International Journal of Research Studies in Science, Engineering and Technology

Volume 10, Issue 1, 2023, PP 20-27

ISSN : 2349-476X
DOI: https://doi.org/10.22259/2349-476X.1001004

Cluster and Principal Component Analysis of Coffee (Coffea

Arabica L.) Diversity Using Quantitative Traits in the South
Western Ethiopian
A. Asegid1*, W. Garedew (PhD)2 and F. Tefera (PhD)3
1
Ethiopia Institute of Agricultural Research, Debre Zeit Agricultural Research Center
2
Jimma University College of Agriculture and Veterinary Medicine, Horticulture and Plant sciences
3
Ethiopia Institute of Agricultural Research, Jimma Agricultural Research Center
*Corresponding Author: A. Asegid, Ethiopia Institute of Agricultural Research, Debre Zeit Agricultural
Research Center, Ethiopia.

ABSTRACT
Coffee (Coffea arabica) is widely used economically important crop in the world. Four replicated standard
check varieties and a total of 133 accessions of coffee from the Bale and West Arsi zones were assessed in
the Gera agricultural research sub center. The study was done to determine the level of genetic diversity
among clusters and to identify major traits that contribute to overall genetic variability for future coffee
breeding works. The experimental design was set out using augmented design with three block of a single
row, with six trees per plot. A study was conducted on four-year-old coffee trees that were planted in July
2015 during the 2018–19 crop seasons. In the univariate analyses of variance, the germplasm accessions
varied significantly for each of the 10 morphological agronomic traits demonstrating existence of variability.
A cluster means analysis for quantitative attributes showed significant variation. Cluster distances between
the majorities of these clusters were highly significant at (P ‹ 0.01); as a result, the distance between clusters
II and VI (142.82) was found to be the greatest, followed by cluster I and VI (100.94). Among the 137
variables, the first four main components accounted for 70.55 percent of the total variation. However, the
variance as a whole was more strongly influenced by the first two principal components (PC1 and PC2).
However, additional traits of interest should be studied over year and locations including physiological,
quality, disease and biochemical analysis with the support of advanced molecular techniques.
Keywords: Coffea arabica, Genetic divergent Cluster analysis, Principal component analysis.

INTRODUCTION both production and consumption of coffee have

risen considerably. Approximately 60 percent of
Coffee (Coffea arabica) is widely used brewed
the world’s coffee production comes from Arabica,
drink (Shukla, S.K. and Kumar, V., 2013) and,
while the remaining 40 percent is contributed by
economically important crop in the world. Coffee
Robusta; the former considered a superior quality
belongs to the genus Coffea of the Rubiaceae
and fetches a higher price (Moat et al., 2017).
family, mostly grown in the tropical and
subtropical regions (Berthaud and Charrier, Globally, total coffee production is estimated to
1988). It is an important commodity crop in be 169. 634 million of 60-kg bags, of which
Ethiopia (WeldeMichael el al., 2016). The genus Arabica coffee production is about 103.60 million of
Coffea L. comprises 124 species (Davis et al., 60-kg bags, while Robusta coffee production was
2011). However, only C. arabica (Arabica estimated to be 65.46 million 60-kg bags (ICO,
coffee), C. Canephora (Robusta coffee); and C. 2021). Economically, coffee is the second most
liberica (Liberian or Liberica coffee, or excels exported commodity after oil, and employs over
coffee) are the economically important species of 100 million people worldwide (Gray et al., 2013).
the genus (Davis et al., 2006). Coffea arabica the Coffee is not only one of the highly preferred
only allopolyploid (2n = 4x = 44) coffee species international beverages, but also one of the
and self-fertile (Silvarolla et al., 2004). Arabica important agricultural commodities in the world.
coffee has its primary center of origin and genetic According to, ICO (2019) Ethiopia is Africa’s
diversity in the high lands of Southwestern, largest coffee producer and the world’s fifth
Ethiopia (Sylvain, 1955). Over the past 50 years, largest exporter of Arabica coffee. The total

