Genes, primers, and probes for qPCR assay.

The farming of common beans (Phaseolus vulgaris) is crucial for global nutrition, culture, and economy, but the crop faces significant challenges from biotic and abiotic stresses. Among these, anthracnose caused by Colletotrichum lindemuthianum, particularly race 65, is notable due to its widespread occurrence and high genetic and virulence diversity, especially in tropical regions such as Brazil. Understanding the molecular basis of resistance and susceptibility to specific pathogen races is key to accelerating the development of superior cultivars. Despite its significance, global gene expression studies addressing the interactions between bean genotypes and race 65 remain scarce. In this study, we explored the molecular basis of resistance and susceptibility to race 65 in two Brazilian common bean cultivars. RNA was extracted from leaves at 0, 48, and 96 hours after inoculation and sequenced using the Illumina NextSeq 500 platform. Our transcriptome analysis identified several candidate genes linked to resistance, including those involved in pathogen recognition, such as kinases and NB-LRR (nucleotide-binding and leucine-rich repeat) genes, as well as genes involved in the phenylpropanoid, glycerolipid biosynthesis, linoleic acid pathways, and cell wall remodeling. In contrast, the susceptible genotype exhibited activation of auxin signaling and sugar transport genes. Additionally, gene coexpression network analysis revealed a strong correlation among resistance-related genes. These findings provide valuable insights into the molecular-genetic mechanisms underlying common bean resistance to race 65 of C. lindemuthianum.

普通菜豆（Phaseolus vulgaris）的栽培对全球营养、文化与经济均具有关键意义，但该作物却面临生物胁迫与非生物胁迫的严峻挑战。其中，由菜豆炭疽菌（Colletotrichum lindemuthianum）引发的炭疽病尤为突出，尤其是其65号生理小种，在巴西等热带地区分布广泛，且遗传与致病力多样性极高，因而备受关注。解析作物对特定病原生理小种的抗病与感病分子基础，是加速优异栽培品种培育的核心关键。尽管该病害的防控具有重要意义，但目前针对菜豆基因型与65号生理小种互作的全球基因表达研究仍较为匮乏。本研究以两个巴西普通菜豆品种为材料，解析其对菜豆炭疽菌65号生理小种的抗病与感病分子机制。我们从接种后0、48、96小时的叶片中提取RNA，并采用Illumina NextSeq 500平台进行测序。转录组分析共鉴定出多个与抗病相关的候选基因，包括参与病原识别的激酶类基因，以及核苷酸结合富亮氨酸重复（nucleotide-binding and leucine-rich repeat，NB-LRR）类基因；同时还涉及苯丙烷代谢、甘油脂生物合成、亚油酸代谢途径及细胞壁重塑相关基因。与之形成鲜明对比的是，感病菜豆基因型则激活了生长素信号通路与糖转运相关基因。此外，基因共表达网络分析显示，抗病相关基因之间存在显著的共表达相关性。本研究结果为解析普通菜豆抵御菜豆炭疽菌65号生理小种的分子遗传机制提供了重要参考。