title: Systems genetics reveals a transcriptional network associated with susceptibility in the maize-grey leaf spot pathosystem.
abstract: We used a systems genetics approach to elucidate the molecular mechanisms of the responses of maize to grey leaf spot (GLS) disease caused by Cercospora zeina, a threat to maize production globally. Expression analysis of earleaf samples in a subtropical maize recombinant inbred line population (CML444 × SC Malawi) subjected in the field to C. zeina infection allowed detection of 20 206 expression quantitative trait loci (eQTLs). Four trans-eQTL hotspots coincided with GLS disease QTLs mapped in the same field experiment. Co-expression network analysis identified three expression modules correlated with GLS disease scores. The module (GY-s) most highly correlated with susceptibility (r = 0.71; 179 genes) was enriched for the glyoxylate pathway, lipid metabolism, diterpenoid biosynthesis and responses to pathogen molecules such as chitin. The GY-s module was enriched for genes with trans-eQTLs in hotspots on chromosomes 9 and 10, which also coincided with phenotypic QTLs for susceptibility to GLS. This transcriptional network has significant overlap with the GLS susceptibility response of maize line B73, and may reflect pathogen manipulation for nutrient acquisition and/or unsuccessful defence responses, such as kauralexin production by the diterpenoid biosynthesis pathway. The co-expression module that correlated best with resistance (TQ-r; 1498 genes) was enriched for genes with trans-eQTLs in hotspots coinciding with GLS resistance QTLs on chromosome 9. Jasmonate responses were implicated in resistance to GLS through co-expression of COI1 and enrichment of genes with the Gene Ontology term 'cullin-RING ubiquitin ligase complex' in the TQ-r module. Consistent with this, JAZ repressor expression was highly correlated with the severity of GLS disease in the GY-s susceptibility network.
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.|Centre for Bioinformatics and Computational Biology, Genomics Research Institute, Department of Biochemistry, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
authors.forename: Nanette
authors.initials: N
authors.lastname: Christie
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Myburg
authors.affiliation: Centre for Bioinformatics and Computational Biology, Genomics Research Institute, Department of Biochemistry, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
authors.forename: Fourie
authors.initials: F
authors.lastname: Joubert
authors.affiliation: Centre for Proteomic and Genomic Research, 0A Anzio Rd, Observatory, Cape Town, 7925, South Africa.|Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa.
authors.forename: Shane L
authors.initials: SL
authors.lastname: Murray
authors.affiliation: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
authors.forename: Maryke
authors.initials: M
authors.lastname: Carstens
authors.affiliation: Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
authors.forename: Yao-Cheng
authors.initials: YC
authors.lastname: Lin
authors.affiliation: Centre for Proteomic and Genomic Research, 0A Anzio Rd, Observatory, Cape Town, 7925, South Africa.|Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Meyer
authors.affiliation: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
authors.forename: Bridget G
authors.initials: BG
authors.lastname: Crampton
authors.affiliation: Center for Medical, Agricultural, and Veterinary Entomology, United States Department of Agriculture, Agricultural Research Service, Chemistry Research Unit, Gainesville, FL, 32608, USA.
authors.forename: Shawn A
authors.initials: SA
authors.lastname: Christensen
authors.affiliation: Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa.
authors.forename: Jean F
authors.initials: JF
authors.lastname: Ntuli
authors.affiliation: Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa.
authors.forename: Sara S
authors.initials: SS
authors.lastname: Wighard
authors.affiliation: Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.|Department of Genetics, Genomics Research Institute, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.affiliation: Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa.
authors.forename: Dave K
authors.initials: DK
authors.lastname: Berger
mesh_terms: D001203:Ascomycota / Q000472:pathogenicity; D032461:Chromosomes, Plant / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics / Q000502:physiology; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D018515:Plant Leaves / Q000235:genetics* / Q000382:microbiology*; D040641:Quantitative Trait Loci / Q000235:genetics; D003313:Zea mays / Q000235:genetics* / Q000382:microbiology*
keywords: 
  Cercospora
  ; 
  Cercospora zeina
  ; 
  Zea mays
  ; co-expression; disease resistance; disease susceptibility; expression quantitative trait loci; gray leaf spot; grey leaf spot; quantitative trait loci