International Journal of Research Studies in Science, Engineering and Technology V10 ● I1 ● 2023 20
Cluster and Principal Component Analysis of Coffee (Coffea Arabica L.) Diversity Using Quantitative Traits in
the South Western Ethiopian

cultivated coffee area in Ethiopia is estimated resistant coffee varieties. The study was conducted
around 758.523.3 ha (CSA, 2021). The annual based on objectives to determine the level of
estimate of national production of coffee is about genetic diversity among clusters and to identify
7.38 million of 60-kg bags (ICO, 2021) and major traits that contribute to overall genetic
national average yield is low (636 kg/ha) (CSA, variability for future coffee breeding works.
2021). Coffee is Ethiopia’s main export commodity,
contributing to the livelihoods of more than 15 MATERIALS AND METHODS
million smallholder farmers and other actors in Experimental Material, Design and Management
the coffee sector (USAD, 2022). It represents the
The experiment was done in South West of
major agricultural export crop, providing 25% of
Ethiopia using One hundred thirty-three C. arabica
the foreign exchange earnings (USDA, 2019).
along with four standard check varieties at Gera
As indicated by Krug and Carvalho, (1951) agricultural research center. The center is located
World arabica coffee production is largely based at 425 km. southwest of Addis Ababa capital city
on using a very small number of cultivars: C. of Ethiopia. It is located at 7046 N latitude and 360
arabica var. typica Cramer, C. arabica var. bourbon. 26’ E longitudes, at an altitude of 1974 meters
The low genetic diversity observed makes this above sea level. The mean annual rainfall of the
crop, vulnerable to biotic and climatic hazards. area is 1880 mm with average maximum and
However, Ethiopia holds a unique position in the minimum air temperatures of 24.5oC and 10.4oC,
world as Coffea arabica the primary center of respectively. The center has contained Acrisols
origin and diversity. The major coffee growing and Nitoso soil with PH of 5-6 and medium to high
area and diversity is found in Oromia Region, of exchangeable cation (Paulos, 1994; Paulos and
South West Ethiopia (Wollega, Illubabor, Jimma- Tesfaye, 2000). The experiment was established in
Limu, Tepi, Kaffa and Bench-Maji). Southern an augmented design with three replications. A
Nations Nationalities Region is the second coffee plot is laid out in a single row with six trees.
producing region. Whereas, Modest coffee Spacing both, between rows and plants were 2m x
production in Amhara region and minor output in 2m (plot area of 4m2) and Spacing between block
Benishangul-Gumuz region (Moat et al., 2017). was 4 meter. All management practices were
applied as per recommendation.
Different research findings illustrate the importance
and existence of natural Arabica coffee genetic Data Collection
variability in Ethiopian, to get highly productivity Data on 25 Quantitative traits were collected on
and disease resistance coffee genetic materials tree basis from three sample trees per row in each
(Adugna, 2005; Labouisse et al., 2008). To make accession using standard coffee descriptor of
use of this genetic potential and seek a solutions IPGRI (1996). The measured accessions for
to pre-existing production constraints, Jima morphological characters is namely: Plant height,
agricultural research center (JARC) conserved stem diameter, number of primary branch (no),
about 6923 coffee accessions from different number of node on main stem (no), canopy
coffee producing areas of the country to its Center diameter(m),average inter node length of main
and its’ Sub-centers over the last five decades and stem (cm), fruit length (mm), fruit thickness
ultimately released about 44 improved varieties (mm), fruit width (mm), bean length (mm), bean
(35 pure lines and nine were hybrids) for different thickness (mm), bean width (mm), leaf length
localities. It is important to plan coffee variability (cm), leaf width (cm), leaf size (mm), petiole
assessment for yield and its component characters length (cm), length of first primary branch (cm),
before doing any breeding improvement program. hundred bean weight (gr), yield (kg/ha), number
As continued breeding efforts, JARC have of secondary branch (no.), number of node on
collected about 133 coffee germplasm from Bale primary branch (no), height up to first primary
and West Arsi Zones of Oromia Regional State. branch (cm), percentage of bearing primary
However, these materials have not been branch. Other traits Coffee berry disease severity
characterized and their genetic potential for and coffee leaf rust severity were recorded
disease resistance and yielding potential is not through visual estimation per three trees.
well known. Hence, it is relevant to characterize
and conserve these coffee accessions to reduce STATISTICAL ANALYSIS
the loss of coffee genetic resources and use in a The statistical analyses of variance were computed
breeding program to improve the productivity of using SAS soft version 9.2 (SAS, 2010) based on
the crop by developing high yielding and disease augmented design for 25 quantitative morphological

