Inter-Simple Sequence Repeat Markers Reveal a Moderate Genetic Diversity among Fusarium Species Causing Common Bean Root Rot in Uganda
Samuel Erima *
National Crops Resources Research Institute, National Agricultural Research Organization, P.O. Box 7084, Kampala, Uganda, Department of Crop Science and Horticulture, Makerere University, P.O. Box 7062, Kampala, Uganda and Faculty of Agriculture and Environmental Sciences, Muni University, P.O. Box 725, Arua, Uganda.
Moses Nyine
Plantain Breeding Program, International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan 200001, Oyo state, Nigeria.
Richard Edema
Department of Crop Science and Horticulture, Makerere University, P.O. Box 7062, Kampala, Uganda.
Allan Nkuboye
National Crops Resources Research Institute, National Agricultural Research Organization, P.O. Box 7084, Kampala, Uganda.
Harriet Orodriyo
Faculty of Agriculture and Environmental Sciences, Muni University, P.O. Box 725, Arua, Uganda.
Agnes Candiru
National Crops Resources Research Institute, National Agricultural Research Organization, P.O. Box 7084, Kampala, Uganda.
Michael Hilary Otim
National Crops Resources Research Institute, National Agricultural Research Organization, P.O. Box 7084, Kampala, Uganda.
Pamela Paparu
National Crops Resources Research Institute, National Agricultural Research Organization, P.O. Box 7084, Kampala, Uganda.
*Author to whom correspondence should be addressed.
Abstract
Aims: The present study aimed to determine the genetic diversity and population structure of Fusarium species causing common bean root rot in Uganda
Study Design: The study used isolates from a previous disease survey in Uganda
Place and Duration of Study: The isolates were collected from 6 different agro-ecological zones of Uganda. Isolation was conducted at the legumes pathology laboratory of the National Agricultural Research Organization at Namulonge, Kampala. The isolates were collected in 2019.
Methodology: DNA was extracted from 101 Fusarium species isolates using a modification of the cetyltrimethylammonium bromide protocol. Seventeen inter-simple sequence repeat primers were used in the polymerase chain reaction. The bands were scored for presence and absence using 1 and 0, respectively. The genetic diversity and population structure were determined using parameters such as polymorphic information content, allele divergence frequency, Principal component analysis, and admixture analysis. Analysis of molecular variance was also conducted.
Results: The average polymorphic information content of the isolates was 84%. The average Wright's fixation index (Fst) and expected heterozygosity were 0.2. The result of the analysis of molecular variance revealed that 0.2% of the variation was between the agro-ecological zones, while 99.8% of the variation was within agro-ecological zones. Admixture analysis showed that the isolates have an admixed ancestry.
Conclusion: Since the isolates from the different agro-ecological zones were similar, released varieties may not face extreme variants when they are planted in agro-ecological zones where they were not screened.
Keywords: Common bean, genetic diversity, Fusarium root rot, intersimple sequence repeat