1. A method for the high throughput discovery, detection and genotyping of one or more genetic markers in one or more samples, comprising the steps of: (a) providing DNA from one or more samples; (b) restricting the DNA with at least one restriction endonuclease to produce at least one restriction fragment comprising sticky remains of a restriction site; (c) ligating at least one adaptor to the at least one restriction fragment to produce at least one adaptor-ligated restriction fragment, wherein one end of the adaptor comprises an overhang that is compatible with the sticky remains of the restriction site of the restriction fragment; (d) amplifying by solution PCR the at least one adaptor-ligated restriction fragment with at least one primer pair to produce a library of at least one amplified adaptor-ligated double stranded restriction fragment, wherein the amplified adaptor-ligated restriction fragment comprises an identifier tag; (e) sequencing a pool of two or more libraries of tagged amplified adaptor-ligated restriction fragments using high throughput sequencing technology, wherein each library comprises a unique identifier tag, wherein the sequencing comprises amplifying by PCR on a solid support; (f) clustering the sequences per library, using the identifier tag; (g) identifying genetic markers within the library and/or between libraries; (h) determining dominant or co-dominant genotypes of the genetic markers in the two or more libraries.