21 International Journal of Research Studies in Science, Engineering and Technology V10 ● I1 ● 2023
Cluster and Principal Component Analysis of Coffee (Coffea Arabica L.) Diversity Using Quantitative Traits in
the South Western Ethiopian

characters and two years yield data. In this study (2018) and Desalegn (2018) also found a
sets of 25 quantitative morphological data were substantial amount of variability for different
subjected to cluster analysis to determine the traits among tested genotypes of arabica coffee,
variability among the accessions. However, ten which shows the possibility to bring improvement
morphological characters that showed statistically through selection. Bayetta (1997) also reported
significant variations among the accessions were high genetic variability within the Arabica coffee
used for principal component analysis. Principal population for yield, growth characters and coffee
component with Eigen values greater than one were berry disease resistance. Moreover, Mesfin and
considered to explain observable variability. Bayyeta (2008) reported the mean square of
Cluster analysis is a process of identification and treatment showing that significant difference
categorization of subsets of objects and a among 100 Hararge coffee accession for 14
multivariate technique whose primary purpose is quantitative characters. In the present studied
to group individuals or objects based on the traits, checks versus accessions were significant
characteristics they possess. Hierarchical clustering for all characters except stem diameter, number
was employed using the similarity coefficients of primary branches, number of nodes on main
among the 137 coffee accessions. Clustering was stem, bean length, bean thickness, number of
performed using the proc cluster procedure of nodes on a primary branch (Table 3). This also
SAS version 9.2 (SAS institute, 2010). The showed that existence of variation among
dendrogram constructed based on the average collected accessions and control check varieties.
linkage and Euclidean distance was used as a
measure of dissimilarity. The number of cluster was
CLUSTER ANALYSIS BASED ON
determined by following the approach suggested by QUANTITATIVE CHARACTERS
Copper and Miligan (1988) by looking in to Six clusters were identified using a cluster
statistics namely Pseudo F, Pseudo t2 and cubic analysis of 137 coffee accessions (Table 9). The
clustering criteria. Genetic divergence between four clusters I, II, III, and IV contained the
and within clusters were calculated using the greatest number of accessions. Smaller accession
generalized Mahalanobis's D2 statistics numbers, however, were grouped in clusters V
(Mahalanobis, 1936) using the equation: and VI. Thus, cluster-II was the largest and had
41 accessions (30%). It was followed by cluster-
I, which had 37 accessions (27%), cluster-IV,
Where, D2 P= the distance between any two which had 29 accessions (21%), cluster-III,
groups i and j, Xi and Xj = the p mean vectors of which had 25 accessions (18%), cluster-V, which
accessions i and j, respectively. S-1 = the inverse had 4 accessions (3%) and cluster-VI, which had
of the pooled covariance matrix. The D2 values 1 accession (1%). 74165 and 74148, perennial
obtained for pairs of clusters were tested for self-pollinated standard check varieties, were
significance at 0.05 level of significance against classified in cluster I, whereas 74110 and 75227
the tabulated values of x2, for ‘P’ degrees of were grouped in clusters III and IV, respectively.
freedom, where p is the number of variables Coffee collections were made in Bale and West
considered (Singh and Chaudhary, 1987). Arsi zones, from three districts: Nensebo,
RESULT AND DISCUSSION Gololcha and Ginir, which was grouped into
different clusters. In this study coffee accessions
The analyzed mean square results for most of collected from the West Arsi zone: Rafisa kebele
measured quantitative traits were significant was grouped in a cluster I, III and IV. Whereas,
difference at (P<0.05) for bean yield, fruit accessions from the same district, Kore kebele
thickness, canopy diameter, fruit length, fruit grouped in cluster I, II, III and IV. This revealed
width, coffee berry disease (CBD), Coffee leaf that existence of higher genetic diversity in
rust (CLR), number of secondary branches, accession collected within same districts.
percent (%) of bearing primary branch and height Variation of accessions revealed that due to
up to first primary branch (Table 1). Thus, it is a admixture of different coffee genotypes through
good chance to improve the accessions through moving by human or other wild animals’ from
selection and breeding using these traits. place to place.
This study result agrees with the findings of These findings agree with Getachew et al.,
Olika et al., (2011) who found that significant (2013) who reported that accessions collected
variations among 49 accession for 22 characters. from different kebeles clustered together, while
(Atinafu and Mohammed, 2017, and Abdulfeta accessions collected from same kebeles were

