Functional genomics to understand molecular mechanisms underlying the phase transitions in small grain cereals

在植物生活史中，种子萌发和开花是两个受遗传和环境因素协同调控的重要发育阶段。种子从休眠到萌发是植物生命周期的重要发育阶段，是农业生产和加工的关键。小粒谷物是养活世界的主要来源，它在很大程度上受到这一生理转变的影响。在没有休眠的情况下，谷物在收获前有提前在穗上发芽的趋势。这种早熟萌发，也被称为收获前发芽(PHS)，是一个复杂的特征。植物激素是种子萌发和休眠的重要驱动力。近年来，赤霉素和脱落酸的拮抗作用被广泛研究，人们对种子休眠/萌发的机制有了更深入的了解。我们正在从一个独特的角度积极研究这一生理现象，其中复杂的萌发过程受到其他机制的调节，这些机制可能不依赖于激素。我们首次报道了谷物中RNA引导的DNA甲基化(RdDM)途径的一个关键基因(AGO4)与PHS的关联，表明AGO4增强了DNA甲基化，并作为种子休眠的负调控因子。从我们的大麦转座子诱变工作中，我们已经发现了发芽减少的DNA沉默途径的转座子突变体。目前还不完全清楚特定的休眠相关基因是否通过RdDM在小粒谷物中受到沉默。有趣的是，AGO4_9基因也与植物繁殖和种子发育有关。越来越多的证据表明，种子休眠和开花事件是相关的。我们对一个大麦mir172转座子突变体的初步鉴定也显示了发芽延迟表型，这表明开花和发芽阶段之间存在潜在的关系。我们推测，这些重要的过渡阶段，如从种子到幼苗(萌发)或从营养到生殖发育(开花)，受到新的表观遗传机制、microRNAs和特定转录因子的调控。我们建议使用基因编辑和其他功能基因组学方法对大麦和其他谷物在这些不同的相变过程中发生的事件进行分子解剖。这将促进对种子休眠到种子萌发和营养到生殖阶段转变所涉及的分子机制的基础知识。建议的研究结果可直接应用于开发分子遗传策略，以提高谷物的质量和数量。该计划中的HQP培训将增强加拿大在作物育种和作物遗传学领域的科学和技术竞争力。

In plant life cycles, seed germination and flowering are two critical developmental transitions which are coordinately regulated by genetic and environmental factors. The transition from seed dormancy to germination is an important developmental step of the plant life cycle, which is the key to agricultural production and processing. Small grain cereals, the major contributors to feeding the world, are largely affected by this physiological transition. In the absence of dormancy, cereal grains have a tendency to germinate prematurely on a spike prior to harvesting. This precocious germination, also known as pre-harvest sprouting (PHS), is a complex trait. Phytohormones are known to be important drivers of seed germination and seed dormancy. The antagonistic action of gibberellin and abscisic acid has been intensively investigated in recent years, leading to an improved understanding of mechanisms underlying seed dormancy/germination. We are actively researching this physiological phenomenon from a unique perspective where an intricate germination process is regulated by alternative mechanisms, which might be independent of hormones. We have reported for the first time the association of a key gene (AGO4) of RNA-directed DNA methylation (RdDM) pathway with PHS in cereals, indicating that AGO4 enhances DNA methylation and acts as a negative regulator of seed dormancy. From our barley transposon-mutagenesis work, we have identified transposon mutants of the DNA silencing pathway with reduced germination. It is not completely understood whether specific dormancy related genes are subjected to silencing through RdDM in small grain cereals. Interestingly, AGO4_9 genes have also been associated with plant reproduction and seed development. Evidence is emerging which indicates that seed dormancy and flowering events are connected. Our preliminary characterization of a barley mir172- transposon mutant having an abnormal, indeterminate spikelet also showed delayed germination phenotype suggests the potential relationship between flowering and germination phases. We hypothesized that these important transition phases such as from seed to seedling (germination) or from vegetative to reproductive development (flowering) are regulated by novel epigenetic mechanisms, micro RNAs and specific transcription factors. We propose to use gene-editing and other functional genomics approaches for molecular dissection of the events in barley and other cereals during these distinct phase transitions. This will advance fundamental knowledge on the molecular mechanisms involved in the transitions from seed dormancy to seed germination and vegetative to reproductive phases. The results of the proposed research can be directly applied to develop molecular genetic strategies to improve the quality and quantity of cereal grains. The training of HQPs in this program will enhance Canada's competitiveness in science and technology in the areas of crop breeding and crop genetics.