Markers

About Markers:

Before the advent of whole genome sequencing, researchers used a variety of "markers" to localize genomic and genetic elements such as Quantitative Trait Loci (QTLs) in relation to each other and to the chromosome.  Often these markers were Simple Sequence Length Polymorphisms or SSLPs.  An SSLP is defined as:

SSLPs, also known as microsatellite DNA, are 1-6 simple nucleotide repeat sequences which are highly polymorphic in length of repeat among strains or between individuals and can be used as genetic markers for genotyping.

Even now that the rat, mouse and human genomes have been sequenced and whole genome assemblies are available, markers such as SSLPs provide an easy way to localize genomic elements.  Because primer sequences are available for many of these and because polymerase chain reactions (PCRs) are routine in most laboratories, such markers are still used for marking the ends of QTLs and the introgressed DNA regions of congenic strains.

RGD stores information about markers obtained directly from researchers through submission forms, through curation of the literature and via downloads of rat, mouse and human data from NCBI's UniSTS database.  Mapping data may be available from any or all of these sources for a particular marker.  UniSTS positions SSLPs on the genome by performing "ePCR" to find where the primers are homologous to chromosome and other sequences.  RGD imports the chromosomal position of each marker via the "UniSTS Import Pipeline".