International Journal of Research Studies in Science, Engineering and Technology V10 ● I1 ● 2023 22
Cluster and Principal Component Analysis of Coffee (Coffea Arabica L.) Diversity Using Quantitative Traits in
the South Western Ethiopian

clustered into different clusters. Seyoum (2003) accessions collected from the same place
also reported that, rather than geographical clustered in to different group, whereas accession
region morphological variation is more important collected from different places grouped into the
because it shows variation in coffee. Generally, same clustered.
////////

Figure1. Tree diagram of 137 accessions using 10 quantitative traits.

23 International Journal of Research Studies in Science, Engineering and Technology V10 ● I1 ● 2023
Cluster and Principal Component Analysis of Coffee (Coffea Arabica L.) Diversity Using Quantitative Traits in
the South Western Ethiopian

Table1. Distribution of Bale and West Arsi coffee accessions clustered based on D 2 analysis.
Clus No. No. ace Percent (%) Name of accessions
I 37 27 B275/07 B317/07 B69/07 B67/07 B265/07 B306/07 74165
B82/07 74148 B110/07 B311/07 B239/07 B326/07 B76/07
B315/07 B303/07 B125/07 B143/07 B155/07 B235/07 B258/07
B157/07 B95/07 B262/07 B113/07 B224/07 B269/07 B264/07
B305/07 B21/07 B293/07 B278/07 B160/07 B240/07 B217/07
B37/07 B281/07
II 41 30 B68/07 B71/07 B79/07 B11/07 B237/07 B165/07 B261/07
B124/07 B57/07 B279/07 B81/07 B225/07 B192/07 B41/07
B191/07 B292/07 B327/07 B117/07 B218/07 B89/07 B231/07
B284/07 B129/07 B204/07 B159/07 B126/07 B107/07 B300/07
B170/07 B202/07 B166/07 B288/07 B172/07 B223/07 B77/07
B144/07 B232/07 B05/07 B274/07 B116/07 B31/07
III 25 18 B285/07 B13/07 B266/07 B287/07 B93/07 B286/07 B313/07
B55/07 B280/07 B307/07 B290/07 B39/07 74110 B309/07
B321/07 B289/07 B56/07 B28/07 B88/07 B282/07 B186/07
B112/07 B270/07 B181/07 B86/07
IV 29 21 B65/07 B298/07 B308/07 B108/07 B271/07 B310/07 B174/07
B291/07 B73/07 B244/07 B251/07 B277/07 B304/07 B318/07
B236/07 75227 B297/07 B276/07 B299/07 B272/07 B267/07
B91/07 B268/07 B109/07 B238/07 B173/07 B20/07 B167/07
B187/07
V 4 3 B175/07 B29/07 B273/07 B145/07
VI 1 1 B184/07
55555

