Methods for Developing Molecular Markers

Molecular markers are essential for breeding major crops today and many molecular marker techniques have been developed. DNA markers are now the most commonly used. This chapter describes the principles of DNA marker techniques and methods to map major genes. DNA markers can be classified into two categories: (1) DNA hybridization-based techniques, including restriction fragment polymorphism and DNA chips, and (2) polymerase chain reaction techniques, including simple sequence repeats, random amplified polymorphic DNA, amplified fragment length polymorphism, and single nucleotide polymorphism. To develop trait-linked markers, segregating populations for the target traits and reliable phenotyping methods are indispensable. With these tools, two approaches can be used to develop trait-linked markers: (1) when there is no biological information for the trait, and (2) when biological information is available. Finally, we describe several case studies for trait-linked marker development.