Molecular Plant Breeding 2016, Vol.7, No.11, 1
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The use of SSR markers in genetic studies of
capsicum varied from constructing linkage maps (Lee
et al., 2004; Mimura et al., 2012), complement tests of
distinctiveness (Kwon et al., 2005), genetic diversity
and structure (Aguilar-Meléndez et al.; 2009, Rai et al.,
2013; Dhaliwal et al., 2014). In the current study 28
SSR markers obtained from the Asian Vegetable
Research and Development Centre, the world
vegetable centre (AVRDC) were used. The objectives
were to determine the genetic diversity and population
structure of local Eritrean pepper germplasm collected
from farmers and research institutions and to evaluate
its relatedness to accessions obtained from Ethiopia,
India, Italy, Mexico and Kenya.
1 Results
1.1 Genetic diversity
A total of 352 alleles were detected. The number of
alleles per locus (Na) ranged from 6 in AVRDC-PP49
and AVRDC-PP129 to 48 alleles in AVRDC-PP147.
Thirteen markers revealed 6 to 10 alleles and 6
revealed 15 to 48 alleles. Average number of alleles
per marker was 13. Mean major allele frequency
(MAF) ranged from 0.17 (AVRDC-PP67) to 0.93
(AVRDC-PP129) with an average of 0.48 (Table 1).
Mean polymorphic information content (PIC) ranged
from 0.13 for AVRDC-PP129 to 0.89 for
AVRDC-PP67 with an average of 0.62. Only 3
markers (AVRDC-PP129, AVRDC-PP146 and
CA519548) of the 28 had PIC value of less than 0.5,
while 10 markers had 0.7 or greater PIC value (Table
1). Populations varied in total number of alleles, mean
number of alleles per locus and number of private
alleles. The highest number of alleles per population
(Na) and highest mean number of alleles per locus
(MNa) was found in Gindae (228 and 8.14
respectively) followed by Mendefera (190 and 6.96),
while the lowest numbers were found in population
KALRO1 (63 and 2.25). The AVRDC population had
the highest number (20) of private alleles, followed by
Gindae (18) and Mendefera (17), while the lowest
number of private allele were 1 (found in KALRO1)
and two alleles (found in Elabered, Dubarwa and
Akurdat). The populations showed high %
polymorphic loci, which was 100% in seven
populations, while in the remaining five populations it
ranged from 82.14 in KALRO1 to 96.43 in Dubarwa
(Table 2).
Partitioning of the molecular variance of the
populations under study (Table 3), showed that 10%
of the variation occurred among the populations, while
30 and 60 % occurred among individuals and within
individuals. The variation in all three partitions was
highly significant (P< 0.001).
Table 2 Allelic distribution pattern within population
Population
N
Na
Na Freq. >= 5%
MNa
NPA
% PL
Elabered
32
139
87
4.96
2
100.00
Dekemhare
18
148
114
5.29
3
100.00
Mendefera
36
190
105
6.79
17
100.00
Dubarwa
18
111
90
3.96
2
96.43
Gindae
82
228
104
8.14
18
100.00
Akurdat
7
94
94
3.36
2
89.29
Afabet
58
187
104
6.68
15
100.00
NARI
14
110
88
3.93
3
89.29
HAC
83
169
95
6.04
13
100.00
AVRDC
48
182
115
6.50
20
100.00
KALRO1
3
63
63
2.25
1
82.14
KALRO2
8
92
92
3.29
9
92.86
Note: N= Population size Na= Total number of alleles per populations MNa= Mean number of alleles per marker NPA=Number of
private alleles per population % PL= % polymorphic loci
