Uncovering the roles of lignin-related genes in disease resistance in maize using mutant and association analysis

Brown midrib (BMR) maize harbors mutations that result in lower lignin levels and higher feed digestibility, making it a desirable silage market class for ruminant nutrition. Northern leaf blight (NLB) epidemics in upstate NY highlighted the disease susceptibility of commercially grown BMR maize hybrids. We found the bm1, bm2, bm3 and bm4 mutants in a W64A genetic background to be more susceptible to foliar fungal (NLB, gray leaf spot, and anthracnose leaf blight) and bacterial (Stewarts wilt) diseases. The bm1, bm2 and bm3 mutants showed enhanced susceptibility to anthracnose stalk rot, and the bm1 and bm3 mutants were more susceptible to Gibberella ear rot. Co-localization of quantitative trait loci and correlations between stalk strength and disease traits in recombinant inbred line families suggest possible pleiotropies. The role of lignin in plant defense was explored using high-resolution, genome-wide association analysis for resistance to NLB in the Goodman diversity panel. Association analysis identified 100 single and clustered SNP associations for resistance to NLB, but did not implicate natural functional variation at bm1-bm5. Strong associations implicated a suite of diverse candidate genes, including lignin-related genes such as a {beta}-glucosidase gene cluster, hct11, knox1, knox2, zim36, lbd35, CASP-like protein 8, and xat3. The candidate genes are targets for breeding quantitative resistance to NLB in maize for use in silage and non-silage purposes. Core IdeasO_LIBrown midrib mutants (bm1-bm4) in maize, characterized as mutations with reduced lignin content, are susceptible to a range of foliar pathogens. C_LIO_LISeveral brown midrib mutants in maize show enhanced susceptibility to stalk rot and ear rot pathogens. C_LIO_LIGenome wide association analysis identified a number of diverse candidate genes associated with resistance to northern leaf blight in maize, including lignin-related genes involved in the monolignol pathway, developmental genes and transcription factors. C_LIO_LIAssociation analysis for resistance to NLB implicated a {beta}-glucosidase gene cluster, including Zmbglu24 and Zmbglu25 known for targeting monolignols and contributing to [~]15% phenotypic variation. C_LIO_LIhct11, which plays an important role in the monolignol pathway, was implicated for resistance to northern leaf blight in maize with potential for multiple stress tolerance. C_LI