Small RNA analysis to study the molecular interaction between F. oxysporum f. sp. ciceris and chickpea

Chickpea is an important source of dietary protein for humans. It is widely grown as food as well as feed crop in different countries. The productivity of chickpea is very low compared to their genetic potential and this is mainly attributed to various biotic and abiotic stresses. Fusarium wilt (FW) is a devastating fungal disease that causes severe wilting that can lead to 100% crop loss. To understand the molecular mechanism behind FW resistance, small RNA sequencing approach was used. The control and stress samples (three biological replicates) from two genotypes, JG 62 (FW-susceptible) and WR 315 (FW-resistant) collected at 10 days post inoculation (dpi), were selected for small RNA sequencing. A total of twelve libraries were constructed and sequenced using Illumina HiSeq 2500 platform. The sequencing and bioinformatics analyses resulted in the identification of 544 miRNAs which included 406 known and 138 novel miRNAs. A total of 136 miRNAs showed differential expression in both genotypes in different combinations. Prediction and functional annotation of miRNA targets revealed that the targets are transcription factors, disease resistance proteins, defense-responsive genes, metabolism-related genes, etc. The study provides a better understanding of microRNA-based regulation of resistance and susceptibility mechanisms in chickpea against Fusarium wilt.