Professor W Thomas Shier

PHARM Medicinal Chemistry
College of Pharmacy
Twin Cities
Project Title: 
Soil Microbiome Studies Related to Rice Yellow Mottle Virus in Mali

This project is to compare bacterial and fungal microbiomes in soil and rice plants from rice production paddies sensitive and resistant to rice yellow mottle virus, a disease first reported in Kenya in 1966, which has been devastating rice production in sub-Saharan Africa since then, including paddy rice irrigated from the Niger River in Mali. The researchers have submitted DNA samples from panels of 40 soil and 40 rice samples to the University of Minnesota Genomics Center; they have conducted next-gen sequencing for bacterial microbiome analysis at the V4V5 site and fungal microbiome analysis at the ITS1 site using a pipeline implemented the Qiime 1.9.1 analysis software. The analysis included filtering raw fastq files for primer and adapter dimer sequences, removing contaminating host sequences and chimeric sequences, clustering sequences into OTUs using the Qiime open-reference OTU calling method with the greengenes 16S reference or UNITE ITS reference, and calculating alpha and beta diversity metrics. The researchers are currently processing the data with the goal of identifying soil microbes able to provide natural control of rice yellow mottle virus.

Project Investigators

Professor W Thomas Shier
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