Abstract: In this paper，the members of Trihelix were identified in the whole genome of apple by bioinformatics method，gene structure，chromosome location，and physical and chemical properties，conservative motifs，evolutionary relationships of Trihelix transcription factor were analyzed. At the same time，based on microarray expression data and qRT-PCR analysis，the differential expression of apple Trihelix in different tissues and stresses was identified. A total of 39 Trihelix transcription factors were identified，with protein sizes ranging from 227 to 917 aa，their molecular weights ranging from 25.751 to 101.294 kD，and their isoelectric points ranging from 4.78 to 9.80. According to the evolutionary relationship，it was divided into five subfamilies，namely GT-1，GT-2，GTγ，SIP1 and SH4. The genetic structure of some subfamily members are similar. Based on the MEME program，the conserved motifs of the apple Trihelix transcription factor family were highly consistent with the results of cluster analysis. The cis-acting element analysis of the 1 kb upstream to the promoter showed that the response of MdTrihelix1，MdTrihelix19 on CGTCA-motif，MdTrihelix6，MdTrihelix13 on ABRE-motif，MdTrihelix2，MdTrihelix7，MdTrihelix14 and MdTrihelix16 on GT1-motif were higher. Gene chip expression found that Trihelix 38，Trihelix 14，Trihelix 9 and Trihelix 11 were hardly expressed in flowers，fruits，leaves，stems，roots，seeds and seedlings，and the remaining 35 genes were expressed at a certain level in various tissues. Among those genes whose expression is up-regulatd in flowers and fruits，except for Trihelix36 belonging to the GT-1 subfamily，the others belong to the members of GT-2 and SIP1 subfamily. Through qRT-PCR analysis，33 MdTrihelix genes showed diversity in response to stress.

Key words: apple, exogenous gene, pollen, viability, tapetum, apple, Trihelix, transcription factor family, bioinformatics, expression analysis