VRS5 (HvTB1) binds to the promoter of tillering and floral homeotic genes to regulate their expression [RNA-seq]

Variation in shoot architecture, or tillering, is an important adaptive trait targeted during the domestication of crops. A well-known regulatory factor in shoot architecture is TEOSINTE BRANCHED 1 (TB1). TB1 and its orthologs have a conserved function in integrating environmental signals to regulate axillary branching, or tillering in cereals. The barley ortholog of TB1, VULGARE ROW-TYPE SIX 5 (VRS5) does not only regulate tillering, but is also involved in regulating row-type by inhibiting lateral spikelet development. These discoveries do mainly come from genetic studies, but how VRS5 regulates these processes on a molecular level remains largely unknown. By combining transcriptome analysis between vrs5 and WT at different developmental stages and DAP-sequencing to locate the genome-wide DNA binding sites of VRS5, we identified bona fide targets of VRS5. We found that VRS5 targets in particular abscisic acid related genes to inhibit tillering in a conserved way. Later, during inflorescence development row-type gene VRS1, and some known floral development genes, like MIKCc type MADS-box genes, are targeted. The study presented here offers a solid and crucial starting point for mutant analyses of a selection of bona fide targets to gain a deeper understanding of the VRS5 network and to enlighten its mode of action in shaping barley development. Overall design: We performed RNA-seq on barley meristems from WT (cv.Bowman) and vrs5 mutants (int-c.5) at four developmental stages, namely Vegetative Apex (VA), Transition apex (TA), triple mound (TM), and lemma and stamen primordia (LP/SP). The samples from VA and TA contain also tiller buds.