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

景天酸代谢(CAM)是一种光合作用的适应性，存在于生活在干旱和半干旱环境中的各种植物物种中。CaM植物可以实现比C3植物高出十倍的水分利用效率。我们的总体目标是通过对参与这一有价值的适应的基因、蛋白质和代谢物的详细了解，建立对CAM的系统水平的看法。对CAM‘零件清单’的全面了解将允许将CAM正向工程应用于C3作物。特别是，我们正在与美国科学家合作一个植物合成生物学项目，旨在将CAM引入杨树(http://cambiodesign.org).我们对我们的模型CAM系统Kalancoëfedtschenkoi和K.laxiflora进行了全基因组和转录组测序(RNA-seq)，包括详细分析了这两个物种的CAM和C3组织中基因转录丰度的模式。这项基因发现工作已经确定了将CAM工程转化为C3作物的候选基因。为了完善候选CAM基因的列表，Hartwell实验室最近的工作集中在沉默Kalancoë转基因株系中的每个候选CAM基因，以完善有效CAM的最小部分列表(例如Dever等人，2015年植物生理学；Boxall等人，2017 The Factory Cell)。此外，我们最近使用详细的气体交换分析来鉴定属于Kalancoë属的弱和强CAM物种。弱CAM种纤细管藻叶片较薄，水分充足时利用C3光合作用，干旱胁迫时弱CAM。它在卡兰乔埃分子系统发展史中占有基础/祖先的位置。相比之下，卡兰乔伊的强CAM物种，如K.Hildebrandtii，肉质丰富，在所有环境条件下都依赖于CAM。这些强大的CAM物种也是进化程度最高的物种。这些发现为Kalancoë的CAM进化的比较基因组分析奠定了基础，这将使我们能够识别与在这个多样化的基因组中从弱的和可诱导的CAM到强的CAM的转变相关的遗传和表观遗传学变化。本项目将专注于对我们现有的K.fedtschenkoi和K.laxiflora基因组和RNA-seq数据与新解码的K.gracilipes和K.Hildebrandtii的基因组和转录本进行比较分析，这些数据将作为我们未来几个月由美国国防部资助的持续研究的一部分进行测序。能源部的“CAM生物设计”项目。这些序列将在这个拟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、水分利用效率更高的生物能源作物和适合沙漠种植的新型生物燃料饲料作物做出实质性贡献。

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.