Characterizing Barley Malting Quality QTL Using a Ds Transposon-Based Functional Genomics and Synteny-Based Comparative Approach

Transposon-based functional genomics approach offers a great potential to characterize genes in plants, especially in barley and wheat, which possess large genomes and genetic transformation is not a routine. Barley is a key ingredient in malting and brewing industry; therefore, gene discovery in relation to malting quality has an industrial perspective. Malting quality is a complex and quantitatively inherited trait. QTL2, one of the important QTL (quantitative trait loci) affecting malting quality traits has been located on chromosome 4H. We employed transposon- and synteny- based approaches to dissect QTL2 region of barley. A Ds transposon insertion line (TNP), TNP- 29 was previously mapped in the vicinity of QTL2. Reactivations of Ds transposon from this TNP line lead to identification of genes harboring in this QTL2 region. Identification of unique flanking sequences, using high-efficiency thermal asymmetric interlaced PCR and inverse PCR confirmed Ds insertion in genes potentially associated with malting quality such as β-GAL1, β-amylase-like gene. Alternatively, barley-rice synteny approach detected 24 candidate genes; one of them shows differential gene expression using qPCR, among malting and non-malting barley varieties. Biochemical analysis like binding assay and ELISA further confirms these findings. Integrated effort of saturation mutagenesis with Ds transposons and synteny- based approach will lead to a better understanding of malting quality traits and candidate genes that display quantitative variation.