Salinity is an important abiotic stress that affects agricultural production and productivity. It is a complex trait
that is regulated by different molecular mechanisms. miRNAs are non-coding RNAs which are highly conserved
and regulate gene expression. Simple sequence repeats (SSRs) are robust molecular markers for studying genetic
diversity. Although several SSR markers are available now, challenge remains to identify the trait-specific SSRs
which can be used for marker assisted breeding. In order to understand the genetic diversity of salt
responsive-miRNA genes in rice, SSR markers were mined from 130 members of salt-responsive miRNA genes
of rice and validated among the contrasting panels of tolerant as well as susceptible rice genotypes, each with
12 genotypes. Although 12 miR-SSRswere found to be polymorphic, only miR172b-SSR was able to differentiate
the tolerant and susceptible genotypes in 2 different groups. It had also been found that miRNA genes were more
diverse in susceptible genotypes than the tolerant one (as indicated by polymorphic index content)which might
interfere to form the stem-loop structure of premature miRNA and their subsequent synthesis in susceptible
genotypes. Thus, we concluded that length variations of the repeats in salt responsive miRNA genes may be responsible
for a possible sensitivity to salinity adaptation. This is the first report of characterization of trait specific
miRNA derived SSRs in plants.