De novo sequencing and analysis of root transcriptome of the Allium mongolicum Regel exposed to drought stress using Illumina/Solexa

Allium mongolicum Regel is a kind of desert plant widely distrib¬uted in the desert lands of China, which showed great resistance to wind erosion, drought and low temperature. Thus, understanding the molecular mechanisms underlying the drought resistance of A. mongolicum Regel is essential for digging drought resistant genes and improving this beneficial trait in other plants. Here, de novo RNA-Seq assembly analysis was conducted using roots of one-month-old seedlings in response to drought stress. By pairwise comparation of non-treated plants (CK), 48 h-droughted plants (G48h) and 96 h-droughted plants (G96h), a total of 2,211 differentially expressed unigenes (DEGs) were obtained. By functional annotation, these DEGs were mainly involved in plasma membrane, photosynthesis, secondary and carbohydrate metabolism. Moreover, genes involved in ABA mediated signaling pathway and secondary metabolism were up-regulated in roots. These results suggest that desert plants may utilize signaling and secondary metabolic pathways as adaptive responses to drought stress. In addition, an average of 244,971, 253,987 and 265,486 putative SNP markers were detected in roots of CK, G48h and G96h respectively. For microsatellite mining, 13,462 SSRs were detected in roots of non-droughted and droughted plants. Collectively, this work will help understanding the molecular mechanisms occurring in A. mongolicum Regel in response to drought stress and aid in the selection of novel drought tolerance genes.