Use of Cleaved Amplified Polymorphic Sequences (CAPS) as Genetic Markers in Arabidopsis thahna

Plant genetic maps can be constructed either wrth phenotyprc or molecular markers. Historically, genetic mapping utrlrzed vtsrble markers, but it is difficult to examme many such markers m a single cross. The recognmon that distantly related individuals differ m DNA sequence throughout then- genome (1 ) led to the rapid mcorporatron of DNA markers into mapping strategies. Until recently, the most commonly used DNA markers were restriction fragment length polymorphtsms (RFLPs), anonymous single copy number genomic clones that reveal a polymorphrsm m the length of a restriction fragment, typically by DNA blot hybrrdrzatron. The RFLP mapping 1s well suited for determmmg the genetic locatron of any newly cloned DNA sequence; the DNA fragment can be used as a hybridrzatron probe (assuming it detects an RFLP) agamst the DNA filters used to construct the RFLP map. However, many Arabzdopszs genes are first identified by mutation. Several years ago, mapping such a mutation on to a pre-existing RFLP map was a lengthy procedure requiring the rsolatron of DNA from mdrvrdual Fz plants or F3 families, and performing DNA blot analysis using each of the RFLP markers as a hybridization probe.