INTER CLUSTER DISTANCE (D2) ANALYSIS Since, the maximum inter-cluster distance was
BASED ON QUANTITATIVE TRAITS observed between clusters II and VI (142.82),
followed by clusters I and VI (100.94), which
The D2 chi-square test for the 6 clusters revealed
helps to get a superior hybrid or recombinant by
that there were highly significant differences (P
crossing between desirable lines of these clusters.
< 0.01 X2 =21.67) between the clusters except
However, the selection of parents should consider
cluster I and II, I and III, I and IV, IV and II, IV
and III, and III and V (Table 2), indicating little the special advantages of each cluster and each
genetic diversity between these clusters. This genotype within a cluster depending on the
suggests that, crossing of genotypes from these specific objective of the hybridization program.
clusters might not give a higher heterotic value in Crosses involving genotypes belonging to the
F1 and a narrow range of variability in the most divergent cluster distances could be used for
segregating F2 population. hybridization programs to obtain good
manifestations of heterosis and wide variability
Clusters II and VI had the highest Inter cluster (Singh and Chaudhary, 1987).
distance (142.82), while clusters I and IV had the
smallest (2.337), followed by clusters VI and IV To get a greater heterotic response in the hybrids
(76.06), II and V (73.89), III and VI (53.76), I and and a wide range of variance among the segregating
V (43.76), IV and V (27.71), and clusters I and population, various genotypes with distant clusters
VI (100.94). On other hand, Clusters I and IV had could be used in the hybridization program. Since
the smallest inter-cluster distance (2.337), while clusters II and VI had the greatest Inter-cluster
clusters II and VI had the greatest (142.82), distance (142.82), followed by clusters I and VI
followed by clusters I and VI (100.94), VI and IV (100.94), crossing between these clusters' desired
(76.06), II and V (73.89), III and VI (53.76), I and lines can result in a superior hybrid or recombinant.
V (43.76), IV and V (27.71), and II and III Moreover, depending on the specific objectives
(26.24), indicating the presence of genetic of the hybridization program, the special benefits
variability between groups of tested genotypes. of each cluster and each genotype within a cluster
Different genotypes with distant clusters could be should be taken into account while choosing
used in the hybridization program to obtain a parents. To get good manifestations of heterosis
higher heterotic response in the hybrids and a and a wide range of variability, hybridization
wide range of variation among the sergeants. procedures could use crosses involving genotypes

International Journal of Research Studies in Science, Engineering and Technology V10 ● I1 ● 2023 24
Cluster and Principal Component Analysis of Coffee (Coffea Arabica L.) Diversity Using Quantitative Traits in
the South Western Ethiopian

