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Genetic Architecture of Resistance to Phylogenetically Diverse Viruses in Maize

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Genetic Architecture of Resistance to Phylogenetically Diverse Viruses in Maize GENETIC ARCHITECTURE OF RESISTANCE TO PHYLOGENETICALLY DIVERSE VIRUSES IN MAIZE DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Jose Luis Zambrano Mendoza, M.S. Graduate Program in Horticulture and Crop Science The Ohio State University 2013 Dissertation Committee: Professor David M. Francis, Advisor Professor Margaret G. Redinbaugh, Advisor Professor Leah K. McHale Professor Peter R. Thomison Copyrighted by Jose Luis Zambrano Mendoza 2013 Abstract Virus diseases of maize can cause severe yield reductions threatening crop production and food supplies in some regions of the world. Genetic resistance to some of the major virus diseases has been characterized. Previously, resistance loci for Maize dwarf mosaic virus, (MDMV), Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV), all members of the Potyviridae; and Maize chlorotic dwarf virus (MCDV) and Maize mosaic virus (MMV), were located to maize map bins 3.04 / 3.05, 6.01, and 10.05 using diverse mapping populations and different environments. For other diseases, including those caused by Maize rayado fino virus (MRFV), Maize fine streak virus (MFSV) and Maize necrotic streak virus (MNeSV), nothing was known about genetic resistance. The main goals of the research reported in this dissertation were to identify the genetic location and mode of inheritance of genes or quantitative trait loci (QTL) conferring resistance to MRFV, MNeSV, and MFSV and to determine whether they are found in the same regions of the maize genome containing resistance to the Potyviridae and the other viruses. MRFV causes one of the most important virus diseases of maize in the Americas. Genetic resistance was previously identified in a tropical highland inbred line and two tropical landraces. The fact that the landraces were populations complicated genetic analysis of the resistance. In this research, novel sources of resistance to MRFV were ii identified, including inbred lines Oh1VI, Cuba, CML287, Ki11 and CML333. The discovery of novel sources of resistance in maize inbred lines facilitated the identification of a QTL conferring resistance to MRFV and will make possible its incorporation and use into breeding programs. The maize line, Oh1VI, is resistant to multiple viruses. To characterize multiple virus resistance in this line, a maize recombinant inbred line (RIL) population, and a number of F1 plants and F2 populations derived from a cross of Oh1VI and the virus- susceptible inbred line Oh28 were genotyped and screened for their responses to: MDMV, SCMV, WSMV, MCDV, MFSV, MMV, MRFV and MNeSV. A genetic map containing 256 markers distributed among 10 linkage groups representing the maize chromosomes was built using genotypic information derived from 768 SNP multiplex assay from the Illumina® BedArray™ platform and 21 informative (polymorphic) SSRs. Composite interval mapping identified 19 significant associations between regions of the genome and resistance to the eight viruses tested. Of these, 15 were clustered on chromosomes 6, 3, and 10. An additional novel cluster of virus resistance QTLs were found in chromosome 2. In Oh1VI, most of the resistance appeared to be dominant and segregation of resistance to specific virus in F2 plants was consistent with one to three resistance genes. It is unknown whether these regions of clustered QTLs contain single or multiple virus resistance genes, but the linkage of genes conferring resistance to multiple virus diseases in this population could facilitate breeding efforts to develop multi-virus resistant maize. Agronomic information of the RIL population and selected multi-virus resistance lines in absence of viral diseases is also presented. iii Dedicated to my family iv Acknowledgments I am grateful to my advisers Dr. Margaret Redinbaugh and Dr. David Francis for their intellectual guidance, discussion and constant support for this project and my academic courses. Their assistance in editing this dissertation is also greatly appreciated. I thank my advisory committee members, Dr. Leah McHale and Dr. Peter Thomison for their advice during the course of my graduate study. I also want to thank Mark Jones, Jane Todd, Kristen Willie, Christopher Nacci, Katia Morales, H. Miao, Rafael Diniz and Erick Brenner, who are/were members or interns of the USDA, ARS Corn, Soybean and Wheat Quality Research Unit (CSWQRU) in Wooster, for technical assistance and friendship. I wish to also thank Dr. Ray Louie and Dr. Lucy Stewart for valuable discussion and encouragement. I thank my laboratory partners Fiorella Cisneros and Bryan Cassone for their help and friendship. I thank my wife Katia for her moral support, patience, company and encouragement during my studies and research. I want to thank Adriana Thomas of DuPont Agricultural Biotechnology and the DuPont Pioneer Marker Laboratory, Johnston, IA for conducting the genotyping of the maize population that was a key addition to this research. I want to thank the Republic of Ecuador and the Instituto Nacional de Investigaciones Agropecuarias for providing a fellowship for my PhD study. This research was supported by the USDA, ARS, CSWQRU. v Vita 1999................................................................Ingeniero Agropecuario, Escuela Politécnica del Ejercito, Sangolquí, Ecuador 1999-2005 ......................................................Research Assistant, Instituto Nacional de Investigaciones Agropecuarias (INIAP), Programa de Maíz, Estación Experimental Santa Catalina, Quito, Ecuador 2005................................................................Visiting Scholar, Department of Plant Pathology, The Ohio State University 2006-2007 .....................................................M.S. Plant Sciences, Wageningen University 2008-2010 .....................................................Research Leader, INIAP, Programa de Maíz, Estación Experimental Pichilingue, Quevedo, Ecuador 2010 to present ..............................................Graduate Student, Department of Horticulture and Crop Science, The Ohio State University vi Publications 1. Zambrano, J.L., M.D. Francis, and M.G. Redinbaugh. 2013. Identification of resistance to Maize rayado fino virus in maize inbred lines. Plant Dis., in press. Fields of Study Major Field: Horticulture and Crop Science vii Table of Contents Abstract ............................................................................................................................... ii Acknowledgments............................................................................................................... v Vita ..................................................................................................................................... vi Table of Contents ............................................................................................................. viii List of Tables ................................................................................................................... xiii List of Figures ................................................................................................................... xv Chapter 1: Introducction and literature review ............................................................ 1 1.1. Introduction .................................................................................................................. 1 1.2. Objectives .................................................................................................................... 3 1.3. Literature review .......................................................................................................... 4 1.3.1. Plant disease resistance ............................................................................................. 4 1.3.2. Qualitative disease resistance ................................................................................... 5 1.3.2.1. Plant basal disease resistance ................................................................................. 5 1.3.2.2. R-gene mediated disease resistance ....................................................................... 6 1.3.3. Quantitative disease resistance ................................................................................. 9 1.3.3.1. QTL mapping ....................................................................................................... 10 1.3.4. Plant resistance to virus diseases ............................................................................ 12 1.3.5. Mechanisms of virus resistance .............................................................................. 16 1.3.6. Genetics of virus resistance in maize ...................................................................... 19 1.3.6.1. Potyviridae (MDMV, SCMV, and WSMV) ........................................................ 20 1.3.6.2. Rhabdoviridae (MMV and MFSV) ...................................................................... 21 1.3.6.3. Tymoviridae (MRFV) .......................................................................................... 22 1.3.6.4. Secoviridae (MCDV) ........................................................................................... 24 viii 1.3.6.5. Tombusviridae (MNeSV) .................................................................................... 25 1.3.7. Clustering of viral resistance genes in maize .......................................................... 26 1.3.8. Breeding for virus
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