Have you tried using a related genome (within wheat family) instead? 

there are some documented workflows in Galaxy for doing a mapping to a related genome. You will have to try out to see which workflow suits your data

There are two ways to do this:

Either you can download the genome from NCBI and for reference genome you can upload the file in galaxy and run RNA-Seq protocol

Second way, is to download tophat2 (assuming that you have a linux OS and proper computer configurations to run the job) and give the command on terminal to run the alignment:

Create a reference index by:

bowtie2-build reference/genome.fa reference/genome.fa

Running tophat:

./tophat2 -p 2 -G reference/genes.gtf -o C1_R1_thout reference/genome.fa data/GSM794483_C1_R1_1.fq data/GSM794483_C1_R1_2.fq

where -p num of threads

 -G reference genome

-o output directory

r1.fastq

r2.fastq

If you are using Galaxy, then you can upload a FASTA file (from NCBI or other source) of the reference genome. Then, when running Tophat, select "Use a genome from history" and select the uploaded FASTA file. This will use that fasta file as a reference (building the index for you).

http://usegalaxy.org

Many thanks for you I tried to download the FASTA file of genome and uploaded it but after running tophat it always return a error that Could not find Bowtie 2 index files (genome.*.bt2)