RNA-seq of downy mildew (Sclerospora graminicola Sacc.): resistant pearl millet genotype (P310-17) control
Two days old grown seedlings of downy mildew resistant (P310-17) and susceptible (7042S) genotypes were inoculated with downy mildew (4x104 zoospores/ml) inoculum and water served as control. Seedlings were harvested 36 hours post inoculation, total RNA was isolated followed by mRNA isolation. The mRNA was fragmented, cDNA libraries were prepared and sequenced on 454 Roche platform. The raw reads were pre-processed and assembled after optimizing using four assemblers. Functional annotation and metabolic pathway analysis were carried out using Blast2GO and KEGG. Bowtei2 was used for aligning the individual reads onto the assembled transcripts. The resulting files of aligned reads (.sam/bam) were input in the eXpress for quantifying the abundances of a set of target sequences. The differential up-regulation or down-regulation of transcripts was determined by edgeR software.
Anand Agricultural University
RNA-seq of downy mildew susceptible pearl millet genotype (7042S) infected with downy mildew