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

在植物的生命周期中，种子萌发和开花是两个重要的发育过程，受到遗传和环境因素的协调调节。种子从休眠到萌发是植物生命周期的重要发育阶段，是农业生产加工的关键。小粒谷物是世界粮食的主要来源，在很大程度上受到这种生理转变的影响。在没有休眠的情况下，谷物在收获前有在穗上过早发芽的倾向。这种早熟发芽，也被称为收获前发芽（PHS），是一种复杂的性状。植物激素是种子萌发和休眠的重要驱动因素。近年来，人们对赤霉素和脱落酸的拮抗作用进行了深入的研究，从而提高了对种子休眠/萌发机制的理解。我们正从一个独特的角度积极研究这一生理现象，其中一个复杂的发芽过程是由其他机制调节的，这可能是独立于激素的。我们首次报道了谷物中RNA-directed DNA methylation （RdDM）通路关键基因AGO4与小灵通（PHS）的关联，表明AGO4增强DNA甲基化，并对种子休眠起到负调控作用。从我们的大麦转座子诱变工作中，我们已经确定了DNA沉默途径的转座子突变体，其萌发率降低。在小粒谷物中，特定的休眠相关基因是否通过RdDM被沉默尚不完全清楚。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有联系的。我们对大麦mir172-转座子突变体的初步鉴定表明，该突变体具有异常的、不确定的小穗，也显示出延迟萌发表型，这表明开花和萌发期之间存在潜在的关系。我们假设这些重要的过渡阶段，如从种子到幼苗（发芽）或从营养发育到生殖发育（开花）是由新的表观遗传机制、微rna和特定的转录因子调控的。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期间发生的事件进行分子解剖。这将促进对从种子休眠到种子萌发和营养到生殖阶段过渡的分子机制的基本认识。本研究结果可直接应用于制定分子遗传策略，以提高谷物的质量和数量。该项目的HQPs培训将提高加拿大在作物育种和作物遗传领域的科技竞争力。

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.