2011年1月15-19日，第19屆動植物基因組大會（Plant and Animal Genome XIX Conference，http://www.intl-pag.org/ ）將在美國圣地亞哥召開。期間，由德國LemnaTec公司和荷蘭Keygene公司合作建立的歐洲第一個植物表型組服務(wù)平臺PhenoFabTM也將同期舉行開幕儀式。
PhenoFabTM結(jié)合了德國LemnaTec公司的高通量植物成像平臺以及荷蘭KeyGene公司分析平臺的強(qiáng)大技術(shù)，可以高通量無損傷的鑒定植物各種表型變異，完美的填補(bǔ)了表型組學(xué)研究的空白，是表型組學(xué)研究的完美解決方案！
PhenoFabTM服務(wù)通過一個巨大的溫室作為植物表型組學(xué)研究的平臺，植物被種于特制的容器中，利用獨(dú)特設(shè)計的傳送裝置，可以將植物有序送至成像暗房中進(jìn)行成像，成像模塊主要包括可見光成像（可以測量植物的結(jié)構(gòu)、寬度、密度、對稱性、葉長、葉寬、葉面積、葉角度、葉顏色、葉病斑、種子顏色、種子顏色面積等等參數(shù)）、近紅外成像（可以分析植物的水分分布狀態(tài)、水力學(xué)研究、脅迫生理學(xué)研究等）和熒光成像（分析植物的生理狀態(tài)），從而獲得植物表型、體內(nèi)水分分布和生理狀態(tài)的數(shù)字化圖像，從不同水平上對植物的性狀特征進(jìn)行選擇和鑒定，極大地提高了工作的效率和質(zhì)量。此外，為了更好的篩選抗逆植株，溫室中還專門提供了環(huán)境條件控制系統(tǒng)，能夠?yàn)橹仓旮叨仍?.6米以下的植物生長提供不同的環(huán)境條件（包括各種脅迫因子），為抗逆單株的鑒定提供了便利的條件。根據(jù)植物的大小，該平臺大約平均容納1100盆植物。
與此同時，德國LemnaTec公司將會在1月18日組織一個“植物表型組學(xué)Workshop”，包括澳大利亞阿德萊德大學(xué)植物加速器、IPK、KeyGene、法國農(nóng)科院等單位的8位專家將會做報告，就植物表型組學(xué)特別是LemnaTec系統(tǒng)在植物表型組學(xué)、遺傳育種中的應(yīng)用做詳細(xì)交流。
澤泉科技作為德國LemnaTec在中國的獨(dú)家合作伙伴，也應(yīng)邀出席PhenoFabTM開幕儀式和“植物表型組學(xué)Workshop”。在此期間，澤泉科技將與國際植物表型組學(xué)、植物功能基因組學(xué)、高通量作物育種等領(lǐng)域的專家交流學(xué)習(xí)，了解國際最新研究趨勢和熱點(diǎn)，更好的為國內(nèi)相關(guān)科研和育種單位提供服務(wù)。
相關(guān)介紹
PhenoFabTM服務(wù)主要包括： ♦? 大于300 m2的現(xiàn)代化溫室；
♦ 帶有特殊硬件的專業(yè)溫室，環(huán)境條件完全可控；
♦ 針對不同的作物，有數(shù)字化表型鑒定、專業(yè)統(tǒng)計分析方法進(jìn)行分析；
♦ 性狀分析主要包括顏色、種芽和生物量、遺傳特性、根系發(fā)育、冠層結(jié)構(gòu)以及生物/非生物因子脅迫等等；
♦ 對植物單株進(jìn)行多層次數(shù)字化的性狀觀察（角度、時間序列、光照等等）；
♦ 專利軟件進(jìn)行植物表型從圖像到數(shù)字化的統(tǒng)計學(xué)分析；
♦ 完全整合的圖像數(shù)據(jù)庫存儲實(shí)驗(yàn)數(shù)據(jù)（類似于實(shí)驗(yàn)室信息管理系統(tǒng)）；
♦ 自動澆水和營養(yǎng)鹽供給系統(tǒng)。
PhenoFabTM服務(wù)主要包括： ♦? 大于300 m2的現(xiàn)代化溫室；
♦ 帶有特殊硬件的專業(yè)溫室，環(huán)境條件完全可控；
♦ 針對不同的作物，有數(shù)字化表型鑒定、專業(yè)統(tǒng)計分析方法進(jìn)行分析；
♦ 性狀分析主要包括顏色、種芽和生物量、遺傳特性、根系發(fā)育、冠層結(jié)構(gòu)以及生物/非生物因子脅迫等等；
♦ 對植物單株進(jìn)行多層次數(shù)字化的性狀觀察（角度、時間序列、光照等等）；
♦ 專利軟件進(jìn)行植物表型從圖像到數(shù)字化的統(tǒng)計學(xué)分析；
♦ 完全整合的圖像數(shù)據(jù)庫存儲實(shí)驗(yàn)數(shù)據(jù)（類似于實(shí)驗(yàn)室信息管理系統(tǒng)）；
♦ 自動澆水和營養(yǎng)鹽供給系統(tǒng)。
植物表型組學(xué)Workshop主要內(nèi)容介紹
Evaluation Of Next Generation Phenotyping: The Australian Plant Phenomics Facility
Geoffrey B Fincher1 , Mark A Tester2 , Robert Furbank3 , Murray Badger4
- 1 Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
- 2 Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
- 3 High Resolution Plant Phenomics Centre, CSIRO Plant Industry, Canberra, ACT 2601, Australia
- 4 High Resolution Plant Phenomics Centre, Australian National University, Canberra, ACT 2601, Australia
Plant phenomics involves the measurement of traits such as leaf length or root architecture and their measurement is important for determining resistance to diseases and environmental stresses such as drought and salinity. Assessment of these characters is usually slow and this has become a bottleneck in the exploitation of genomic and related data for crop improvement. The science of genomics has accelerated so rapidly in the past few years that advances in manipulation of the genome now far exceed the ability and capacity to measure the effects of these manipulations (phenomics).
The Australian Plant Phenomics Facility (APPF) is a $50 million project that has two nodes. At the first node, located at CSIRO Plant Industry and ANU in Canberra, new non-destructive phenomics technologies such as high resolution infra-red imaging are being adapted for in-depth application to individual plants and for use in the field.
