Genetic basis of resistance to southern corn leaf blight in the maize multi‐parent population and diversity panel

Abstract

Summary Southern corn leaf blight (SLB), caused by the necrotrophic pathogen Cochliobolus heterostrophus, is one of the maize foliar diseases and poses a great threat to corn production around the world. Identification of genetic variations underlying resistance to SLB is of paramount importance to maize yield and quality. Here, we used a random‐open‐parent association mapping population containing eight recombinant inbred line populations and one association mapping panel consisting of 513 diversity maize inbred lines with high‐density genetic markers to dissect the genetic basis of SLB resistance. Overall, 109 quantitative trait loci (QTLs) with predominantly small or moderate additive effects, and little epistatic effects were identified. We found 35 (32.1%) novel loci in comparison with the reported QTLs. We revealed that resistant alleles were significantly enriched in tropical accessions and the frequency of about half of resistant alleles decreased during the adaptation process owing to the selection of agronomic traits. A large number of annotated genes located in the SLB‐resistant QTLs were shown to be involved in plant defence pathways. Integrating genome‐wide association study, transcriptomic profiling, resequencing and gene editing, we identified ZmFUT1 and MYBR92 as the putative genes responsible for the major QTLs for resistance to C. heterostrophus. Our results present a comprehensive insight into the genetic basis of SLB resistance and provide resistant loci or genes as direct targets for crop genetic improvement.

Genetic basis of maize stalk strength decoded via linkage and association mapping

“…One canonical example is flowering time, the wide variation of which is caused by the cumulative effects of numerous small-effect QTLs in NAM and CUBIC populations (Buckler et al, 2009;, whereas only a few major QTLs were identified in a set of natural inbred lines in maize (Lu et al, 2015;Yang et al, 2013). Similarly, a recent GWAS using ROAM and association mapping populations in a study of southern corn leaf blight resistance showed that <30% of loci overlapped with those identified in populations with different backgrounds, although the genetic variation in resistance to southern leaf blight is controlled mainly by major genetic factors (Chen et al, 2023). Therefore, multi-parent populations, along with diversity panels, have their own unique advantages for dissecting the genetic architecture of complex quantitative traits.…”

“…In comparison with traits such as kernel quality, ear and plant architecture, and resistance to disease (Chen et al., 2023; Hu et al., 2021; Liu, Huang, et al., 2017; Pan et al., 2017; Xiao et al., 2016), the phenotypic variation explained by all RPR QTLs detected via SLM (16.01–33.03%), JLM (33.71%), and GWAS (15.94%) in the ROAM population was relatively small, and was far below the broad‐sense heritability (77.40%–90.00%). The complex genetic structure of RPR and the relatively small number of effective loci carried by the parents might be the major reasons for this discrepancy.…”

“…Among these multi‐parent populations, the ROAM population was developed from the existing recombinant inbred line (RIL) populations without an a priori requirement to interconnect across populations (Xiao et al., 2016), which saves substantial time in comparisons with other multi‐parent populations. The ROAM approach has been widely used in dissecting the genetic architecture of a set of complex traits in maize, such as ear traits, plant architecture, kernel size and weight, starch content, and disease resistance (Chen et al., 2023; Hu et al., 2021; Liu, Huang, et al., 2017; Pan et al., 2017; Xiao et al., 2016).…”

Infection‐specific transcriptional patterns of the maize pathogen Cochliobolus heterostrophus unravel genes involved in asexual development and virulence

“…Each year, despite the deployment of extensive use of fungicides and resistant varieties, about 10%–20% of maize harvest is lost due to SCLB (Balint‐Kurti et al., 2007 ; Wang et al., 2014 ). SCLB is caused by the necrotrophic fungus Cochliobolus heterostrophus , which infects leaves, sheaths and ear husks of maize (Chen et al., 2023 ). In 1970, a new virulent race (race T) appeared in Florida and swept up the east coast of the United States in a single growing season, destroying more than 15% of the maize crop (Condon et al., 2018 ).…”

“…leaves, sheaths and ear husks of maize (Chen et al, 2023). In 1970, a new virulent race (race T) appeared in Florida and swept up the east coast of the United States in a single growing season, destroying more than 15% of the maize crop (Condon et al, 2018).…”