Additional file 1: Grey leaf spot (GLS) severity quantitative trait loci
(QTLs) identified for the CML444 X SC Malawi maize recombinant inbred
line population identified in the Baynesfield trial. List of disease severity
QTL identified in RIL population [21, 50] and corresponding alleles in
RIL165 and RIL387
Additional file 2: RNA-Seq data analysis pipeline. Read quality was
evaluated by the fastQC application v0.11.2. Illumina 1.5 encoded quality
scores (Q) were converted to Sanger scale (phred) using FASTQ Groomer
Galaxy v1.0.4. Thereafter, sequence reads were mapped to v2 of the B73
reference genome (5b.60 annotation; sequence obtained from
Phytozome v9.1), using TopHat v2.0.9 (http://ccb.jhu.edu/software/tophat/
index.shtml/), by implementing Bowtie2 v1.0.0. Cufflinks v2.0.2 (http://
cole-trapnell-lab.github.io/cufflinks//) was used to calculate transcript
abundance, reported as fragments per kilobase pair of exon model per
million fragments mapped (FPKM). Transcript assemblies were merged
with the reference annotation into a single .gtf file using Cuffmerge.
Differential expression analysis was conducted on the merged file using
Cuffdiff with a False Discovery Rate (FDR) threshold set to 0.05
Additional file 3: Expression levels, protein annotation and GO
annotation of differentially expressed genes. Statistically significant
differentially expressed genes between the two genotypes are reported.
The Log2FC derived from the comparisons of the fragments per kilobase
of transcript per million fragments mapped (FPKM) expression values of
RIL165 vs RIL387 is depicted. For each gene, the putative annotation of
the protein according to the RefSeq database (provided by the National
Center for Biotechnology Information (NCBI), www.ncbi.nlm.nih.gov/
refseq/), Uniprot (Universal Protein Resource; www.uniprot.org) and
GenBank sequence database (provided by the NCBI,
www.ncbi.nlm.nih.gov/genbank/) is described. Gene ontology terms
mapped to each gene by AgriGo are included, in addition to the
chromosomal positions of the genes in v2 of the B73 reference genome.
Where the DE gene overlapped with the genomic position of a disease
severity QTL [21, 50] this was indicated
Additional file 4: Comparison of RNA-Seq and RT-qPCR expression
analyses of genes between RIL165 and RIL387. Expression profiles of (a) entcopalyl
diphosphate synthase 2 (GRMZM2G044481), (b) syn-copalyl
diphosphate synthase (GRMZM2G068808), (c) Terpene synthase 6
(GRMZM2G127087_T03), (d) β-glucosidase1 (GRMZM2G031660), (e) Bx3
(GRMZM2G167549), (f) Bx5 (GRMZM2G063756), (g) Bx8 (GRMZM2G085054),
and (h) Bx9 (GRMZM2G161335) is depicted
Additional file 5: Significant enriched GO terms and associated genes
responsive to C. zeina infection in a susceptible (RIL165) maize line. Gene
ontology enrichment analysis was carried out using agriGO v1.2 of
statistically significant differentially expressed genes with a Log2FC > 1 or <
−1. Singular enrichment analysis (SEA) was performed using a
hypergeometric test, Hochberg FDR adjustment method parameters, a
significance level of 0.05, and a minimum number of five mapped entries
using the complete set of gene ontology terms
Additional file 6: Overview of pathways where differentially expressed
genes participate as reported by MADIBA. Up-regulated gene products
were mapped onto metabolic pathways using the KEGG representation.
The number of enzymes in each pathway is portrayed for both RIL165
and RIL387
Additional file 7: Photographs depicting GLS disease progression in
RIL165 and RIL387 greenhouse material inoculated with C. zeina. Material
was harvested at three time points based on development of GLS
disease symptoms: immediately after inoculation (0dpi, control),
development of chlorotic spots (14 dpi) and development of grey leaf
spot lesions (24 dpi for RIL165 and 28 dpi for RIL387)
Additional file 8: Zealexin defences are induced in response to C. zeina.
Leaves were treated with a spore solution (3 × 105 conidia/ml) and
harvested at 0 days post inoculation (dpi), 14dpi and 24 or 28dpi (RIL165
and RIL387 respectively). The metabolite content of each sample was
analysed using gas chromatography/chemical ionization – mass
spectrometry. Zealexins were quantified based on the internal standard 13C18-linolenic acid and presented in ng/μg FW. Average levels of total
zealexin metabolites depicted for RIL165 and RIL387 (n = 3–5; ±SEM)
Additional file 9: Biosynthesis of benzoxazinoids in maize. The
biosynthetic pathway of DIMBOA is depicted as per [112]. The expression
profiles of DIMBOA biosynthetic genes in glass house leaf material is
presented
Additional file 10: Primer sequences and descriptive information of
genes studied