ABSTRACT
This chapter discusses the practical aspects of designing marker-assisted selection (MAS) strategy and high-throughput genotyping techniques that increase the efficiency significantly. Conventional plant breeding is primarily based on phenotypic selection of superior individuals among segregating progenies resulting from hybridization. A molecular marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. Molecular markers intended for MAS can be selected based on their genome distribution; haplotype diversity and polymorphic information content indices; and their association with candidate genes and other agronomic traits excluding target introgression trait. In practical MAS, a breeder is also concerned about how the markers should be detected, how many generations of MAS have to be conducted, and how large a size of the population is needed. The power and efficiency of genotyping are expected to improve with the advent of markers like single nucleotide polymorphism.