from the most dissimilar cluster distances (Singh coffee yield (0.3), number of secondary branch
and Chaudhary, 1987). (0.75%), canopy diameter (0.46%) and percent
(%) of bearing primary branch (-0.53%).
Table2. Inter cluster distance for 10 quantitative
traits of Bale and Wet Arsi zone coffee collection in
Likewise, the fourth PC variation revealed by
Gera southwest Ethiopia. coffee leaf rust (-0.30%) and height up to first
primary branch (0.90%).
I II III IV V VI
However, Chahal and Goal (2002) revealed that
I 0 5.528 ns 8.718ns 2.377 ns 43.831** 100.935**
II 0 26.242** 13.993 ns 73.890** 142.817** characters with the largest absolute values closer
III 0 2.553 ns 15.906 ns 53.762** to unit within the first principal component
IV 0 27.713** 76.058** influence the clustering more than those with
V 0 19.723* lower absolute values closer to zero.
VI 0 Accordingly, fruit length (0.75%), fruit thickness
(0.87%), fruit width (0.86%), coffee berry
*, **=Highly significant, (p<0.01) x2=21.67,
disease (0.42%) and number of secondary branch
(p<0.05) x2=16
(0.32%), percent (%) of bearing primary
PRINCIPAL COMPONENT ANALYSIS branches (0.39%) and canopy diameter (0.42%)
had more contribution to the total variation and
The first four principal components with Eigen
were the one that most differentiated the clusters
values greater than unity explained 70.55 percent
and should be considered in selection diverse of
of the total variation among the 137 genotypes
parent for future crossing and breeding program.
for the 10 quantitative characters measured
However, in PC2 and PC4 coffee berry disease (-
(Table 3). Principal component analysis showed
0.72) and coffee leaf rust (-0.3) were negatively
4 PC (PC1, PC2, PC3, and PC4) exhibited greater
contributed for total variation, respectively.
than one Eigen value (2.59, 2.09, 1.31 and 1.07)
(Table 2). Accordingly, the first PCA accounted This finding partially agrees with Masreshaw,
25.88% of total variation, followed by the second (2018) who had reported that first principal
(20.86%), the third (13.12%) and the fourth component that accounted the highest total
(10.7%). However, the first two principal variation (21.99%) was due to the chief
components (PC1 and PC2) were contributed contribution of positive discriminatory traits like
more to the total variation. The first PC average length of primary branches, fruit width,
contributes higher to the total variation (25.88%) fruit thickness and hundred bean weights. The
due to greater contribution of positive result partially coincided with Tounekti et al.,
discriminatory traits of fruit length (0.75%), fruit (2017) who report that PC1 accounted for
thickness (0.87%), fruit width (0.86%), coffee 51.01% of the total variation, which were due to
berry disease (0.42%) and number of secondary greater contribution of fruit length (0.29), fruit
branch (0.32%). Variation in the second PC width (0.30), fruit thickness (0.30), bean length
(20.86 %) was mainly influenced by fruit length (0.30), bean width (0.26) and bean thickness
(0.75%), fruit width (0.86%), and coffee berry (0.22). Similarly, Yigzaw (2005) also reported
disease (0.60), percent (%) of bearing primary characters contributing for variation for coffee
branches (0.39%) and canopy diameter (0.42%). genotypes includes inter-node lengths, tree
The third PC (13.12% ) variation was exhibited height, canopy diameter, number of branches,
also due to greater contributory traits of clean bean and fruit character.
Table3. Eigen values and Eigenvectors of the first four principal components (PCA) for some important traits.
Variables PCA1 PCA2 PCA3 PCA4
Bean yield (kg/ha) -0.20 0.79 0.30 0.17
Fruit length (mm) 0.75 0.33 -0.23 0.00
Fruit thickness (mm) 0.87 0.17 -0.09 -0.07
Fruit width (mm) 0.86 0.31 -0.15 -0.14
Coffee berry disease (%) 0.42 -0.72 0.17 -0.11
Coffee leaf rust (%) -0.29 0.60 0.22 -0.30
Number of secondary branch(no) 0.32 -0.13 0.75 -0.21
Height up to first primary branch (cm) 0.18 -0.05 0.00 0.90
Canopy diameter 0.22 0.42 0.46 0.22
% of bearing Primary branch -0.17 0.39 -0.53 -0.12
Eigenvalue 2.59 2.09 1.31 1.07
Difference 0.50 0.77 0.24 0.23

25 International Journal of Research Studies in Science, Engineering and Technology V10 ● I1 ● 2023
Cluster and Principal Component Analysis of Coffee (Coffea Arabica L.) Diversity Using Quantitative Traits in
the South Western Ethiopian

Percent of variation (%) 25.88 20.86 13.12 10.7

Cumulative variance (%) 25.88 46.74 59.85 70.55

CONCLUSION under its specialty coffee growing area, Awada,

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districts cluster into different group indicates variety release. Protection and seed quality
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Citation: A. Asegid, W. Garedew (PhD), F. Tefera (PhD), "Cluster and Principal Component Analysis of Coffee
(Coffea Arabica L.) Diversity Using Quantitative Traits in the South Western Ethiopian", International Journal of
Research Studies in Science, Engineering and Technology, vol. 10, no.1, pp. 20-27, 2023.
Copyright: © 2023 A. Asegid., et al. This is an open-access article distributed under the terms of the Creative
Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium,
provided the original author and source are credited.

27 International Journal of Research Studies in Science, Engineering and Technology V10 ● I1 ● 2023