Charcoal rot is an economically important fungal disease of soybean. The molecular basis of charcoal rot pathogen Macrophomina phaseolina and soybean pathogenesis is largely unknown, limiting breeding programs to develop genetic resistance. Hence, the present study was targeted to study the transcriptome of susceptible (JS 95–60) and resistant (JS 20–29) soybean genotypes infected with M. phaseolina to identify the molecular basis of its host-pathogen interaction. Illumina HiSeq 2500 platform was used to generate an overall of 25560 paired end reads. A total of 1683 and 1219 differentially expressed genes were obtained in resistant and susceptible genotypes, respectively. The expression of several signaling genes viz, calcium, kinases, pathogenesis related, etc. were differentially induced in both the genotypes. However, the expression of several leucine-rich repeat genes was differentially up-regulated in R6. Ca²⁺ ion-mediated basal defense response was observed in both the genotypes. Several WRKY-genes were up-regulated in resistant response, contributing to up-regulation of phenylpropanoid pathway genes. Several other genes differentially expressed in two contrasting genotypes, comprised those involved in hormone-signaling, biosynthesis of secondary metabolism and transcriptional reprogramming during infection. The charcoal rot resistance trait seems to be quantitative, and we propose that genes like WRKY, LysM-RLKs, NBS-LRR, flavonoid pathway genes can be effectively utilized to introgress resistance trait in soybean.

炭腐病是一种经济上重要的大豆真菌病害。木炭腐病病原Macophhomina phaseolina和大豆发病机制的分子基础在很大程度上是未知的，这限制了育种计划发展遗传抗性。因此，本研究的目标是研究易感 (JS 95–60) 和抗性 (JS 20–29) 大豆基因型的转录组，这些基因型感染了豆豉确定其宿主-病原体相互作用的分子基础。Illumina HiSeq 2500 平台用于生成总共 25560 个配对末端读数。在抗性和易感基因型中分别获得了1683和1219个差异表达基因。几种信号基因的表达，即钙、激酶、发病机制相关等，在两种基因型中被差异诱导。然而，几个富含亮氨酸的重复基因的表达在 R6 中差异上调。钙²⁺在两种基因型中都观察到了离子介导的基础防御反应。几个 WRKY 基因在抗性反应中上调，有助于苯丙烷途径基因的上调。其他几种基因在两种不同的基因型中差异表达，包括参与激素信号传导、次级代谢的生物合成和感染过程中的转录重编程的基因。木炭抗性性状似乎是定量的，我们建议 WRKY、LysM-RLKs、NBS-LRR、类黄酮途径基因等基因可以有效地用于大豆的抗性性状渗入。