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.

Genetic diversity ofColletotrichum gloeosporioidesspecies complex associated withCitruswither‐tip of twigs in Tunisia using microsatellite markers

“…Comparatively, a high genetic diversity was observed on C. gloeosporioides in yam in Nigeria using 51 SSR markers (Abang et al, ) and on strawberry in the United States using 40 genetic loci with RAPD and SSR markers (Urena‐Padilla, Mackenzie, Bowen, & Legard, ). Using 50 SSR markers, including the 10 SSR markers we tested, Moges et al () found a higher level of genetic diversity between 163 Ethiopian Citrus C. gloeosporioides isolates. Because polyacrylamide gels are less sensitive to detect small size variations of SSR amplicons than capillary electrophoresis used by Moges et al (), we may have detected fewer alleles in the present study.…”

“…Using 50 SSR markers, including the 10 SSR markers we tested, Moges et al () found a higher level of genetic diversity between 163 Ethiopian Citrus C. gloeosporioides isolates. Because polyacrylamide gels are less sensitive to detect small size variations of SSR amplicons than capillary electrophoresis used by Moges et al (), we may have detected fewer alleles in the present study. However, our genetic diversity was higher than previously reported in Tunisia (Rhaiem & Taylor, ).…”

“…To study the genetic diversity of the 54 Tunisian isolates of Colletotrichum sp., 10 pairs of microsatellite primers were selected from a list of 23 SSR markers developed by Moges et al () for C. gloeosporioides , based on their high polymorphism information content (PIC value > 0.4). Amplification reactions were performed in a final volume of 25 µl with 0.4 µM of each primer, 0.2 mM dNTPs, 1× reaction buffer, 0.8 U of GoTaq DNA polymerase, 1.5 mM MgCl 2 and 50 ng genomic DNA.…”

“…ciggaro and C. siamense ) (Huang et al, ; Liu et al, ; Weir, Johnston, & Damm, ) and C. truncatum species complex ( C. truncatum ) (Damm, Woudenberg, Cannon, & Crous, ). Currently, the advances made in next‐generation sequencing and in modern molecular techniques provide appropriate methods for taxonomic studies, population genetic structure and phylogenetic analyses (Capote, Pastrana, Aguado, & Sánchez‐Torres, ; Moges et al, ; Penet, Briand, Pétro, Bussière, & Guyader, ; Rampersad, ; Sharma & Kulshrestha, ). Because of their high level of polymorphisms and their easy application via multiplexing (Cai et al, ; Capote et al, ), simple sequence repeat (SSR) markers have been widely used for genetic diversity analysis of various plant pathogenic fungi (Bahri, Leconte, Vallavieille‐Pope, & Enjalbert, ; Szabo, ; Winton, Krohn, & Leiner, ).…”

“…Very few studies have been conducted on the causative agent of Citrus anthracnose disease worldwide (Keuete Kamdoum, Noumbo, & Kuiate, ). Understanding pathogen population structure, its spatio‐temporal dynamics and its genetic diversity leading to host adaptation and fungicide resistance are essential for the development of effective disease management strategies (Mahmodi et al, ; Marulanda et al, ; Moges et al, ; Rampersad, ; Ranathunge et al, ). The objectives of the study were (a) to identify the causative agent of anthracnose disease, associated with twig wither‐tip symptoms, across major Citrus growing areas in Tunisia and (b) to analyse the genetic diversity and population structure of Colletotrichum sp.…”