Comparison of tGBS and AFLP Technologies for Molecular Marker Development and Gene/QTL Mapping

Amplified fragment length polymorphism (AFLP) is a molecular marker system that has been used for gene/QTL mapping for nearly two decades. Genotyping-by-sequencing (GBS), based on the Next-generation sequencing (NGS) technology, is the newest molecular marker system that was developed several years ago. AFLP and tGBS (tunable GBS) were compared for effectiveness of marker development and mapping in two F₂ populations in lettuce. In one population in which the two parents were closely related, AFLP generated 86 polymorphic markers that failed to form linkage groups for mapping, whereas tGBS yielded 1726 SNPs that generated 23 linkage groups and were successfully used for mapping of the target QTLs. In the other population of two diverse parents, AFLP produced 176 markers that generated 11 linkage groups and the target gene was mapped to one linkage group at 11.2 cM to the closest AFLP marker. The tGBS method yielded 2632 SNPs that generated 14 linkage groups and the same target gene was mapped to one linkage group with the closest SNP marker being 13.1 cM from the gene. It appears that tGBS is more effective in mapping than AFLP when the parents are closely related but these two methods have similar effectiveness in molecular mapping if the parents are diverse in genetic backgrounds.