Molecular Plant Breeding 2016, Vol.7, No.11, 1
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interest within the population under study
(Mohammadi and Prasanna, 2003). Molecular markers
are useful tools for diversity studies, and are usually
more reliable than morphological markers. Random
amplified polymorphic DNA (RAPD) was one of the
most popular markers used. Baral and Bosland (2002)
and Sanatombi et al. (2010), used RAPDs for diversity
studies of germplasm from Nepal and India. RAPDs
were also used for characterizing and comparing
genetic structure of landraces (Votava et al., 2005) and
wild versus domesticated populations (Oyama et al.,
2006). Similarly, Amplified Fragment Length
Polymorphism (AFLP) markers were useful to reveal
genetic diversity among pepper genotypes from
Ethiopia compared to germplasm from other countries
(Geleta et al., 2006).
Simple sequence repeats (SSR) markers also called
Microsatellites are tandem repeated motifs of 1-6
nucleotides abundant in most eukaryotic and
prokaryotic genomes (Kalia et al., 2011). More
recently these markers have become more widely used
in genetic studies of pepper and other plants. The
information value of microsatellites is high compared
to AFLPs and RAPDs (Lee et al., 2004). SSR markers
are co-dominant, stabile, with capacity of multi-allelic
detection, ease of application, excellent sensitivity and
transferability (González-Pérez et al., 2014). They
have been widely used in many plant species
including cereals, vegetables and fruits for genetic
diversity studies, population genetics and evolutionary
studies, as well as genome analysis, gene mapping and
marker-assisted selection (Kalia et al., 2011).
González-Pérez et al. (2014) described microsatellites
to have proven superior power than other markers in
resolving population structure and still remain very
attractive for breeding purposes.
Table 1 Extent of genetic diversity revealed by parameters using the 28 SSR marker
Marker
No. of alleles Major Allele Frequency Gene Diversity Heterozygosity Polymorphic Information Content
AVRDC-PP95
19
0.58
0.62
0.46
0.59
AVRDC-PP128 10
0.35
0.77
0.53
0.74
AGi101
12
0.30
0.80
0.57
0.78
AVRDC-PP49
6
0.46
0.67
0.60
0.61
AGi121
11
0.48
0.70
0.35
0.66
CAMS-855
9
0.56
0.62
0.36
0.58
CA526211
11
0.29
0.79
0.54
0.76
AVRDC-PP133 10
0.48
0.68
0.24
0.64
AVRDC-PP121 12
0.65
0.55
0.51
0.53
BM59622
11
0.42
0.71
0.37
0.66
AVRDC-PP37
9
0.45
0.72
0.41
0.69
AVRDC-PP87
13
0.52
0.67
0.31
0.64
CA524065
7
0.49
0.68
0.25
0.64
GPMS-169
8
0.39
0.74
0.36
0.70
AVRDC-PP126 14
0.38
0.79
0.43
0.76
CA519548
7
0.81
0.33
0.13
0.31
AGI096
12
0.37
0.72
0.31
0.68
AVRDC-PP24
15
0.65
0.55
0.27
0.52
AVRDC-PP129 6
0.93
0.13
0.04
0.13
AVRDC-PP146 7
0.85
0.26
0.10
0.24
AVRDC-PP155 15
0.30
0.79
0.68
0.76
AVRDC-PP88
13
0.39
0.74
0.52
0.70
AVRDC-PP5
8
0.65
0.54
0.54
0.51
AVRDC-PP19
7
0.54
0.58
0.34
0.50
AVRDC-PP144 9
0.38
0.68
0.42
0.63
AVRDC-PP67
20
0.17
0.89
0.51
0.89
AVRDC-PP120 23
0.26
0.81
0.46
0.78
AVRDC-PP147 48
0.32
0.79
0.87
0.76
Mean
13
0.48
0.65
0.41
0.62
