Engineering more water-use efficient crops: functional genomics of weak and strong Crassulacean acid metabolism in diverse species of the genus Kalanc

天冬酸代谢（CAM）是一种适应光合作用的机制，存在于干旱和半干旱环境中的多种植物物种中。CAM植物的水分利用效率是C3植物的10倍。我们的首要目标是通过对这种有价值的适应所涉及的基因、蛋白质和代谢物的详细了解，开发CAM的系统级视图。全面了解CAM“零件清单”将允许CAM进入C3作物的前瞻性工程。特别是，我们正在与美国科学家合作开展植物合成生物学项目，旨在将CAM引入杨树（http://cambiodesign.org）。我们对模型CAM系统Kalanchoë fedtschenkoi和K. laxiflora进行了全基因组和转录组测序（RNA-seq），包括对两种物种CAM和C3组织中基因转录丰度的详细分析。这项基因发现工作已经确定了C3作物CAM工程的候选基因。为了完善候选CAM基因列表，Hartwell实验室最近的工作重点是沉默Kalanchoë转基因系中的每个候选CAM基因，以完善有效CAM的最小部件列表（例如Dever等人，2015 Plant Physiology； Boxall等人，2017 the Plant Cell）。此外，我们最近使用详细的气体交换分析来鉴定属于Kalanchoë属的弱和强CAM物种。弱CAM物种，K. gracilipes，叶片相对较薄，在水分充足时使用C3光合作用，但在干旱胁迫下弱CAM。它在Kalanchoë分子系统发育中处于基础/祖先的位置。相比之下，Kalanchoë的强CAM物种，如K. hildebrandtii，是高度多肉的，在任何环境条件下都依赖CAM。这些强大的CAM物种在进化方面也是最衍生的。这些发现为Kalanchoë中CAM进化的比较基因组分析奠定了基础，这将使我们能够确定与这个多样化属中从弱和诱导CAM到强CAM过渡相关的遗传和表观遗传变化。该项目将重点对我们现有的K. fedtschenkoi和K. laxiflora的基因组和RNA-seq数据与新解码的K. gracilipes和K. hildebrandtii的基因组和转录组进行比较分析，这些基因组和转录组将在未来几个月内作为我们正在进行的研究的一部分进行测序，该研究由我们的美国能源部“CAM生物设计”项目资助。这些序列将在这个建议的博士项目开始之前提供。从长远来看，这项工作将为开发更耐旱、用水效率更高的生物能源作物和适合沙漠栽培的新型生物燃料原料作物做出重大贡献。

Crassulacean acid metabolism (CAM) is an adaptation of photosynthesis found in a diverse range of plant species that inhabit arid and semi-arid environments. CAM plants can achieve water use efficiencies up to ten-times greater than C3 species. Our over-arching goal is to develop a systems level view of CAM by developing a detailed understanding of the genes, proteins and metabolites involved in this valuable adaptation. Comprehensive knowledge of the CAM 'parts-list' will permit forward engineering of CAM into C3 crops. In particular, we are collaborating with US scientists on a plant synthetic biology project that aims to introduce CAM into poplar trees (http://cambiodesign.org). We have performed whole genome and transcriptome sequencing (RNA-seq) for our model CAM systems, Kalanchoë fedtschenkoi and K. laxiflora, including detailed analysis of patterns of gene transcript abundance in CAM and C3 tissues of both species. This gene discovery work has identified candidate genes for engineering CAM into C3 crops. In order to refine the list of candidate CAM genes, recent work in the Hartwell lab has focused on silencing each candidate CAM gene in transgenic lines of Kalanchoë in order to refine the minimal parts-list for efficient CAM (e.g. Dever et al., 2015 Plant Physiology; Boxall et al., 2017 The Plant Cell).In addition, we have recently used detailed gas exchange analysis to identify both weak and strong CAM species belonging to the genus Kalanchoë. The weak CAM species, K. gracilipes, is relatively thin leaved and uses C3 photosynthesis when well-watered, but weak CAM when drought stressed. It occupies a basal/ ancestral position in the Kalanchoë molecular phylogeny. By contrast, strong CAM species of Kalanchoë, such as K. hildebrandtii, are highly succulent and rely on CAM under all environmental conditions. These strong CAM species are also the most derived in evolutionary terms. These discoveries set the stage for comparative genomic analysis of CAM evolution in Kalanchoë, which will allow us to identify the genetic and epigenetic changes that are associated with the transition from weak and inducible CAM through to strong CAM in this diverse genus.This project will focus on comparative analysis of our existing K. fedtschenkoi and K. laxiflora genomes and RNA-seq data with the newly decoded genomes and transcriptomes of K. gracilipes and K. hildebrandtii, which will be sequenced as part of our ongoing research in the coming months funded by our US Dept. of Energy "CAM biodesign" project. The sequences will be available prior to the start of this proposed PhD project. In the long term, this work will make a substantial contribution to the development of more drought tolerant, water use efficient bioenergy crops and new biofuel feedstock crops suitable for desert cultivation.