Status and epidemiology of maize lethal necrotic disease in Northern Tanzania

Fatma Hussein Kiruwa; Samuel Mutiga; Joyce Njuguna; Eunice Machuka; Senait Senay; Tileye Feyissa; Patrick Alois Ndakidemi; Francesca Stomeo

doi:10.3390/pathogens9010004

Status and epidemiology of maize lethal necrotic disease in Northern Tanzania

Fatma Hussein Kiruwa, Samuel Mutiga, Joyce Njuguna, Eunice Machuka, Senait Senay, Tileye Feyissa, Patrick Alois Ndakidemi, Francesca Stomeo

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Abstract

Sustainable control of plant diseases requires a good understanding of the epidemiological aspects such as the biology of the causal pathogens. In the current study, we used RT-PCR and Next Generation Sequencing (NGS) to contribute to the characterization of maize lethal necrotic (MLN) viruses and to identify other possible viruses that could represent a future threat in maize production in Tanzania. RT-PCR screening for Maize Chlorotic Mottle Virus (MCMV) detected the virus in the majority (97%) of the samples (n=223). Analysis of a subset (n=48) of the samples using NGS-Illumina Miseq detected MCMV and Sugarcane Mosaic Virus (SCMV) at a co-infection of 62%. The analysis further detected Maize streak virus with an 8% incidence in samples where MCMV and SCMV were also detected. In addition, signatures of Maize dwarf mosaic virus, Sorghum mosaic virus, Maize yellow dwarf virus-RMV and Barley yellow dwarf virus were detected with low coverage. Phylogenetic analysis of the viral coat protein showed that isolates of MCMV and SCMV were similar to those previously reported in East Africa and Hebei, China. Besides characterization, we used farmers’ interviews and direct field observations to give insights into MLN status in different agro-ecological zones (AEZs) in Kilimanjaro, Mayara, and Arusha. Through the survey, we showed that the prevalence of MLN differed across regions (P = 0.0012) and villages (P < 0.0001) but not across AEZs (P > 0.05). The study shows changing MLN dynamicsin Tanzania and emphasizes the need for regional scientists to utilize farmers’ awareness in managing the disease.

Original language	English (US)
Article number	4
Journal	Pathogens
Volume	9
Issue number	1
DOIs	https://doi.org/10.3390/pathogens9010004
State	Published - Jan 2020

Bibliographical note

Funding Information:
This research was funded by theTanzania Commission for Science and Technology (COSTECH) and the Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub through the Africa Biosciences Challenge Fund (ABCF) Fellowship, grant number BS01 NBO SID004 SID004C2 ABC 132. The ABCF Program is funded by the Australian Department for Foreign Affairs and Trade (DFAT) through the BecA-CSIRO partnership; the Syngenta Foundation for Sustainable Agriculture (SFSA); the Bill & Melinda Gates Foundation (BMGF); the UK Department for International Development (DFID) and; the Swedish International Development Cooperation Agency (Sida). Acknowledgments: We would like to acknowledge Dr. Mbwambo of ARI Mlingano for the GIS dataset for the Tanzania agro-ecological zones (AEZs) map, Tanzania Ministry of Agriculture for the permission of accessing AEZs dataset and Francis Mwatuni of CIMMYT, Nairobi for providing MCMV primers.

Funding Information:
Funding: This research was funded by theTanzania Commission for Science and Technology (COSTECH) and the Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub through the Africa Biosciences Challenge Fund (ABCF) Fellowship, grant number BS01 NBO SID004 SID004C2 ABC 132. The ABCF Program is funded by the Australian Department for Foreign Affairs and Trade (DFAT) through the BecA-CSIRO partnership; the Syngenta Foundation for Sustainable Agriculture (SFSA); the Bill & Melinda Gates Foundation (BMGF); the UK Department for International Development (DFID) and; the Swedish International Development Cooperation Agency (Sida).

Publisher Copyright:
© 2019 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

MLN prevalence
Maize chlorotic mottle virus
Next-generation sequencing
Phylogenetic analysis
Sugarcane mosaic virus

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title = "Status and epidemiology of maize lethal necrotic disease in Northern Tanzania",

abstract = "Sustainable control of plant diseases requires a good understanding of the epidemiological aspects such as the biology of the causal pathogens. In the current study, we used RT-PCR and Next Generation Sequencing (NGS) to contribute to the characterization of maize lethal necrotic (MLN) viruses and to identify other possible viruses that could represent a future threat in maize production in Tanzania. RT-PCR screening for Maize Chlorotic Mottle Virus (MCMV) detected the virus in the majority (97%) of the samples (n=223). Analysis of a subset (n=48) of the samples using NGS-Illumina Miseq detected MCMV and Sugarcane Mosaic Virus (SCMV) at a co-infection of 62%. The analysis further detected Maize streak virus with an 8% incidence in samples where MCMV and SCMV were also detected. In addition, signatures of Maize dwarf mosaic virus, Sorghum mosaic virus, Maize yellow dwarf virus-RMV and Barley yellow dwarf virus were detected with low coverage. Phylogenetic analysis of the viral coat protein showed that isolates of MCMV and SCMV were similar to those previously reported in East Africa and Hebei, China. Besides characterization, we used farmers{\textquoteright} interviews and direct field observations to give insights into MLN status in different agro-ecological zones (AEZs) in Kilimanjaro, Mayara, and Arusha. Through the survey, we showed that the prevalence of MLN differed across regions (P = 0.0012) and villages (P < 0.0001) but not across AEZs (P > 0.05). The study shows changing MLN dynamicsin Tanzania and emphasizes the need for regional scientists to utilize farmers{\textquoteright} awareness in managing the disease.",

