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A suppression subtraction hybridization (SSH) cDNA library of alfalfa (Medicago sativa L.) cv. Zhongmu NO.1 had been constructed to identify differentially expressed genes under stress. Based on the sequence of a 460 bp expressed sequence tags (ESTs), a cDNA of 1652 bp was cloned by rapid amplification of cDNA ends (RACE) method. This gene (MsPBL) was predicted to encode a 434-amino-acid protein, which contained a Phox and Bem1 (PB1) domain. PB1 domain is a functional domain comprising about 80 amino acid residues, which exists in many signal transduction proteins and mediates dimerization in the proteins. PB1 domain is mostly involved in two cell signal transduction pathways: MAPK and NF-KB. When fused to the green fluorescent protein, we found MsPBL localization in the nucleus of onion (Allium cepa L.) epidermal cells. The transcripts of MsPBL rose significantly when alfalfa was treated with 300 mM NaCl, 0.1 mM ABA, and 20 % polyethylene glycol (PEG-6000). These results indicated that MsPBL may be functional within the nucleus as a signal transduction protein to allow alfalfa to rapidly respond to the environmental stress signals.