International Journal of Horticulture, 2015, Vol.5, No.21, 1-45
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variability within and among several species. During recent decades several techniques have been introduced that
detect molecular variability within and among several crop species as well as the ornamentals. PCR based
techniques have been used successfully in DNA fingerprinting of plant genomes and in genetic diversity studies.
These techniques include RAPD (Randomly amplified polymorphic DNA), RFLP (Restriction Fragment Length
Polymorphism), SSR (Simple Sequence Repeats) or microsatellites, STS (Sequence Tagged Sites), SNP (Single
Nucleotide Polymorphism), VNTR (Variable number tandem repeat), STR (Short tandem repeat), SFP (Single
feature polymorphism) and AFLP (Amplified fragment Length Polymorphism) (Nei, 1987; Williams et al., 1991;
Loh, 1999; Barcaccia et al., 1999; Han et al., 1999; Escaravage et al., 1998; Visser, 1997; Dubouzet et al., 1997;
Han et al., 2000; Picton and Hughes, 1997; Anastassopoulos and Keil, 1996; Tsuchiya et al., 1987; Welsh and
MCclelland, 1990; Gebhardt and Salamini, 1992; Vos et al., 1995; Dubouzet et al., 1998; Walker and Werner,
1997; Wol et al., 1993; Arús, 2000; Debener 2001a, 2001b; Debener, 2004; Dosda and Baril, 2001; Anand, 2000;
Anderson and Fairbanks, 1990; Bernatsky and Tanksley, 1989; Rajapakse et al., 1997; Rayburn et al., 1993; Rout,
2005; Rout and Mohapatra, 2006). Molecular markers have been developed for most ornamentals to a limited
extent when compared to the main food crops. Applications have been essentially studies of cultivar identification,
pedigree analysis or germplasm variability using isozyme or RAPD markers. These results opened new avenues
for the development of useful markers for crops, like the ornamentals. RAPD technique has also been used in
plants for the construction of genetic maps (Reiter et al., 1992), genotype identification, taxonomical studies etc.
(Whitkus et al., 1994; Wolfe and Liston, 1998; Guang et al., 1996; Mehmood et al., 2008). In the last few decades,
these new DNA molecular markers, based on the PCR technique, such as random amplified polymorphic DNA
(RAPD) (Williams et al., 1990; Welsh and McClelland, 1990) and inter simple sequence repeats (ISSRs)
(Zietkiewicz et al., 1994), among others, have become excellent tools for plant breeders (Hern´andez and Mart´ın,
2003). It is being widely used to amplify a specific segment of DNA by using random primers. One can compare
the genetic makeup between different species of plants and even different varieties or cultivars of a species by
using RAPD markers. The genetic diversities can be understood in more details by using this molecular biological
technique.
In RAPD method, by using a single arbitrary primer (10 mer) and amplifying DNA by polymerase chain reaction
(PCR), the resulting DNA markers can easily be separated on an agarose gel by electrophoresis(Williams et al.,
1990). The advantages of RAPD are its simplicity, rapidity, the requirement for only a small quantity of DNA, and
the ability to generate numerous polymorphisms (Cheng et al., 1997). Therefore, it has been a powerful technique
for species identification, genetic analysis(Williams et al., 1990; Cheng et al., 1997; Tzuri et al., 1991;Kiss et al.,
1993; Landry et al., 1993; Wight et al., 1993; Mohan et al., 1997; Chung et al., 2002; Lim et al., 2006) and for
elucidation of genetic relationships of numerous plant species, and parentage testing (Fu et al., 2008; Williams et
al., 1991; Halward et al., 1992; Keil et al., 1994; Novy et al., 1994;Kindiger and Dewald, 1996; Cjuric and Smith,
1996). RAPDs have been widely used for determining the genetic relationships between different related species
and identification of cultivars (Hu and Quiros, 1991) and for estimating genetic relationships and diversity among
crop germplasms (Thomas et al., 1993; Hallden et al., 1996). Many crop species as well as ornamental plants have
been characterized using this procedure such as
Chrysanthemum
, roses,
Alstroemeria
L., Amaranthus, Hibiscus,
Pelargonium, Poinsettia, Orchid and Sunflower (Wolff et al., 1995;Martin et al., 2002; Hubbard et al., 1992;
Rajapakse et al., 1992; Torres et al., 1993; Vainstein and Ben Meir, 1994; Matsumato and Fukui, 1996; Ben -Meir
and Vainstein, 1994; Debener and Mattiesch, 1996; 1998; 1999a; 1999b; Debner et al., 1996; Reynders and
Bollereau, 1996; Millan et al., 1996; Esselink et al., 2003; Dubouzet et al., 1997; 1998; Mandal and Das, 2002;
Faseela and Salkutty, 2007; Zhou et al., 2002; Bakker et al., 2000; James et al., 2004; Lesur et al., 2001; Ling et
al., 1997; Xiang et al., 2003; Chen et al., 2006). RAPD markers have been efficiently used in the routine
assessment of variety identification and hybrid seed purity in Calycanthaceae (Zhou et al., 2007), Orchid (Xiang
et al., 2003) and Calla lily (Hamada and Hagimori, 1996).
Recently use of molecular markers has been proposed for identification of animal diversity and demonstrated on a
large scale through the use of a short DNA sequence in the cytochrome
c
oxidase 1 (
CO1
) gene (Hebert et al.,
2003, 2004a, 2004b). Methods for identifying species by using short orthologous DNA sequences, known as