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author = "Kiruwa, {Fatma Hussein} and Samuel Mutiga and Joyce Njuguna and Eunice Machuka and Senait Senay and Tileye Feyissa and Ndakidemi, {Patrick Alois} and Francesca Stomeo",

note = "Funding Information: This research was funded by theTanzania Commission for Science and Technology (COSTECH) and the Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub through the Africa Biosciences Challenge Fund (ABCF) Fellowship, grant number BS01 NBO SID004 SID004C2 ABC 132. The ABCF Program is funded by the Australian Department for Foreign Affairs and Trade (DFAT) through the BecA-CSIRO partnership; the Syngenta Foundation for Sustainable Agriculture (SFSA); the Bill & Melinda Gates Foundation (BMGF); the UK Department for International Development (DFID) and; the Swedish International Development Cooperation Agency (Sida). Acknowledgments: We would like to acknowledge Dr. Mbwambo of ARI Mlingano for the GIS dataset for the Tanzania agro-ecological zones (AEZs) map, Tanzania Ministry of Agriculture for the permission of accessing AEZs dataset and Francis Mwatuni of CIMMYT, Nairobi for providing MCMV primers. Funding Information: Funding: This research was funded by theTanzania Commission for Science and Technology (COSTECH) and the Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub through the Africa Biosciences Challenge Fund (ABCF) Fellowship, grant number BS01 NBO SID004 SID004C2 ABC 132. The ABCF Program is funded by the Australian Department for Foreign Affairs and Trade (DFAT) through the BecA-CSIRO partnership; the Syngenta Foundation for Sustainable Agriculture (SFSA); the Bill & Melinda Gates Foundation (BMGF); the UK Department for International Development (DFID) and; the Swedish International Development Cooperation Agency (Sida). Publisher Copyright: {\textcopyright} 2019 by the authors. Licensee MDPI, Basel, Switzerland.",

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AU - Feyissa, Tileye

AU - Ndakidemi, Patrick Alois

AU - Stomeo, Francesca

N1 - Funding Information: This research was funded by theTanzania Commission for Science and Technology (COSTECH) and the Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub through the Africa Biosciences Challenge Fund (ABCF) Fellowship, grant number BS01 NBO SID004 SID004C2 ABC 132. The ABCF Program is funded by the Australian Department for Foreign Affairs and Trade (DFAT) through the BecA-CSIRO partnership; the Syngenta Foundation for Sustainable Agriculture (SFSA); the Bill & Melinda Gates Foundation (BMGF); the UK Department for International Development (DFID) and; the Swedish International Development Cooperation Agency (Sida). Acknowledgments: We would like to acknowledge Dr. Mbwambo of ARI Mlingano for the GIS dataset for the Tanzania agro-ecological zones (AEZs) map, Tanzania Ministry of Agriculture for the permission of accessing AEZs dataset and Francis Mwatuni of CIMMYT, Nairobi for providing MCMV primers. Funding Information: Funding: This research was funded by theTanzania Commission for Science and Technology (COSTECH) and the Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub through the Africa Biosciences Challenge Fund (ABCF) Fellowship, grant number BS01 NBO SID004 SID004C2 ABC 132. The ABCF Program is funded by the Australian Department for Foreign Affairs and Trade (DFAT) through the BecA-CSIRO partnership; the Syngenta Foundation for Sustainable Agriculture (SFSA); the Bill & Melinda Gates Foundation (BMGF); the UK Department for International Development (DFID) and; the Swedish International Development Cooperation Agency (Sida). Publisher Copyright: © 2019 by the authors. Licensee MDPI, Basel, Switzerland.

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N2 - Sustainable control of plant diseases requires a good understanding of the epidemiological aspects such as the biology of the causal pathogens. In the current study, we used RT-PCR and Next Generation Sequencing (NGS) to contribute to the characterization of maize lethal necrotic (MLN) viruses and to identify other possible viruses that could represent a future threat in maize production in Tanzania. RT-PCR screening for Maize Chlorotic Mottle Virus (MCMV) detected the virus in the majority (97%) of the samples (n=223). Analysis of a subset (n=48) of the samples using NGS-Illumina Miseq detected MCMV and Sugarcane Mosaic Virus (SCMV) at a co-infection of 62%. The analysis further detected Maize streak virus with an 8% incidence in samples where MCMV and SCMV were also detected. In addition, signatures of Maize dwarf mosaic virus, Sorghum mosaic virus, Maize yellow dwarf virus-RMV and Barley yellow dwarf virus were detected with low coverage. Phylogenetic analysis of the viral coat protein showed that isolates of MCMV and SCMV were similar to those previously reported in East Africa and Hebei, China. Besides characterization, we used farmers’ interviews and direct field observations to give insights into MLN status in different agro-ecological zones (AEZs) in Kilimanjaro, Mayara, and Arusha. Through the survey, we showed that the prevalence of MLN differed across regions (P = 0.0012) and villages (P < 0.0001) but not across AEZs (P > 0.05). The study shows changing MLN dynamicsin Tanzania and emphasizes the need for regional scientists to utilize farmers’ awareness in managing the disease.

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Status and epidemiology of maize lethal necrotic disease in Northern Tanzania

Abstract

Bibliographical note

Keywords

Access

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