Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia

Abstract

Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (FST = 0.049) as evidenced by high level of gene flow estimate (Nm = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia.

Fig 1. Unweighted Neighbor-joining tree using the simple matching similarity coefficient based on 23 microsatellite markers for the 163 isolates of Colletotrichum gloeosporioides isolated from citrus in Ethiopia.

The tree shows the clustering pattern of isolates from the four C. gloeosporioides populations. The populations are color coded as follows: Central region (red), Northwest region (green), South region (blue) and Southwest region (violet).

Fig 2. Principal coordinates analysis (PCoA) bi-plot showing the clustering of the 163Colletotrichumgloeosporioides isolates based on 23 microsatellite loci.

The four populations are color coded as follows: Central region (red), Northwest region (green), South region (blue) and Southwest region (yellow). Percentages of variation explained by the first 3 axes (1, 2, and 3) are 36.16%, 11.6% and 8.68%, respectively.

Fig 3. Bayesian model-based estimation of population structure (K = 3) for the 163 Colletotrichum gloeosporioides isolates in four pre-determined populations (x-axis): Central Ethiopia (CE), Northwest Ethiopia (NEW), South Ethiopia (SE) and Southwest Ethiopia (SWE).

Each group is separated by a black vertical line. Numbers in the y-axis show coefficient of membership/assignment.