Transposable element-based molecular markers can be utilized to investigate genetic diversity and to create genetic linkage maps. In this study, Class I and class II transposons were employed to obtain a comparative account of genetic diversity between wild and cultivated barley genotypes. Three types of PCR-based techniques were used: IMP (Inter MITE Polymorphism), IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism). Specific primer pairs for IMP, IRAP, and REMAP detected a total of 200 bands with an average of 20 bands per marker. The mean polymorphic information content (PIC) and discrimination power (D) values in all 47 genotypes from these three types of transposon-based polymorphisms were 0.910 and 0.935, respectively. Unweighted Pair Group Method with Arithmetic mean (UPGMA)-based cluster analysis classified all 47 genotypes, both wild and cultivated, into separate groups consistent with their geographical origins. Sequencing followed by chromosome location of polymorphic bands enables precise gene introgression from wild gene pool to cultivated barley. The highly polymorphic nature of these marker systems makes them suitable for use in varietal identification and MAS-based breeding programs in barley and other cereals.

Among various functional genomics tools used to characterize genes in plants, transposon-based mutagenesis approaches offer great potential, especially in barley and wheat, which possess large genomes and in which genetic transformation is not routine. Two Ds transposon flanking sequences (TNPs), TNP-29 (27.4cM (centiMorgan)) and TNP-79 (70.3cM), were mapped in the vicinity of a malting quality QTL located on chromosome 4H of barley. Reactivation of the Ds transposon sequence from these TNP lines led to the identification of genes in the malting QTL regions. Several Ds (dissociation) lines were generated by crossing TNP-29 and TNP-79 with an AcTPase (activator) expressing line (25-B), and F₂ progenies were subsequently screened for Ds insertions at new locations. To further characterize these Ds mutants, we mapped the new Ds flanking sequences on a barley genetic map and found that 29% of Ds were located in regions associated with the malting QTL located on chromosome 4H and in close proximity to other important malting-associated QTL across the barley chromosome. Using a sequence based approach, a linkage map was generated that confirmed the position of Ds loci in the barley genome map. Locating these Ds loci on the barley map opens avenues to dissect important malting QTL for facilitating identification of candidate malting genes.

Field pea (Pisum sativum L.) is an important protein-rich pulse crop produced globally. Increasing the lipid content of Pisum seeds through conventional and contemporary molecular breeding tools may bring added value to the crop. However, knowledge about genetic diversity and lipid content in field pea is limited. An understanding of genetic diversity and population structure in diverse germplasm is important and a prerequisite for genetic dissection of complex characteristics and marker-trait associations. Fifty polymorphic microsatellite markers detecting a total of 207 alleles were used to obtain information on genetic diversity, population structure and marker-trait associations. Cluster analysis was performed using UPGMA to construct a dendrogram from a pairwise similarity matrix. Pea genotypes were divided into five major clusters. A model-based population structure analysis divided the pea accessions into four groups. Percentage lipid content in 35 diverse pea accessions was used to find potential associations with the SSR markers. Markers AD73, D21, and AA5 were significantly associated with lipid content using a mixed linear model (MLM) taking population structure (Q) and relative kinship (K) into account. The results of this preliminary study suggested that the population could be used for marker-trait association mapping studies.