Genome-wide identification and expression analysis of genes in alfalfa () in response to cold stress.

Dehydration-responsive element-binding proteins (DREBs) belong to members of the AP2/ERF transcription factor superfamily, which has been reported to involve various abiotic-stress responses and tolerance in plants. However, research on the -family is still limited in alfalfa ( L.), a forage legume cultivated worldwide. The recent genome-sequence release of the alfalfa cultivar "XinJiangDaYe" allowed us to identify 172 by a multi-step homolog search. The phylogenetic analysis indicated that such s could be classified into 5 groups, namely A-1 (56 members), A-2 (39), A-3 (3), A-4 (61) and 13 (A-5 (13), thus adding substantial new members to the -family in alfalfa. Furthermore, a comprehensive survey in of conserved motif, gene structure, molecular weight, and isoelectric point (pI) as well as gene expression was conducted. The resulting data showed that, for cold-stress response, 33 differentially expressed s were identified with a threshold of Log2-fold > 1, and most of which were transcriptionally upregulated within 48 h during a cold treatment(s). Moreover, the expression profiling of s from two ecotypes of alfalfa subspecies i.e. ssp. (F56, from a colder region of Central Asia) and ssp. (B47, from Near East) revealed that most of the cold-stress responsive exhibited a significantly lower expression in F56, leading to a proposal of the existence of a distinct mechanism(s) for cold tolerance regulated by DREB-related action, which would have been evolved in alfalfa with a genotypic specificity. Additionally, by examining the transcriptome of a freezing-tolerance species ( cv. Zhaodong), eight were found to be implicated in a long-term freezing-stress adaptation with a great potential. Taken together, the current genome-wide identification in alfalfa points to the importance of some s in the cold-stress response, providing some promising molecular targets to be functionally characterized for the improvement of cold tolerance in crops including alfalfa.