International Journal of Horticulture, 2015, Vol.5, No.21, 1-45
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of a variety, the genetic similarity between original variety and mutant will be very high (close to 100%) as shown
in roses (Debener et al., 2000). Molecular markers then constituted a viable alternative (Rick et al., 2001; Debener
et al., 1996, 2000; Bredemeijer et al., 2002; Heckenberger et al., 2002; Ro¨der et al., 2002; Esselink et al., 2003),
as they provide a more accurate methodology for the determination of genetic similarity. Accurate identification of
plants is desired for patent protection, however, it is difficult to distinguish phenotypically similar cultivars using
morphological and physiological methods or isozyme analyses. The limitation of these analyses is that they are
observations of the phenotype. In contrast, DNA polymorphisms offer direct observation of the plant genotype,
and it has been shown that restriction fragment length polymorphism (RFLP) analysis was useful for cultivar
identification in rose (Hubbard et al., 1992; Rajapakse et al., 1992). RAPD technique (Williams et al., 1990;
Welsh and MCclelland, 1990; Caetano-Anolles et al., 1991) based on the polymerase chain reaction (PCR) has
been used to detect polymorphism in five rose cultivars (Torres et al., 1993). It was also demonstrated that
cultivars from one family, differing for flower colour, could not be distinguished with several DNA techniques
(Wolff et al., 1995). RAPD fingerprinting techniques have been used for the identification of horticultural crop
varieties, description of cultivar genotypes and for protecting breeder’s rights (Debener, 2001; Williams, 1990;
Camlin, 2001). RAPD markers have been extensively used to distinguish intraspecific genetic variation in
ornamental crops and detection of hybrids and clones (Arús, 2000; Debener, 2001a; Collins et al., 2003).
Ranamukhaarachchi et al. (Ranamukhaarachchi et al., 2001) showed that RAPD markers had the ability to
identify pot-plant anthurium cultivars. In ornamentals, DNA markers are currently used to identify varieties and to
analyze inter- and intra-speciÞc genetic relatedness (Rajapakse et al., 1997; Ben-Meir and Vainstein, 1994;
Yamagishi, 1995; Torres et al., 1993).
The RAPD analysis is rapid, simple, and does not involve radioactive material. On the other hand, the RAPD
technique is highly sensitive to reaction conditions, dominant in nature, and does not usually enable detection of a
single locus (Williams et al., 1991; Mohan et al., 1997; Yang and Korban, 1996). Hence this marker is not useful,
for example, in markerassisted breeding programs. In contrast to RAPD amplification, the ISSR markers are more
feasible and reproducible (Godwin et al., 1997), and the distribution of ISSRs in the eukaryotic genome makes
them highly informative (Tautz et al., 1984). They are also highly polymorphic and their use is cost effective,
requiring no prior information of the sequence (Bornet et al., 2002).
Authors have very successfully utilized RAPD analysis for the identification of cultivars, documentation,
estimation of genetic diversity, to trace out the molecular affinity of origin of unknown group and correct
identification of induced mutants in Amaryllis, Bougainvillea, Chrysanthemum and rose. The resolution of the
molecular markers is much higher than morpho-agronomic characters to identify individual cultivars. The
information obtained will facilitate choosing the appropriate breeding program to incorporate beneficial genes in
desirable genotypes lacking the particular trait. Through the study, parentages of some of the hybrids of Amaryllis
and Bougainvillea have been confirmed on one hand, and the groupings of the cultivars based on their diversity
have been successfully carried out on the other hand. They have suggested RAPD an efficient and reliable
alternative to the conventional methods those are based on morphological markers.
The use of RFLPs for characterization overcomes the limitation of RAPD, since they provide substantial
polymorphism and they can be unlimited in number. In general, the AFLP technique has been claimed to be
suitable for molecular discrimination at the species level because of its extraordinary capacity to generate
polymorphisms within individuals with narrow genetic distances (Han et al., 2000). AFLP technique (Vos et al.,
1995) is highly reproducible and polymorphic, and it has been widely applied to investigate genetic relationship
among species, closely related cultivars and even clones of plants (Loh et al., 1999; Zhang, 2000; Hagen et al.,
2002; Steiger et al., 2002; Carr et al., 2003; Sensia et al., 2003; Lanteri et al., 2004; Owen et al., 2005; Zhao et al.,
2005).
Recently a novel technique ‘DNA barcoding’ has been designed to provide rapid, accurate, and automatable
species identifications by using short, standardized gene regions as internal species tags (Paul and Hebert, 2005;
Janzen et al., 2005; Smith, 2005; Smith et al., 2005). This will facilitate the species discovery by allowing
