De Novo Transcriptional Analysis of Alfalfa in Response to Saline-Alkaline Stress

Saline-alkaline stress, caused by high levels of harmful carbonate salts and high soil pH, is a major abiotic stress affecting crop productivity. Alfalfa, a perennial forage legume, expresses some tolerance to biotic and abiotic stress, especially to saline-alkaline stress. To elucidate the mechanism underlying plant saline-alkaline tolerance, we conducted ion torrent sequencing and transcriptome analysis of whole alfalfa seedlings treated with saline-alkaline solutions. Transcriptome database was generated from 53,853 unigenes. Of 4,137 differentially expressed genes, 2,752 and 2,633 genes altered significantly their expression levels after 1 d and 7 d of treatment, respectively. Gene ontology analysis recognized 14 pathways highly enriched in biological process, metabolic, and signal pathway categories and demonstrated the differential response of metabolic pathways after both treatments. The expression levels of 109 and 96 transcription factors were altered significantly after 1 d and 7 d of treatment, respectively. Specific responses of peroxidase, flavonoid, and light pathway component indicate that the antioxidant capacity is one of the central mechanisms of saline-alkaline stress tolerance in alfalfa. Responses of eight genes specific to saline-alkaline stress were screened among 18 different expression genes comparing to salt stress-induced genes to uncover different mechanisms involved in plant tolerance to saline and alkaline stress. Among them, the expression levels of an NAC transcription factor and a glutathione S-transferase were altered significantly in treatments; they were upregulated under saline-alkaline stress and downregulated under salt stress. The transcriptome analysis in this study provides a novel insight into the understanding of saline-alkaline stress tolerance mechanisms in alfalfa.