Molecular and Culture-based Assessment of Root/crown Rot Fungal/Oomycete Complex of Bean in Mozambique

Dry edible beans (Phaseolus vulgaris) play an important role in food security, alleviating hunger and malnutrition and adding value to the economy in Mozambique. Recently, root/crown rot (RCR) has caused yield losses in bean fields in Mozambique. A diverse taxa of fungi and oomycetes have been associated with RCR. However, in Mozambique little information on root rot is available. The purpose of this study is to use Illumina sequencing platform, polymerase chain reaction (PCR) and culture-based methods to identify the primary pathogens associated with RCR in Mozambique. A total of 88 plants showing symptoms of RCR disease were collected from two locations, Gurué and Chokwé, over a 2-year period. DNA was extracted from a portion of the interface of healthy and infected RCR diseased plant tissue and spotted on Flinders Technologies Associated (FTA) cards, and the remaining matching plant tissue used for DNA extraction and plated directly in culture media. Illumina sequencing platform with universal primers to amplify the 18S (ribosomal RNA) rRNA region were used. Polymersase Chain Reaction (PCR), using species and genus specific primer was used for isolate detection and identification. There was high correlation between results from DNA extracted from FTA cards and plant tissue (PFusarium oxysporum and Fusarium solani were the most prevalent groups found through the Illumina platform. A high frequency of isolation of Fusarium spp. was detected through PCR. Similarly, the majority of the pathogenic isolates identified through sequencing were also within Fusarium spp. Overall using all methods Fusarium spp. were the most fungal species detected in both locations and years when compared to Rhizoctonia solani, Pythium spp. or Macrophomina phaseolina.Advisor: James Steadman