Marigold black spot caused by Alternaria tagetica is a major disease that can decrease marigold production by 40%, resulting in serious economic losses. In this study, we identified many genes responsive to A. tagetica in the resistant and susceptible marigold genotypes. Analyses of differentially expressed genes, expression trends, and a weighted gene co-expression network revealed a series of hub genes with key roles in different A. tagetica infection stages. Additionally, 1 216 unigenes encoding transcription factors from eight families were differentially expressed between Ts and Ma. Moreover, R genes from various families (e.g., N, NL, RLP, and TNL) were differentially expressed in the two marigold genotypes before and after the inoculation with A. tagetica. Pathway diagrams were used to visualize the leaf transcriptional changes in the two marigold genotypes infected by A. tagetica to clarify the effects of A. tagetica on the expression patterns of genes involved in phosphatidylinositol signaling, plant–pathogen interactions, and plant hormone signal transduction. We identified candidate genes related to disease resistance and generated valuable resources for analyzing the candidate gene functions related to black spot resistance in marigold. The study data may be useful for the molecular marker-assisted screening and breeding of marigold lines with increased disease resistance.

由Alternaria tagetica引起的万寿菊黑斑病是一种重大病害，可使万寿菊减产40%，造成严重的经济损失。在这项研究中，我们在抗性和易感万寿菊基因型中发现了许多对A. tagetica有反应的基因。对差异表达基因、表达趋势和加权基因共表达网络的分析揭示了一系列在不同的A. tagetica感染阶段具有关键作用的中枢基因。此外，来自 8 个家族的 1 216 个编码转录因子的 unigenes 在 Ts 和 Ma 之间差异表达。此外，来自不同家族的 R 基因（例如，N、NL、RLP和TNL) 在接种A. tagetica 之前和之后的两种万寿菊基因型中差异表达。通路图用于可视化被A. tagetica感染的两种万寿菊基因型的叶片转录变化，以阐明A. tagetica对涉及磷脂酰肌醇信号传导、植物-病原体相互作用和植物激素信号转导的基因表达模式的影响。我们确定了与抗病性相关的候选基因，并为分析与万寿菊黑斑病抗性相关的候选基因功能提供了宝贵的资源。该研究数据可能对分子标记辅助筛选和选育抗病性增强的万寿菊品系具有重要意义。