Fig. 1

Correlation analysis of repeated measurements and BLUE values across locations for maize common smut resistance traits A-C: heatmaps of correlation coefficients for disease index (DI), incidence rate (IR), and area under the disease progress curve (AUDPC) across three replicates at two locations, Shenyang and Jinzhou, in two years, 2023 and 2024. 23SY, 24SY, 23JZ, and 24JZ represent Shenyang in 2023, Shenyang in 2024, Jinzhou in 2023, and Jinzhou in 2024, respectively; 1, 2, and 3 indicate the three replicates. D: SY-DI, JZ-DI, All-DI, SY-IR, JZ-IR, All-IR, SY-AUDPC, JZ-AUDPC, and All-AUDPC denote the best linear unbiased estimation (BLUE) values for disease index in Shenyang across two years, disease index in Jinzhou across two years, disease index across two years and two locations, incidence rate in Shenyang across two years, incidence rate in Jinzhou across two years, incidence rate across two years and two locations, AUDPC in Shenyang across two years, AUDPC in Jinzhou across two years, and AUDPC across two years and two locations, respectively. BLUE: best linear unbiased estimation; *, **, and *** indicate P < 0.05, P < 0.01, and P < 0.001, respectively. NS indicates no significant difference."

Fig. 2

Frequency distribution of incidence rate, disease index, and area under the disease progress curve for maize common smut 23SY, 24SY, 23JZ, 24JZ, and BLUE represent Shenyang in 2023, Shenyang in 2024, Jinzhou in 2023, Jinzhou in 2024, and the overall BLUE value across two years and two locations, respectively. BLUE: best linear unbiased estimation."

Fig. 3

Comprehensive assessment of maize inbred lines for resistance to common smut HS, S, MR, R, and HR represent highly susceptible, susceptible, moderately resistant, resistant, and highly resistant, respectively."

Fig. 4

Analysis of critical environmental time windows affecting maize common smut resistance traits A: identification of critical environmental time windows for disease index (DI). B: identification of critical environmental time windows for incidence rate (IR). C: identification of critical environmental time windows for area under the disease progress curve (AUDPC). Tmax, Tmin, Tmean, PTT, RH and SD represent maximum temperature, minimum temperature, mean temperature, precipitation, relative humidity, and sunshine duration, respectively."

Table 1

Grey relational grades between maize common smut resistance traits and meteorological factors"

Fig. 5

Genetic structure analysis of the maize association panel A: scatter plot of principal component analysis (PCA) based on genome-wide SNPs. B: heatmap of the kinship matrix among individuals; diagonal elements approaching 1 indicate complete genotypes and high homozygosity of the inbred lines; the off-diagonal region is predominantly light blue, with generally low kinship coefficients, indicating substantial genetic divergence and relatively distant relationships among individuals; the absence of distinct high-kinship blocks is consistent with the PCA results, suggesting that this panel does not contain strong subpopulation-driven kinship clusters and has a relatively dispersed genetic structure. C: population structure analysis, with different colors representing the proportion of each accession assigned to different ancestral subpopulations (K = 6). The x-axis represents 421 maize inbred lines, and the y-axis indicates the probability of each inbred line being assigned to different subpopulations."

Fig. 6

Manhattan plots from genome-wide association analysis of maize common smut resistance traits A: disease index (DI); B: incidence rate (IR); C: area under the disease progress curve (AUDPC). The red horizontal dashed line indicates the significance threshold (P = 2.87×10-6)."

Fig. 7

Venn diagram of SNP loci associated with disease index, incidence rate, area under the disease progress curve, and their combined maize common smut resistance index"

Fig. 8

Integrative analysis of GWAS candidate genes and transcriptome differentially expressed genes Heatmap of expression patterns for 79 candidate genes at different time points (1, 2, 4, 6, 8, and 10 days) after inoculation with the standard Ustilago maydis strain SG200. Blue to red indicates expression values from low to high. Inf1 d, Inf2 d, Inf4 d, Inf6 d, Inf8 d, and Inf10 d represent 1, 2, 4, 6, 8, and 10 days post-inoculation, respectively; Mock1 d, Mock2 d, Mock4 d, Mock6 d, Mock8 d, and Mock10 d represent the corresponding mock-inoculated controls at 1, 2, 4, 6, 8, and 10 days post-inoculation, respectively. FPKM: fragments per kilobase of transcript per million mapped reads."

Table S1

List of important candidate genes for common smut resistance in maize and their functional annotations"

Fig. 9

Gene ontology (GO) enrichment analysis of differentially expressed candidate genes for common smut resistance in maize FDR (false discovery rate) is a statistical error control metric used in multiple hypothesis testing, defined as the expected proportion of incorrectly rejected null hypotheses among all rejected null hypotheses."