de novo Assembly and Molecular Marker Development in Tall Fescue Using RNA Seq Data

Tall fescue (Festuca arundinacea Schreb.) is a widely grown open important forage in USA. To enhance the molecular breeding of tall fescue markers development initiative has been take using transcriptome profiling between a drought tolerant (B400) and a susceptible (W279) genotype Both the genotypes were evaluated under drought conditions. RNA samples from leaf, shoot, root, and inflorescence were pooled and sequenced through Illumina paired-end sequencing. A total of 199,399 contigs were assembled with an average length of 585 bp. Between the two genotypes, 2,986 reference transcripts (RTs) were significantly differentially expressed and 1,048 of them could be annotated and found to associate with metabolic pathways and enzyme coding genes. A total of 6,348 SSRs and 6,658 SNPs were identified in the contig sequences. Primers were developed from the corresponding sequences which might be used as candidate gene markers in tall fescue. This study will lead to develop a comprehensive molecular marker system to facilitate marker-assisted breeding in tall fescue.