Genome-wide identification, expression profiling, and SSR marker development of the bZIP transcription factor family in Medicago truncatula

• We identified 75 bZIP transcription factor-encoding genes in the Medicago truncatula genome.
• The functions of MtbZIP genes may involve in organ development, drought-responses and salt-responses.
• We developed and validated MtbZIP gene specific SSR markers that useful for alfalfa genetic diversity evaluation.

The basic leucine zipper (bZIP) transcription factors have been shown to play great roles in pathogen defense, light and stress signalling, seed maturation and flower development in plants. However, no reports about this transcription factor family have been reported in grass species, including the model dicotyledonous grass species Medicago truncatula. In the present study, we have identified 75 bZIP transcription factor-encoding genes in the M. truncatula genome. The phylogenetic analysis of these bZIP protein sequences permits classification of them into 12 groups. The chromosome distribution analyses suggesting that bZIP genes in M. truncatula are not recently generated by gene duplication. The results of the identification of intron/exon structural and conserved motifs showed that there is a high group-specificity in all MtbZIP genes. Expression of bZIP transcription factor-encoding genes indicates specific or coexpression patterns of MtbZIP genes involved in organ development, drought-responses and salt-responses. In addition, 104 SSRs specific to 53 MtbZIP genes were detected and 97 primer pairs were developed. The validation of 30 randomly selected primer pairs in 20 alfalfa cultivars showed 17 of them were true-to-type SSR loci and highly transferable among alfalfa cultivars. These results will be important for further cloning and functional characterization of bZIP transcription factors in M. truncatula.