LAUSR

Abstract The miRNAs are a part of large gene regulatory networks, and the identification of molecular markers linked to miRNA genes can be useful for breeding programs. In this study, 10 microsatellite markers were mined from drought-responsive miRNA genes in rice. Based on the analysis of genetic diversity, a total of seven polymorphic miRNA-SSR markers from among 83 diverse rice genotypes showed high levels of genetic diversity. The structure analysis based on 34 SSR markers and seven miRNA-SSR markers divided the genotypes into two distinct groups. The association analysis between seven miRNA-SSR markers and 21 phenotypic traits using the population structure data as covariates showed five pairs of associations at the significant levels of P ≤ .01 when tested using the two statistical models. In this study, we demonstrated a relation between miRNA-SSR markers and some quantitative traits, and also defined useful consistent linked markers in reproductive stress and non-stress conditions.