Method for high-throughput aflp-based polymorphism detection

A method for genotyping of one or more polymorphisms, comprising:

• pooling a first library of amplified DNA fragments and a second library of amplified DNA fragments to obtain a pooled DNA library, the amplified DNA fragments of the first library comprising DNA sequences amplified from a first sample by solution PCR and a first unique identifier sequence which is not derived from the first sample, the amplified DNA fragments of the second library comprising DNA sequences amplified from a second sample by solution PCR and a second unique identifier sequence which is not derived from the second sample, wherein the first and second unique identifier sequences indicate different sample origins of the first and second libraries;
• sequencing the pooled DNA library using high throughput sequencing technology, comprising amplifying on a solid support;
• clustering sequences of the first and second libraries of amplified DNA fragments;
• and
• determining dominant or co-dominant genotype(s) of one or more polymorphisms in the first and second libraries of amplified DNA fragments using the first and second unique identifier sequences.

A method for genotyping of one or more polymorphisms, comprising:

• pooling a first library of amplified DNA fragments and a second library of amplified DNA fragments to obtain a pooled DNA library, the amplified DNA fragments of the first library comprising DNA sequences amplified from a first sample by solution PCR and a first unique identifier sequence which is not derived from the first sample, the amplified DNA fragments of the second library comprising DNA sequences amplified from a second sample by solution PCR and a second unique identifier sequence which is not derived from the second sample, wherein the first and second unique identifier sequences indicate different sample origins of the first and second libraries;
• sequencing the pooled DNA library using high throughput sequencing technology, comprising amplifying on a solid support;
• and
• determining dominant or co-dominant genotype(s) of one or more polymorphisms in the first and second libraries of amplified DNA fragments using the first and second unique identifier sequences.