利用植物表型组学挖掘基因组学的成果

2020.4.04

王辉

致力于为分析测试行业奉献终身

到2050年，全球人口将达到97亿，预计作物产量翻一番才能满足全球人口的粮食需求。为了达到这一目标，作物产量需每年增长2.4%，但目前作物产量平均增长率仅为1.3%。作物生产性能的遗传改良仍然是提高作物生产力的关键因素，但当前的改善速度无法满足可持续性和粮食安全的需要。为了确保粮食安全、生态系统的可持续发展，必须培育高产、适应新气候和多变气候的作物。

基因组学和表型组学的进展正在提供对复杂的生物学机制的洞察，这些机制是植物对环境变化作出反应的基础。然而，将基因型与表型联系起来培育气候适应性作物品种仍然是一个巨大的挑战，阻碍了高通量基因组学和表型组学在育种中的最佳应用。

本文综述了植物表型系统化、快速化、微创化和低成本化的必要性，讨论了其向现代高通量表型的演变、适应高通量表型的性状、高通量表型与基因组学的整合以及高通量表型在提高育种效率和加快作物品种培育中的意义。

根系表型（a，g为微根管法原位测量）

鹰嘴豆耐热表型分析研究中的叶片叶绿素荧光成像

叶片上半部分没有经过热处理，下半部分在46°C下热处理1小时。深蓝色为高光合活性（高fv/fm），而橙色、黄色和绿色或完全黑色代表低光合活性。

红外热成像表征冠层温度

不同品种苹果花粉的活性（微流控阻抗流式细胞法）

表1常用的作物高通量植物表型平台（HTPPS）

Name	Target Plant Organ	Parameters	Description
PHENOPSIS	Leaf	Plant growth parameters	An automated platform for reproducible phenotyping of plant responses to soil water deficit in Arabidopsis thaliana
WIWAM	Leaf	Growth parameters	Used to impose stress early during leaf development
PHENOSCOPE	Shoots	Vegetative growth and homogeneity	An integrated device, allowing a simultaneous culture of individual Arabidopsis plants and high-throughput acquisition, storage, and analysis of quality phenotypes
GROWSCREEN	Leaf	3D surface area of leaf discs	Platform to study plant leaf growth fluorescence and root architecture from seedling under control conditions in Arabidopsis thaliana, barley and maize
TraitMill	Flowers, grains, etc.	Growth and yield parameters	Automated high resolution phenotypic platform, uniquely placed to identify genes that improve the yield of cereals
PlantScan	Whole plant	Vegetative growth parameters	Automated high-resolution phenomic center providing non-invasive analysis of plant structure, morphology and function in Gossypium, wheat and maize
LemnaTec	Leaf	Growth and yield parameters	Visualize and analyze 2D/3D non-destructive high-throughput imaging, monitor plant growth and behavior under fully controlled conditions
LeasyScan	Leaf, whole plant	Canopy traits	Phenotyping for traits controlling plant water use with precision in pearl millet
HRPF	Whole plant	Growth and yield parameters	High-throughput rice phenotyping facility
GlyPh (self-construction)	Whole plant	Soil water content and growth estimation	Low-cost platform for phenotyping plant growth and water use under a broad range of conditions
BreedVision	Whole plant	Growth and physiological parameters	Measures various agronomic traits and leads to non-destructive phenotyping for crop improvement and plant genetic studies
PlantScreenTM	Shoot	Chlorophyll fluorescence imaging and non-imaging chlorophyll fluorescence, growth parameters	Evaluates various parameters of chlorophyll fluorescence obtained from kinetic chlorophyll fluorescence imaging
OloPhen	Whole plant	Rosette area, growth and survival rate	Suitable for analysis of rosette growth in multi-well plates, suitable to evaluate plant stress tolerance.
Color eye (RBG scanner)	Leaf	Leaf greenness, lesions	Data can be overlayed over laser triangulation data obtained by plant eye
LabVIEW	Canopy	Growth parameters	Low-cost, accurate, and high-throughput phenotyping system with custom algorithms
Shovelomics	Root	Root growth parameters	Identification and selection of useful root architectural phenotypes for annual legume or dicotyledonous crops.
Phenodyn/Phenoarch	Leaf	Leaf elongation rate	Follows QTL-dependent daily patterns in maize lines under naturally fluctuating conditions, located in INRA, France
LemnaGrid	Root and leaf	Plant and root growth parameters	Compares growth behaviors of different genotypes, discriminates plant root zone water status
Integrated Analysis Platform (IAP)	Leaf	Plant leaf orientation	Provides user-friendly interfaces with highly adaptable core functions, supports image data transfer from different acquisition environments and large-scale image analysis
LAMINA	Leaf	Leaf parameters	Tool for automated analysis of images of leaves, designed to provide classical indicators of leaf structure
Rosette Tracker	Shoot	Area, perimeter diameter stockiness	Allows to simultaneously quantify plant growth, photosynthesis, and leaf temperature-related parameters
Leaf Analyser	Leaf	Leaf architecture	Provides a high-throughput method to evaluate leaf shape variation in higher-dimensional phenotypic space
Self-construction	Root	Root growth parameters	Algorithms allow the automatic extraction of many root traits in a high-throughput fashion
Phenovator	Leaf	Photosynthesis	High-throughput phenotyping facility for photosynthesis developed at Wageningen University and Research

表2常用的高通量植物表型分析软件包（节选）

Name of the Software	Target Plant Organ	Parameters	Description
MATLAB	Leaf	Leaf architecture	Uses image processing algorithms for high-throughput analysis of images for estimating phenotypes/traits associated with tested plants
HTPheno	Shoot	Height, width and shoot area	Analyzes colour images of plants and different phenotypical parameters for each plant
GiaRoots	Root	Morpho-geometric parameters	Semi-automated software tool for high-throughput analysis of root system images
RootReader 3D	Roots	Root types and phenotypic root traits	Imaging and software platform for HTP of 3-D root traits during seedling development
PhenoPhyte	Leaf	Leaf and plant growth parameters	Tool to analyze the non-destructive imaging of plants can be used in suboptimal imaging conditions also
RootNav	Root	Root system architecture	Image analysis tool for semi-automated quantification of complex root system architecture in a range of plant species
SmartGrain	Seed	Seed structure parameters	Software for high-throughput measurement of seed shape, makes possible to distinguish between lines with small differences in seed shape
SmartRoot	Root	Root system architecture	Operating system-independent freeware and relies on cross-platform standards for communication with data-analysis software
DART	Root	Root system architecture	Uses human vision tracing to avoid analytical biases
Tomato analyzer	Fruit	Fruit colour	Analyzes tomato fruit colour