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Background  MADS-box genes constitute a large family of transcription factors functioning as key regulators of many processes during plant vegetative and reproductive development.  Type II MADS-box  genes have been intensively investigated and are mostly involved in vegetative and flowering development. A growing number of studies of  Type I MADS-box  genes in Arabidopsis, have assigned crucial roles for these genes in gamete and seed development and have demonstrated that a number of  Type I MADS-box  genes are epigenetically regulated by DNA methylation and histone modifications. However, reports on agronomically important cereals such as barley and wheat are scarce.    Results  Here we report the identification and characterization of two  Type I-like MADS-box  genes, from barley ( Hordeum vulgare ), a monocot cereal crop of high agronomic importance. Protein sequence and phylogenetic analysis showed that the putative proteins are related to Type I MADS-box proteins, and classified them in a distinct cereal clade. Significant differences in gene expression among seed developmental stages and between barley cultivars with varying seed size were revealed for both genes. One of these genes was shown to be induced by the seed development- and stress-related hormones ABA and JA whereas  in situ  hybridizations localized the other gene to specific endosperm sub-compartments. The genomic organization of the latter has high conservation with the cereal  Type I-like MADS-box  homologues and the chromosomal position of both genes is close to markers associated with seed quality traits. DNA methylation differences are present in the upstream and downstream regulatory regions of the barley  Type I-like MADS-box  genes in two different developmental stages and in response to ABA treatment which may be associated with gene expression differences.    Conclusions  Two barley MADS-box genes were studied that are related to  Type I MADS-box  genes. Differential expression in different seed developmental stages as well as in barley cultivars with different seed size was evidenced for both genes. The two barley  Type I MADS-box  genes were found to be induced by ABA and JA. DNA methylation differences in different seed developmental stages and after exogenous application of ABA is suggestive of epigenetic regulation of gene expression. The study of barley  Type I-like MADS-box  genes extends our investigations of gene regulation during endosperm and seed development in a monocot crop like barley.

The study of two barley Type I-like MADS-boxgenes as potential targets of epigenetic regulation during seed development