Chapter 9 Using Random Amplified Polymorphic DNAs in Zebrafish Genomic Analysis

Abstract

Publisher Summary This chapter explores random amplified polymorphic DNAs (RAPDs) and its help in zebrafish genomic analysis. The chapter discusses its identification, various types of RAPDs and their advantages and disadvantages with respect to other genetic markers and, finally, the use of RAPDs in constructing maps and mapping mutations. RAPDs have been used extensively as a method to generate a genetic map for a species in a short period of time. RAPDs are only one of the many types of genetic markers that are suitable for building genetic maps. There are several ways to detect DNA polymorphisms that have been used with success in zebrafish research. These can be divided into two basic strategies: the first requires availability of a locus as a clone, which is either directly used as a probe, or which is sequenced to provide information for the design of polymerase chain reaction (PCR) primers. This category includes classical restriction fragment length polymorphisms (RFLPs), microsatellite markers, and single strand conformation polymorphisms (SSCPs). Another category of DNA polymorphisms requires no previous knowledge of the loci identified; these include RAPDs and arbitrary fragment length polymorphisms (AFLPs). Each type has its own peculiar advantages, and different methods are more useful under different situations.