A combination of joint linkage and genome-wide association study reveals putative candidate genes associated with resistance to northern corn leaf blight in tropical maize

Abstract

Northern corn leaf blight (NCLB), caused by Setosphaeria turcica, is a major fungal disease affecting maize production in sub-Saharan Africa. Utilizing host plant resistance to mitigate yield losses associated with NCLB can serve as a cost-effective strategy. In this study, we conducted a high-resolution genome-wide association study (GWAS) in an association mapping panel and linkage mapping with three doubled haploid (DH) and three F₃ populations of tropical maize. These populations were phenotyped for NCLB resistance across six hotspot environments in Kenya. Across environments and genotypes, NCLB scores ranged from 2.12 to 5.17 (on a scale of 1-9). NCLB disease severity scores exhibited significant genotypic variance and moderate-to-high heritability. From the six biparental populations, 23 quantitative trait loci (QTLs) were identified, each explaining between 2.7% and 15.8% of the observed phenotypic variance. Collectively, the detected QTLs explained 34.28%, 51.37%, 41.12%, 12.46%, 12.11%, and 14.66% of the total phenotypic variance in DH populations 1, 2, and 3 and F₃ populations 4, 5, and 6, respectively. GWAS, using 337,110 high-quality single nucleotide polymorphisms (SNPs), identified 15 marker-trait associations and several putative candidate genes linked to NCLB resistance in maize. Joint linkage association mapping (JLAM) identified 37 QTLs for NCLB resistance. Using linkage mapping, JLAM, and GWAS, several QTLs were identified within the genomic region spanning 4 to 15 Mbp on chromosome 2. This genomic region represents a promising target for enhancing NCLB resistance via marker-assisted breeding. Genome-wide predictions revealed moderate correlations with mean values of 0.45, 0.44, 0.55, and 0.42 for within GWAS panel, DH pop1, DH pop2, and DH pop3, respectively. Prediction by incorporating marker-by-environment interactions did not show much improvement. Overall, our findings indicate that NCLB resistance is quantitative in nature and is controlled by few major-effect and many minor-effect QTLs. We conclude that genomic regions consistently detected across mapping approaches and populations should be prioritized for improving NCLB resistance, while genome-wide prediction results can help incorporate both major- and minor-effect genes. This study contributes to a deeper understanding of the genetic and molecular mechanisms driving maize resistance to NCLB.

Keywords: genome-wide association study (GWAS); genomic selection (GS); northern corn leaf blight (NCLB); quantitative trait locus (QTL) mapping; sub-Saharan Africa (SSA); tropical maize.

Figure 1

Phenotypic distribution of NCLB disease severity scores (on a 1-to-9 scale) in IMAS association panel, three DH populations, and combined DH populations, and three F₃ populations evaluated across locations.

Figure 2

Pairwise phenotypic correlations between northern corn leaf blight scores and other traits in combined three DH populations evaluated in three environments. Correlation values > 0.10 and >0.15 were interpreted as significant at 0.05 and 0.01 levels, respectively. GYG, grain yield; AD, days to anthesis; PH, plant height; EH, ear height; EPO, ear position; HC, husk cover; GLS, gray leaf spot; NCLB, Northern corn leaf blight; ER, ear rot; EA, ear aspect; PA, plant aspect.

Figure 3

Mapping of NCLB resistance-associated QTLs detected based on individual biparental-based linkage mapping, joint linkage association mapping (JLAM), and IMAS association mapping panel (AMP). Red, green, and blue colors represent QTL detected under biparental-based linkage mapping (pop 1, pop 2, pop 3, pop 4, pop 5, and pop 6), JLAM, and AMP approaches, respectively.

Figure 4

Manhattan and quantile-quantile (Q-Q) plots generated using a mixed linear model for NCLB scores across environments. The x-axis indicates the SNP location along the 10 chromosomes, with chromosomes separated by different colors. The significance level was set at P = 2 × 10^–5 at 0.05 false discovery rate (FDR) and is represented on the plot by the dashed horizontal line. The position of SNPs along the 10 maize chromosomes is shown on the x-axis, with each color indicating distinct maize chromosomes. The −log10(P observed) is shown on the y-axis.

Figure 5

Genome-wide prediction correlations for NCLB resistance in biparental and IMAS association panel based on three different scenarios. WW (within-within) scenario, estimation and prediction sets are derived within populations; AW (across-within) scenario, combined populations serve as a training set and an estimation set is from single biparental population; and combined scenario, where combine all populations and randomly derive both training and testing set and evaluate with five-fold cross-validation.