Analysis of BAD gene expression in Oryza sativa using qRTPCR

Fragrance in rice (Oryza sativa), known to be primarily associated with grain 2-Acetyl-1-Pyrroline (2AP) concentration, is a highly valued trait. It has previously been determined that a non-functional betaine aldehyde dehydrogenase (BAD2) encoding gene homologue is responsible for fragrance in rice. It is hypothesized that in non-fragrant rice BAD2 catalyses the breakdown of a precursor to 2AP while the presence of a non-functional BAD2 encoding gene in fragrant varieties leads to an increase in the concentration of this precursor and a consequent increase in the concentration of 2AP. Functional BAD1 encoding genes have been identified in both fragrant and non-fragrant rice varieties, and it may be BAD1 and BAD2 have different in vivo activity and or functions. There are several possible mechanisms by which this could be achieved including different substrate specificities, different optimum conditions and different compartmentalization of the homologues. In addition, BAD1 and BAD2 gene homologues may be expressed at different levels within any one variety and the expression levels of BAD2 may differ between non- fragrant and fragrant varieties. The expression levels of the BAD1 and BAD2 encoding genes were assayed using quantitative real time reverse transcriptase PCR (qRTPCR) in leaf tissue from three fragrant (Kyeema, Basmati 370, Khao Dawk Mali) and three non-fragrant (Amaroo, Nipponbare, Teqing) rice varieties. The relative expression of the functional (non-fragrant) and non-functional (fragrant) BAD2 encoding alleles has also been assessed between non-fragrant and fragrant varieties.