A procedure for mapping <i>Arabidopsis</i> mutations using co‐dominant ecotype‐specific PCR‐based markers

TLDR

Mapping markers for Arabidopsis thaliana have been developed that correspond to PCR‑amplified DNA fragments. The method employs 18 PCR primer sets that amplify unique sequences from Columbia and Landsberg erecta ecotypes, and restriction enzymes generate ecotype‑specific digestion patterns to identify the origin of each fragment. Co‑dominant CAPS markers enable unambiguous mapping of an Arabidopsis gene to one of ten chromosome arms in a single cross using few F₂ progeny.

Abstract

A set of mapping markers have been designed for Arabidopsis thaliana that correspond to DNA fragments amplifed by the polymerase chain reaction (PCR). The ecotype of origin of these amplified fragments can be determined by cleavage with a restriction endo‐nuclease. Specifically, 18 sets of PCR primers were synthesized, each of which amplifies a single mapped DNA sequence from the Columbia and Landsberg erecta ecotypes. Also identifed was at least one restriction endonuclease for each of these PCR products that generates ecotype‐specific digestion patterns. Using these co‐dominant cleaved amplified polymorphic sequences (CAPS), an Arabidopsis gene can be unambiguously mapped to one of the 10 Arabidopsis chromosome arms in a single cross using a limited number of F 2 progeny.