Abstract: MdWRKY gene family，gene classification，chromosome location，sequence alignment and conserved structure domains of MdWRKY proteins were predicted and analyzed with bioinformatics methods，alignment of amino acid sequences and phylogenetic analysis. The amino acid sequences of the WRKY domain of all MdWRKY and possible orthlogs in Arabidopsis were aligned with Clustal W and the phylogenetic analysis tree was constructed using the neighbor-joining method in MEGA 5.0. The results showed that MdWRKY family contained 116 genes，which was further divided into three groups（GroupⅠ，GroupⅡ and Group Ⅲ）. In addition，members in GroupⅡ can be further divided into five sub-groups（from Ⅱa to Ⅱe）. A total of 112 MdWRKY genes were mapped to 17 chromosomes，whereas only 4 MdWRKY genes were not mapped to any particular chromosome. For example，Chr 1 encompasses the largest number of 12 MdWRKY genes，while the lowest number（Chr 14）contained 2 MdWRKY genes. MdWRKY proteins contained from 118 to 965 amino acids and the isoelectric point is from 4.81 to 10.16. Expression analysis showed that the expression levels of most MdWRKY genes were altered during the ripening process and rootstock-scion interactions process.

Key words: apple, Malus domestica, WRKY, transcription factor, bioinformatics