Various functional genomic tools are being used to identify and characterize genes in plants. The Activator/Dissociation (Ac/Ds) transposon-based approach offers great potential, especially in barley, due to its limited success of genetic transformation and its large genome size. The bias of the Ac/Ds system towards genic regions and its tendency toward localized transpositions can greatly enhance the discovery and tagging of genes linked to Ds. Barley is a key ingredient in malting and brewing industry; therefore, gene discovery in relation to malting has an industrial perspective. Malting quality in barley is a complex and quantitatively inherited trait. Two major quantitative trait loci (QTLs) affecting malting quality traits have been located on chromosome 4H. In this study, Ds was reactivated from parent transposants (TNP) lines, TNP-29 and TNP-79, where Ds was mapped in the vicinity of important malting QTLs. Reactivation of Ds was carried out both by conventional breeding and in vitro approaches. A threefold increase in reactivation frequency through the in vitro approach enabled the development of a new genomic resource for the dissection of malting QTL and gene discovery in barley. Identification of unique flanking sequences, using high-efficiency thermal asymmetric interlaced PCR and inverse PCR from these populations, has further emphasized the new location of Ds in the barley genome and provided new transposon mutants especially in β-GAL1, β-amylase-like gene and ABC transporter for functional genomic studies.

The brown planthopper (BPH) is the leading cause of insect damage to rice plants. It has caused profound losses in rice production since the late 1970’s and continues to be a major pest problem. Therefore, there is an urgent need to discover new BPH resistance genes to ensure the successful production of rice. Here, a new BPH resistance source provided by SeedWorks International Pvt. Ltd., SWD10, was used for this purpose. A total of 232 F2 progenies were genotyped with 216 polymorphic markers. Results revealed two dominant QTLs located on the short and long arms of chromosome 4. These QTLs are referred to as BPH41 and BPH42, respectively. BPH resistance mechanism test revealed that antibiosis and antixenosis mechanisms both play a role in BPH resistance conferred by these two QTLs. To further reduce the size of each QTL, 14,368 recombinant lines were screened, and the QTLs were delimited between markers SWRm_01617 and SWRm_01522 for BPH41, and SWRm_01695 and SWRm_00328 for BPH42. Additionally, using RNA-seq data of lines containing the QTLs, we further shortlisted four and three gene candidates for BPH41 and BPH42, respectively. Differential gene expression analysis of lines containing the QTLs suggested that SWD10 BPH resistance is contributed by the plant’s innate immunity and the candidate genes may be part of the rice innate immunity pathway. The newly identified QTLs are currently being utilized for breeding BPH resistant rice varieties and hybrids.