We used a systems genetics approach to elucidate molecular mechanisms of maize
responses to gray leaf spot (GLS) disease, caused by Cercospora zeina, a threat to maize
production globally. Expression analysis of earleaf samples in a sub-tropical maize RIL
population (CML444 X SC Malawi) subjected in field to C. zeina infection allowed
detection of 20,206 expression QTLs (eQTL). 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 transeQTLs
in hotspots on chromosomes 9 and 10, which also coincided with phenotypic
QTLs for GLS susceptibility. 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 defense 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
COI-1 and enrichment of genes with the GO term “cullin-RING ubiquitin ligase complex”
in the TQ-r module. Consistent with this, JAZ repressor expression was highly
correlated with GLS disease severity in the GY-s susceptibility network.
Table S1. Co-expression module membership of all 19,281 reporters and correlation of
reporter expression with GLS disease scores across 100 RILs of the CML444 X SC Malawi
Table S2. Co-expression modules identifed by WGCNA of microarray data from 100 RILs of
the CML444 X SC Malawi population.
Table S3. Reporters in the GY-s co-expression module of the maize RIL population, and
expression in B73-C. zeina.
Table S4. Reporters and enriched GO term in the PT-s co-expression module of the maize RIL
Table S5. Reporters in the TQ-r co-expression module of the maize RIL population, and
expression in B73-C. zeina.
Table S6. Enriched GO-terms for the TQ-r module.
Table S7. All eQTLs identified from microarray data from the CML444 X SC Malawi maize
Table S8. Global eQTL summary and cis/trans-eQTL classification.
Table S9. All trans-eQTL hotspots, and co-expression modules enriched for reporters in these
Table S10. Reporters with cis-eQTLs that overlap the GLS QTLs.
Table S11. Reporters in the GY-s module with eQTLs in eQTL_HS9a(S) and/or
Table S12. Reporters in the TQ-r module with eQTLs in eQTL_HS9a(R) and eQTL_HS9b(R).
Table S13. Differentially expressed genes in maize inbred B73 challenged with C. zeina
Table S14.1 GO enrichment of B73 genes significantly induced by C. zeina (RNAseq;
FDR<0.05) that are present in the GY-s co-expression module
Table S14.2 Maize B73 genes significantly induced by C. zeina (RNAseq; FDR<0.05) that are
present in the GY-s co-expression module
Table S15. Comparison of co-expression module gene lists and list of DEGs in B73 challenged
with C. zeina.