Exploiting anatomical traits to accelerate breeding of novel stress tolerant crops

干旱和土壤肥力低是制约全球作物生产的主要因素。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，这些限制变得更加具有挑战性。在这种背景下，最近的发现已经确定了一些根系解剖特征，这些特征可以通过改善水分和养分的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，在根皮质组织中形成空气空间（称为通气组织）。这大大减少了根组织的养分需求和呼吸，使植物在干旱和营养条件不理想的情况下获得更多的土壤资源，提高作物产量。除了通气组织的形成，其他特征，如皮层组织中活细胞的数量和层数的减少（分别称为皮质细胞计数和皮质细胞文件数）也具有类似的益处。然而，尽管有这些知识，由于解剖表型的采样和定量相关的挑战，解剖性状作为作物育种的选择标准很少受到关注。“解剖学”是一种新颖的跨学科方法，现在首次可以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了5年多的数百种玉米品种生成了根系解剖数据。接下来，我使用集成的基因发现管道分析该数据集，该管道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。该分析强调了解剖数据与玉米多样性面板中数十万个DNA多态性之间的相关性，从而确定了控制玉米根系解剖性状的关键基因。例如，我的管道鉴定了两种与通气组织形成功能相关的新型转录因子。对这些转录因子的玉米插入突变体和水稻同源突变体的突变分析发现，与野生型相比，突变体的通气率显著降低。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BBSRC的发现研究员，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。我的第一个目标是确定玉米气孔组织介导的恢复力的分子机制。接下来，我将使用激光捕获显微解剖和单细胞RNA测序方法来生成玉米根系的细胞分辨率基因表达图谱，并绘制根系生长发育过程中控制气孔形成的基因和信号。最后，我将把在玉米方面产生的知识转化为其他重要但往往投资不足的作物，如珍珠粟，以加速育种和遗传改良计划。通气组织的形成是一个发育过程，同一皮质层内的特定细胞经历程序性细胞死亡，而邻近细胞存活。我的玉米根系时空基因表达图谱的细胞分辨率将是一个无与伦比的资源表征通气组织以及其他根系解剖特征和发育程序。此外，这项研究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主食。因此，我的研究也将有助于英国的全球粮食安全努力。

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.