1. A method for the discovery and genotyping of one or more genetic markers, comprising: (a) ligating at least one adaptor to at least one DNA restriction fragment to produce at least one adaptor-ligated restriction fragment; (b) 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; (c) 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; (d) clustering the sequences; and (e) identifying genetic markers within the library and/or between libraries using the identifier tag and determining dominant or co-dominant genotypes of the identified genetic markers in the two or more libraries.