Analysis of soybean transcriptome uncovers differential genomic regulations in response to charcoal rot in resistant and susceptible genotypes

Abstract

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.