Exploiting anatomical traits to accelerate breeding of novel stress tolerant crops

干旱和土壤肥力低是全球作物生产的主要制约因素。随着时间的推移，由于土壤质量恶化、人口压力增加和气候变化，这些制约因素变得更具挑战性。在这种情况下，最近的发现已经确定了几个根系解剖特征，可以通过改善水分和养分吸收来大幅提高作物产量和气候适应能力。例如，当活细胞经历程序性细胞死亡时，根皮层组织中的空气空间（称为通气组织）的形成发生。这显著降低了养分需求和根组织的呼吸作用，使植物能够在干旱和次优养分条件下获得更多的土壤资源并提高作物产量。除了通气组织形成之外，其他性状如皮质组织中活细胞的数量和层数减少（分别称为皮质细胞计数和皮质细胞列数）也具有类似的益处。然而，尽管有这些知识，解剖性状作为作物育种的选择标准很少受到关注，因为与解剖表型的取样和定量相关的挑战。“解剖学”是一种新的跨学科方法，现在首次能够快速成像和分析大量作物品种的植物解剖特征。使用这种方法，我的美国合作者为南非种植5年以上的数百种玉米品种生成了根部解剖数据。接下来，我使用集成的基因发现管道分析了这个数据集，其中包括全基因组关联研究（GWAS），文献挖掘和增强的数据可视化技术。这项分析突出了玉米多样性小组中解剖数据与数十万DNA多态性之间的相关性，从而确定了控制玉米根解剖性状的关键基因。例如，我的管道确定了两个新的转录因子功能相关的通气组织形成。突变分析的玉米亩插入和水稻直系同源突变体的这些转录因子发现一个显着减少通气组织的百分比相比，野生型的突变体。这些研究证实了从Anatomics数据集获得的代表性基因在通气组织形成中的作用。然而，通气组织发育调控的分子机制在很大程度上是未知的。作为一名BBSRC发现研究员，我将在诺丁汉大学率先在谷类作物中使用解剖学和功能基因组学方法。我的第一个目标将是确定通气组织介导的玉米恢复力的分子机制。接下来，我将使用激光捕获显微切割和单细胞RNA测序方法来生成玉米根的细胞分辨率基因表达图谱，并绘制在根生长和发育过程中控制通气组织形成的基因和信号。最后，我将把玉米方面的知识转化为其他重要但往往投资不足的作物，如珍珠粟，以加快育种和遗传改良计划。通气组织形成是一个发育程序，其中同一皮层内的特定细胞经历程序性细胞死亡，而相邻细胞存活。我的时空基因表达图谱的玉米根在细胞分辨率将是一个无与伦比的资源，通气组织以及其他根解剖性状和发展计划。此外，从这项研究中揭示的基因调控机制也将帮助我们了解这些性状如何赋予玉米和珍珠粟作物的抗逆性，这些作物是经济上重要的膳食斯台普斯。因此，我的研究也将有助于英国的全球粮食安全的努力。

Drought and low soil fertility are major constraints to global crop production. These constraints are becoming even more challenging over time due to deteriorating soil quality, increasing population pressure and changing climate. In this context, recent discoveries have identified several root anatomical traits that can substantially improve crop yield and climate resilience by improving water and nutrient uptake. For example, the formation of air spaces (termed aerenchyma) in root cortex tissue occurs when living cells undergo programmed cell death. This significantly reduces nutrient demand and respiration of root tissues, enables plant to acquire more soil resources and improve crop yield under drought and suboptimal nutrient conditions. In addition to aerenchyma formation, other traits such as reduced number and layers of living cells in the cortex tissue (termed cortical cell count and cortical cell file number respectively) confer similar benefits. However, despite this knowledge, anatomical traits have received little attention as selection criteria in crop breeding because of the challenges associated with sampling and quantification of anatomical phenotypes."Anatomics" is a novel interdisciplinary approach that now makes it possible for the first time to rapidly image and analyse plant anatomical traits in large numbers of crop varieties. Using this approach, my US collaborators generated root anatomical data for hundreds of maize varieties grown over 5 years in South Africa. Next, I analysed this dataset using an integrated gene-discovery pipeline that includes Genome wide association studies (GWAS), literature mining and enhanced data visualisation techniques. This analysis highlighted correlations between the anatomical data and hundreds of thousands of DNA polymorphisms in the maize diversity panel and thus pinpointed key genes that control root anatomical traits in maize. For instance, my pipeline identified two novel transcription factors functionally associated with aerenchyma formation. Mutation analysis of a maize mu insertion and a rice ortholog mutant for these transcription factors found a significant reduction in aerenchyma percentage in the mutants compared to the wild type. These studies confirmed the role of representative genes obtained from the Anatomics datasets in aerenchyma formation. However, the molecular mechanisms underlying the regulation of aerenchyma development are largely unknown. As a BBSRC Discovery Fellow, I will pioneer the use of anatomics and functional genomics approaches in cereal crops at University of Nottingham. My first objective will be to determine the molecular mechanism for aerenchyma mediated resilience in maize. Next, I will use Laser Capture Microdissection and Single-Cell RNA sequencing approaches to generate a cellular resolution gene expression atlas for the maize root and map genes and signals that control aerenchyma formation during root growth and development. Finally, I will translate the knowledge generated in maize to other important and often under-invested crops such as pearl millet to accelerate breeding and genetic improvement programmes. Aerenchyma formation is a developmental programme where specific cells within the same cortical layer undergo programmed cell death while neighboring cells survive. My spatiotemporal gene expression atlas of maize root at cellular resolution will be an unparalleled resource to characterise aerenchyma as well as other root anatomical traits and developmental programmes. Further, the gene regulatory mechanisms unravelled from this research will also help us to understand how such traits confer stress tolerance in maize and pearl millet crops which are economically important dietary staples. Thus, my research will also contribute to UK's global food security efforts.