Investigating reproductive development in Brachypodium distachyon focussing on the YABBY family of transcription factors

Brachypodium, as a sister to the core pooids containing wheat, barley, oats and rye, represents a good model and point of comparison for the study of development and evolution in temperate cereals. Using a comparative cellular developmental and transcriptomic approach, we investigated regulation of key stages in grain development. This was achieved by generating a transcriptome incorporating several distinct developmental stages of Brachypodium grains; pre-anthesis ovaries, young grain (1-3 DAA), mid-length grain (3-8 DAA), full-length (8-15 DAA) and mature grain (15-24 DAA), mature grain (without embryo), germinating grains and seedlings stage. By looking at the differential expression of genes through grain development we identified clusters that coincide with the initiation of key developmental stages, such as the initiation of endosperm proliferation, cellularisation and differentiation, as well as the activation of specific metabolic pathways, such as starch and protein biosynthesis. Focus was given to members of the YABBY gene family that have an established role in promoting abaxial cell fate and as master regulators of reproductive development in eudicots, but with less clarity in grass species. Using Brachypodium as the model plant for cereal crops, the orthologues of YABBY genes in grasses were identified and subjected to detailed phylogenetic, expression and functional analyses using Bayesian Interference (BI) analyses, RT-PCR, transcriptomics, mRNA in situ hybridization (ISH) and RNAi. Based on several analyses, YABBY6 was suggested as a novel candidate of transcription factors regulating seed development in Brachypodium. Metadata from Chapter 2 were used to extract similar expression genes of YABBY family members and potential motifs regulated in polarity networks involving YABBY genes were suggested.