Molecular Plant Breeding 2016, Vol.7, No.11, 1
-
16
1
Research Article
Open
Access
Genetic Diversity and Population Structure of Eritrean Pepper (
Capsicum
species
) as Revealed by SSR Markers
Brhan Khiar Saleh
1,2
, Remmy W. Kasili
2
, Eduard G. Mamati
2
, Kouadio Nasser Yao
3
, Santie M. deVilliers
4
, Woldeamlak Araia
1
,
Aggrey B. Nyende
2
1 Hamelmalo Agricultural College. P.O.Box 397, Keren, Eritrea
2 Jomo Kenyatta University of Agriculture and Technology. P.O.Box 62000-0020, Nairobi, Kenya
3 Biosciences eastern and central Africa (BecA). P.O Box 30709 Nairobi 00100, Kenya
4 Pwani University, P.O.Box 195-80108, Kilifi, Kenya
Corresponding
author
email
Molecular
Plant
Breeding,
2016,
Vol.7,
No.09
doi:
Received: 20 Jan., 2016
Accepted: 5 Mar., 2016
Published: 01 Mar., 2016
Copyright
© 2016
Brhan et al.,
This
is
an
open
access
article
published
under
the
terms
of
the
Creative
Commons
Attribution
License,
which
permits
unrestricted
use,
distribution,
and
reproduction
in
any
medium,
provided
the
original
work
is
properly
cited.
Preferred
citation
for
this
article:
Saleh B.K., Kasili R., Mamati G.E., Yao K.N., de Villeirs S.M., Araia W., and Nyende A.B., 2016, Genetic Diversity and Population Structure of Eritrean Pepper
(
Capsicum species
) as Revealed by SSR Markers, Molecular Plant Breeding, 7(09): 1-16 (doi
Abstract
Pepper (Capsicum spp.) is one of the most important vegetable crops and the most widely used spice worldwide including
Eritrea. Diversity studies are an essential step for crop breeding and improvement. Therefore, the objectives of the study were to
determine the diversity and population structure of local Eritrean pepper collected from farmers and research institutions and to
evaluate the relatedness of the Eritrean pepper with accessions obtained from five other countries. A total of 407 individual pepper
plants from 150 seed samples were evaluated using 28 SSR markers. The results showed that varieties maintained in situ by farmers
were heterogeneous. Diversity parameters indicated extensive genetic variation among the Eritrea genotypes. The 28 markers
revealed a total of 352 alleles with an average of 13 alleles per marker. Mean Polymorphic Information Content was 0.62 and, mean
Observed Heterozygosity was 0.41. The analysis of molecular variance showed only 10% variation was among populations, 30%
among individuals within populations and 60% within individuals. This can be explained by the high mean number of effective
migrants (2.25) that ranged from 1.01 to 10.45 among populations indicating movement of germplasm among farmers in different
geographic and agro-ecological regions. A factor analysis, neighbour joining clustering and the model based clustering (Structure)
classified the 407 individuals into 3 groups. However, in the model based clustering; increasing the number of populations to 4 (K=4 )
caused all non-Eritrean genotypes to fall in a separate cluster suggesting availability of potentially rich diversity within the Eritrean
populations justified by the large number of private alleles observed.
Keywords
Eritrean pepper; SSR markers; Genetic diversity; Population structure; Farmer variety; Germplasm
Introduction
Chilli pepper belongs to the genus
Capsicum
of the
Solanceae
family. This genus contains 31 species of
which five,
C. annuum
L.,
C. chinense
Jacq.,
C.
frutescens
L.,
C. baccatum
L.
and
C. pubescens
Ruiz
& Pav.
are
domesticated (Moscone et al., 2006).
Pepper is the most widely used spice and one of the
important vegetable crops in the world. In Eritrea,
pepper is used on both dry and fresh forms in almost
all traditional dishes. The average weekly household
consumption of dry pepper is estimated at 140 grams
(Saleh et al., 2013). It is consumed as powder
prepared from dry pods called ‘
berbere
’, which is
added to dishes as a food dye and spice. The dry red
pods are also one of the main ingredients of the
chickpea-based ‘
shiro
’ powder, a popular sauce in
Eritrea, while green pods are eaten raw as a salad or
appetizer (Saleh et al., 2013). Pepper is one of the four
most widely grown vegetable crops in Eritrea. The
total cultivated area under pepper in 2010 was
estimated at 2 873.55 ha and the production was 21
010 tons with an average yield of 7.3 tons/ha of green
pepper (Ministry of Agriculture, 2011). In the last ten
years, Eritrea has shown a continuous increase in both
area under pepper and production, while productivity
declined from 10.1 t/ ha in 2003 to 7.3 in 2010
(Ministry of Agriculture, 2011).
The study of genetic variation among individuals,
groups of individuals or populations is a pre-requisite
for plant breeding. Knowledge about germplasm
diversity and genetic relationships among breeding
materials informs crop improvement strategies. It
allows exploration of variability in available traits of
