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Table 1. Advantages and disadvantages of most commonly-used DNA markers for QTL analysis
Molecular Codominant (C)
marker or Dominant (D) Advantages Disadvantages References

Restriction C Robust Time-consuming, laborious Beckmann & Soller (1986),

fragment length Reliable and expensive Kochert (1994), Tanksley
polymorphism Transferable across Large amounts of DNA required et al. (1989)
(RFLP) populations Limited polymorphism
(especially in related lines)
Random D Quick and simple Problems with reproducibility Penner (1996), Welsh &
amplied Inexpensive Generally not transferable McClelland (1990),
polymorphic Multiple loci from a single Williams et al. (1990)
DNA (RAPD) primer possible
Small amounts of
DNA required
Simple sequence C Technically simple Large amounts of time and McCouch et al. (1997),
repeats (SSRs) Robust and reliable labour required for production Powell et al. (1996),
or microsatellites Transferable between of primers Taramino & Tingey (1996)
populations Usually require polyacrylamide
electrophoresis
Amplied D Multiple loci Large amounts of DNA required Vos et al. (1995)
fragment Length High levels of Complicated methodology
Polymorphism (AFLP) polymorphism generated
SSRs are also known as sequence tagged microsatellite site (STMS) markers (Davierwala et al., 2000; Huettel et al., 1999; Mohapatra et al.,
2003; Winter et al., 1999). Euphytica (2005) 142: 169196
DOI: 10.1007/s10681-005-1681-5