It is well suited for fine-mapping of genomic regions, genome-wide studies, and detection of marker-trait associations.
Whole genome sequencing or screening and mapping of genomic libraries has confirmed single LWS opsins in two species of pufferfish [ 29], and two LWS opsins in both the zebrafish [ 16] and medaka [ 17], while screening and Southern blotting of a genomic library suggests the presence of two (or possibly three) LWS loci in the cavefish (Astyanax fasciatus) [ 21].
Extreme instability of pyrimidine motif triplex DNA at physiological pH severely limits its use in wide variety of potential applications, such as artificial regulation of gene expression, mapping of genomic DNA, and gene-targeted mutagenesis in vivo.
Optical mapping of genomic DNA from representatives of ST 23 and ST 240 leave little doubt that the horizontal transfer of tca occurred via plasmid exchange.
However, it can also be used for comparative mapping of genomic fragments onto the chromosomes of closely related species, without additional cloning or DNA sequencing, as shown in [27], [28].
However, systemic mapping of genomic DNA rearrangements has lagged behind, due to technical difficulties in detecting smaller deletions, tumor heterogeneity, and the necessity to purify malignant from normal cells [1].
This approach (random DNA shearing followed by barcode tagging) works very well for species with small genomes, including organellar and microbial DNAs, and has been used to rapidly determine the complete chloroplast genome sequences of spruce and several pine species [15] and for discovery and mapping of genomic SNPs in rice [16], [17].
This would include, for example, molecular mapping of genomic regions associated with fruit quality control and, eventually, marker assisted selection.
An essential step to achieve this is the accurate mapping of genomic loci that contribute to the trait.
