Tissue-Specific Expression Profiles of Fiber Genes in the Root-Rot Resistant Perfect Variety of Alfalfa Show Preferences for Cellulose Production in the Stem

Medicago sativa (alfalfa) is an important agriculture crop for livestock forage that is highly valued for its perennial nature, ability to fix nitrogen and tolerance to environmental stress. Given alfalfa’s agricultural strengths and relatively high biomass, it has received considerable attention lately as a candidate biofuel for ligno-cellulosic energy production. Here we describe our effort to generate a high quality transcriptome and better characterize the genes and pathways involved in cell-wall biosynthesis. We used a single propagule from the alfalfa cultivar Perfect in order to minimize genetic variation within our sample and thereby increase the quality of our assembly. We used RNA-seq to investigate gene expression in root, shoot and leaf tissues of the plant, and sequenced genomic DNA enriched for genic regions via reduced representation libraries in order to enhance our gene models. A transcriptome assembled using the closely related Medicago truncatula genome as a reference, in combination with de novo methods, resulted in 62,502 annotated transcripts. An examination of the primary fiber biosynthesis genes and their relative differential expression between tissues revealed that genes involved in cellulose synthesis are expressed more than those involved in hemicellulose biosynthesis, which are in turn more highly expressed than pectin and lignin synthesis genes. Meanwhile, fiber production as measured by relative gene expression, is most abundant in the stem, followed by the root. Our transcriptomic reference and expression results should serve as a valuable resource for ongoing cellulosic biofuel research on this important North American crop.