting WA-CMS mitochondria,
the other set consisting of five markers
targeting male fertile mitochondria in addition to
development of a set of eight co-dominant PCR-based
markers targeting both the genomes. When a set of
candidate genes/ORFs reported earlier to be associated
with WA-CMS trait in rice were analyzed
through RT-PCR of RNA isolated from immature
rice florets, it was observed that the chimeric ORF,
WA352 is expressed only in WA-CMS line and hybrid
(i.e. genotypes containing sterile mitochondria),
indicating it’s candidacy for the WA-CMS trait.
Targeting the functional nucleotide polymorphism
between WA-CMS and maintainer mitochondria with
respect to WA352, two dominant markers, one
targeting sterile and another targeting fertile mitochondria
were developed. In addition, a robust, codominant
functional marker targeting the candidate
gene was also developed and validated for its utility
in identification of genetic impurities in seed lots of
WA-CMS lines.Not Availabl