The SvFUL2 transcription factor is required for inflorescence determinacy and timely flowering in Setaria viridis

Inflorescence architecture in cereal crops directly impacts yield potential through regulation of seed number and harvesting ability. Extensive architectural diversity found in inflorescences of grass species is due to spatial and temporal activity and determinacy of meristems, which control the number and arrangement of branches and flowers, and underlie plasticity. Timing of the floral transition is also intimately associated with inflorescence development and architecture. Here, we show that a single mutation in a gene encoding an AP1 A-class MADS-box transcription factor significantly delays flowering time and disrupts multiple levels of meristem determinacy in panicles of the C4 model panicoid grass, Setaria viridis. Poly-A+ RNA-seq libraries were generated from pools of hand-dissected inflorescence primordia from wild-type and ful2 mutant seedlings. Wild-type primordia were sampled at 8, 11, and 17 DAS while, accounting for the mutant’s developmental progression, ful2 primordia were sampled at 9, 15, and 21 DAS. For each developmental stage, four biological replicates were collected, for a total of 24 data points. In addition to these samples, we included previously described wild-type S. viridis inflorescence primordia samples (Zhu et al., 2018): 23 additional data points from six inflorescence stages (10, 12, 14, 15, 16, and 18 DAS). Form these data We built a signed gene regulatory network using the WGCNA R package (Langfelder and Horvath, 2008) and integrated it with information derived from regulatory interactions among TFs and their putative targets based on the GENIE3 algorithm (Huynh-Thu et al., 2010). This complementary approach helped us to resolve the directionality and connectivity of important hub genes within the GRN.

谷类作物的花序架构通过调控籽粒数量与收获特性，直接影响产量潜力。禾本科物种的花序存在广泛的架构多样性，这源于分生组织的时空活性与决定特性——后者控制分枝与小花的数量与排布，并构成可塑性的基础。开花转变的时序同样与花序发育及架构密切相关。本研究发现，编码AP1类MADS-box转录因子的基因发生单突变后，会显著延迟C4模式黍亚科禾草青狗尾草（Setaria viridis）圆锥花序的开花时间，并破坏其分生组织确定性的多个层级。我们从野生型与ful2突变体幼苗的手工解剖花序原基混合样本中构建了polyA+ RNA测序（Poly-A+ RNA-seq）文库。野生型原基分别于播种后8、11和17天（DAS）取样；考虑到突变体的发育进程，ful2突变体原基则于播种后9、15和21天取样。每个发育阶段设置4个生物学重复，总计获得24个数据点。除此以外，我们纳入了此前已发表的野生型青狗尾草花序原基样本（Zhu等，2018）：来自6个花序发育阶段（播种后10、12、14、15、16和18天）的23个额外数据点。基于上述数据，我们使用WGCNA R包（Langfelder与Horvath，2008）构建了带符号的基因调控网络（Gene Regulatory Network, GRN），并结合基于GENIE3算法（Huynh-Thu等，2010）得到的转录因子（Transcription Factor, TF）与其潜在靶基因间的调控互作信息。这种互补分析方法帮助我们解析了基因调控网络中关键枢纽基因的方向性与连接性。