Molecular characterization of mitochondrial genome of WA CMS maintainer restorer lines of rice

Abstract

A majority of rice hybrids that are being grown in several Asian countries including India are based on wild abortive cytoplasmic male sterility (WA-CMS). Despite the innumerable reports on mitochondrial factors as prime cause for the WA-CMS trait, the genes/orfs newlineunderlying the trait of WA-CMS are unclear. On the other hand, Rf4 and Rf3, two major nuclear fertility restoration genes have been implicated with fertility restoration trait in WA-CMS system in many newlinestudies, but the candidate genes reported to be controlling the trait need to be validated for their efficient application in hybrid breeding program. In the present study, the genome wide comparative newlinesequence analysis of two complete mitochondrial genomes of WA-CMS and maintainer was performed in order to identify significant sequence polymorphisms associated with different mitochondrial regions between the two types of cytoplasm. Targeting these newlinepolymorphisms, two different sets of dominant PCR-based markers, first set composing of six markers targeting WA-CMS mitochondria, another set comprising of five markers specific to male fertile newlinemitochondria and an additional set of eight codominant PCR-based markers targeting both the mitochondrial genomes were developed and validated.