**3. Development of genetic markers**

An alternative approach to improving selection efficiency in tomato is to discover genetic markers that are associated through linkage or pleiotropy with genes that control the trait(s) of interest. Genetic markers are biological features that can be transmitted from one generation to another. They can be used as experimental probes or tags to track an individual, a tissue, a cell, a nucleus, a chromosome or a gene. The value of genetic markers as indirect selection criteria has been known to breeders since early 1900s. Genetic markers can be classified into two categories namely classical markers and DNA markers [23, 24]. Classical markers comprise morphological markers, cytological markers and biochemical markers. DNA markers such as restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), rapid amplified polymorphic DNA (RAPD), simple sequence repeats (SSR), single nucleotide polymorphism (SNP), etc. have been developed. These DNA markers have developed into many systems based on different polymorphism detecting techniques or methods including northern and southern blotting of nucleic acid hybridization, polymerase chain reaction (PCR), and DNA sequencing [25].

### **4. Classical markers**

Breeders have used morphological markers to select for superior phenotypes for many decades. During the history of plant breeding, markers mainly used included visible traits such as flower color, leaf shape, seed shape, fruit shape, flesh color, stem length, etc. These morphological markers can easily be identified and therefore usually used in the construction of linkage maps. Some of these markers are also linked with other agronomic traits and thus can be used as indirect selection criteria in breeding. However, morphological markers available are limited, and many of these markers are not associated with important economic traits like yield and quality. In addition, some even have undesirable effects on the development and growth of the plant. In tomato, there are over 1300 morphological, physiological (e.g., male sterility, fruit ripening, and fruit abscission), and disease-resistance genes [26] of which only less than 400 have been mapped [27].

Cytological markers are represented by chromosome karyotype and banding patterns. These markers are not directly used in plant breeding but serve as landmarks on the chromosomes thereby used for identifying linkage groups and subsequently genetic maps are constructed. Biochemical markers or isozymes are alternative forms or structural variants of an enzyme with different molecular weights and electrophoretic mobility but have the same catalytic activity or function. The second generation of isozymes became more popular during 1970s and early 1980s. Although some 41 isozymic genes in tomato have been identified, characterized and mapped [28], these markers are few and less polymorphic [29].
