**4.3.1 Random Amplified Polymorphis DNA (RAPD)**

In cacao, the first study of the use of molecular markers in cacao was reported by Wilde *et al*. (1992). These authors used Random Amplified Polymorhism DNA (RAPD) to study relationships among cocoa groups. Their work was soon followed by those of several authors who also used RAPD to determine genetic relationships among cacao populations (Russel *et al*., 1993; Laurent *et al*., 1994; Lerceteau *et al*., 1997; Whitkus *et al*., 1998). N'Goran *et al*. (1994) analyzed the genetic diversity of 106 genotypes in Cote d'Ivoire belonging to the various morphogeographic groups within Criollo, using 49 repeatable polymorphic RAPD products. They showed a clear structure among Forastero and Criollo groups with clear differentiation between Upper and Lower Amazon Forastero. Lerceteau *et al*. (1997) analysed the genetic diversity of Ecuadorian Nacional clones, Forastero, Trinitario and Criollo cacao clones using forty-three genomic probes. They found that within-group genetic diversity was almost identical between Forastero, Trinitario and Criollo. Their results showed that the populations of Amazon Forasteros and Criollo studied were highly diverse and that the Criollo and Trinitario populations showed some overlap.

#### **4.3.2 Restriction Fragment Length Polymorphisms (RFLP)**

RFLPs are generally found to be moderately polymorphic and can be applied in comparisons ranging from the individual level to closely related species. Because of their high genomic abundance and random distribution throughout the genome, RFLPs have been used by several workers to determine the genetic diversity of cacao populations (N'Goran *et al*., 2000; Lerceteau *et al*., 1997; Motamayor and Lanaud, 2002; Motamayor *et al*., 2002).

#### **4.3.3 Microsatellites**

Microsatellites, also known as Simple Sequence Repeats (SSRs) are molecular marker loci consisting of tandemly repeated DNA of short oligonucleotide sequences of two to six bases in length. They form a class of genetic markers that show variation in the number of repeats of a simple DNA sequence. They are extremely common in eukaryotic genome (Tautz and Rentz, 1984) and are highly polymorphic in length. The development and application of SSRs facilitate the acquisition of a large quantity of genetic information relevant to genotype identification, which provides opportunities to characterize germplasm collections (Mitchell *et al*., 1997). Such information generated are used by plant breeders to better understand their germplasm, guide breeding plans and better exploit genetic variation available (Lu *et al*., 2005). Microsatellites are recommended as an international standard for defining genetic identity and has been widely used in the study of genetic diversity of cacao genetic resources (Aikpokpodion *et al*., 2009, 2010; Saunders *et al*., 2000; Zhang *et al*., 2006).
