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Resistance to Gray Leaf Spot of Maize: Genetic Architecture and Mechanisms Elucidated through Nested Association Mapping and Near-Isogenic Line Analysis

  • Jacqueline M. Benson ,

    jmb565@cornell.edu

    Affiliation School of Integrative Plant Sciences, Cornell University, Ithaca, New York, United States of America

  • Jesse A. Poland,

    Affiliation Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America

  • Brent M. Benson,

    Affiliation 203 Solutions LLC, Baltimore, Maryland, United States of America

  • Erik L. Stromberg,

    Affiliation Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute, Blacksburg, Virginia, United States of America

  • Rebecca J. Nelson

    Affiliation School of Integrative Plant Sciences, Cornell University, Ithaca, New York, United States of America

Resistance to Gray Leaf Spot of Maize: Genetic Architecture and Mechanisms Elucidated through Nested Association Mapping and Near-Isogenic Line Analysis

  • Jacqueline M. Benson, 
  • Jesse A. Poland, 
  • Brent M. Benson, 
  • Erik L. Stromberg, 
  • Rebecca J. Nelson
PLOS
x

Abstract

Gray leaf spot (GLS), caused by Cercospora zeae-maydis and Cercospora zeina, is one of the most important diseases of maize worldwide. The pathogen has a necrotrophic lifestyle and no major genes are known for GLS. Quantitative resistance, although poorly understood, is important for GLS management. We used genetic mapping to refine understanding of the genetic architecture of GLS resistance and to develop hypotheses regarding the mechanisms underlying quantitative disease resistance (QDR) loci. Nested association mapping (NAM) was used to identify 16 quantitative trait loci (QTL) for QDR to GLS, including seven novel QTL, each of which demonstrated allelic series with significant effects above and below the magnitude of the B73 reference allele. Alleles at three QTL, qGLS1.04, qGLS2.09, and qGLS4.05, conferred disease reductions of greater than 10%. Interactions between loci were detected for three pairs of loci, including an interaction between iqGLS4.05 and qGLS7.03. Near-isogenic lines (NILs) were developed to confirm and fine-map three of the 16 QTL, and to develop hypotheses regarding mechanisms of resistance. qGLS1.04 was fine-mapped from an interval of 27.0 Mb to two intervals of 6.5 Mb and 5.2 Mb, consistent with the hypothesis that multiple genes underlie highly significant QTL identified by NAM. qGLS2.09, which was also associated with maturity (days to anthesis) and with resistance to southern leaf blight, was narrowed to a 4-Mb interval. The distance between major leaf veins was strongly associated with resistance to GLS at qGLS4.05. NILs for qGLS1.04 were treated with the C. zeae-maydis toxin cercosporin to test the role of host-specific toxin in QDR. Cercosporin exposure increased expression of a putative flavin-monooxygenase (FMO) gene, a candidate detoxification-related gene underlying qGLS1.04. This integrated approach to confirming QTL and characterizing the potential underlying mechanisms advances the understanding of QDR and will facilitate the development of resistant varieties.

Author Summary

Gray leaf spot (GLS), a necrotrophic, foliar fungal disease of maize, contributes to maize yield losses worldwide. We identified and characterized regions of the maize genome that confer resistance to GLS and gained insight into the mechanisms associated with these quantitative trait loci (QTL). We provide evidence for structural and detoxification-related mechanisms underlying quantitative resistance. The distance between major veins of the maize leaf was positively correlated with the quantity of fungal conidiophores (reproductive structures) produced. Four of the GLS QTL were associated with inter-vein distance, and co-localization was confirmed for one of these QTL in near-isogenic lines. In addition, up-regulation of a putative detoxification-related flavin-monooxygenase gene was correlated with a fine-mapped QTL. Plant breeding decisions regarding development and deployment of disease resistance traits can be improved with better understanding of the mechanisms underlying quantitative disease resistance.

Introduction

Plants resist attack by many plant pathogens by inducing localized cell death. This strategy can provide effective defense against pathogens that require living host tissue (biotrophs or hemibiotrophs) and is the basis for most monogenic resistance. However, it is not effective for pathogens that feed on dead tissue (necrotrophs) [1]. For this reason, complete, single-gene resistance is typically unavailable for diseases caused by necrotrophic pathogens [2,3]. Gray leaf spot (GLS), a foliar disease of maize caused by the polycyclic pathogens Cercospora zeae-maydis and Cercospora zeina [4,5], is a necrotrophic pathogen that is mostly controlled by quantitative forms of host plant resistance. Understanding the mechanisms underlying resistance to GLS may further elucidate the biology of host-pathogen interactions since there are contrasting mechanisms of defense against necrotrophic and biotrophic pathogens [6]. GLS is one of the most important maize diseases in the United States and in maize-growing regions worldwide [7]. It can cause yield losses over 70% due to associated severe blighting, stalk deterioration and lodging [8,9].

Although it is critical for the management of most plant diseases (not only those caused by necrotrophic pathogens), the genetic basis of quantitative disease resistance is not well understood. A better understanding of the genetic architecture and the underlying genes and mechanisms could contribute to crop improvement and disease management. Previous QTL studies have improved understanding of the genetic architecture by identifying regions of the genome that confer resistance to GLS [4,1022]. The aim of this study was to improve understanding of the locations, sizes and interactions among loci controlling GLS resistance using nested association mapping (NAM) [23] and to develop hypotheses concerning the underlying mechanisms of resistance.

Quantitative resistance can be divided into a range of sub-phenotypes at the macroscopic and microscopic levels. These phenotypes include reduction in total number of infections, reduction in lesion expansion, reduction of sporulation, lengthening of the latent period, and increasing the number of propagules necessary to establish infection [24]. Individual QTL may differentially affect specific sub-phenotypes [25]. Poland et al. [26] provided six hypotheses regarding mechanisms that underlie QDR loci: (1) genes that underlie plant development and architecture, (2) genes with mutations or allelic changes in genes involved in basal defense, (3) genes involved in secondary metabolite production known to fend off pathogen attacks, (4) genes involved in signal transduction, (5) weak forms of R-genes, and (6) genes previously unassociated with pathogen defense. Cloning of several disease QTL has provided hints about the underlying molecular mechanisms involved in resistance [2732].

Poland’s third hypothesis above indicates that such mechanisms might include those involved in chemical warfare between plant pathogens and their hosts