Use of a subset of doubled-haploid lines for RAPD interval mapping in barley

Area of Science:

• Plant genetics and breeding
• Molecular marker technology
• Genomic mapping in barley

Background:

• Molecular markers are crucial for gene and quantitative trait loci localization in barley.
• Previous efforts have limited the placement of Random Amplified Polymorphic DNA (RAPD) markers on barley genetic maps.

Purpose of the Study:

• To integrate RAPD markers into specific intervals on the Steptoe (S) x Morex (M) barley linkage map.
• To analyze the distribution patterns of these RAPD markers across the barley genome.
• To compare the efficiency of Taq DNA polymerase versus the Stoffel fragment for RAPD marker amplification.

Main Methods:

• Screening of 362 decamer primers against S and M barley DNA to identify reliable RAPDs.
• Utilizing a subset of 15 doubled-haploid (DH) lines from a 150 DH line population for marker placement.
• Employing additional DH lines for refining marker positions and comparing amplification efficiencies.

Main Results:

• Identified 127 reliable RAPDs from 85 primers, with four codominant markers found.
• RAPD markers exhibited non-uniform distribution, with significant clustering around centromeric regions.
• The Stoffel fragment demonstrated higher reliability in detecting RAPDs (44%) compared to Taq DNA polymerase (17%).

Conclusions:

• Established a method for rapid placement of new markers on the S x M linkage map using a DH line subset.
• RAPD marker distribution suggests potential for targeted genetic studies and marker-assisted selection in barley.
• The Stoffel fragment is a more efficient tool for reliable RAPD marker generation in barley.