The second node consists of the Plant Accelerator, which has recently been constructed on the Waite Campus of the University of Adelaide. It provides automated, high throughput, non-destructive imaging of plant populations in controlled environments. The Plant Accelerator node includes four “smarthouses”, which contain conveyor systems to deliver potted plants automatically to four imaging stations for high resolution, multi-aspect imaging at a range of visible and infra-red wavelengths. The Plant Accelerator has been used to generate data on the tolerance of wheat and barley lines to abiotic stresses such as salinity and borate toxicity, and the data have been compared with those obtained previously using several manual phenotyping protocols.
The Australian Plant Phenomics Facility (APPF) is a $50 million project that has two nodes. At the first node, located at CSIRO Plant Industry and ANU in Canberra, new non-destructive phenomics technologies such as high resolution infra-red imaging are being adapted for in-depth application to individual plants and for use in the field.
The second node consists of the Plant Accelerator, which has recently been constructed on the Waite Campus of the University of Adelaide. It provides automated, high throughput, non-destructive imaging of plant populations in controlled environments. The Plant Accelerator node includes four “smarthouses”, which contain conveyor systems to deliver potted plants automatically to four imaging stations for high resolution, multi-aspect imaging at a range of visible and infra-red wavelengths. The Plant Accelerator has been used to generate data on the tolerance of wheat and barley lines to abiotic stresses such as salinity and borate toxicity, and the data have been compared with those obtained previously using several manual phenotyping protocols.
High-Throughput Phenotyping In Barley – The IPK Plant Phenomics Facilities
Anja Hartmann , Tobias Czauderna , Roberto Hoffmann , Christian Klukas , Thomas Altmann , Falk Schreiber , NILs Stein
Leibniz Institute of Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
Automated high-throughput or high precision phenotyping remains one of the major bottlenecks in plant research since more and more plant genomes are being sequenced. In order to facilitate ways of automated phenotyping in the analysis of natural genetic diversity in cereal crops as well as in crop response to abiotic stresses, we are in the process of establishing a Lemnatec Scanalyzer system, which can accommodate 312 barley plants. Initial steps were made and lessons learned in course of setting up standardized calibration experiments. An image analysis software was developed (HT-Pheno) based on open source tools to allow for flexible basic determination of plant area. Extensive calibration experiments were performed to learn about the influence of environmental effects of the surrounding glasshouse. An overview of the initial experiences will be provided and discussed.
Keytrack Root Phenotyping - At The Root Of Development
Gert-Jan Speckmann , Bas de Regt , Shital Dixit , Koen Huvenaars , Jose Guerra , Harold Verstegen , Marco G.M. van Schriek
Keygene N.V., Agro Business Park 90, 6708 PW, Wageningen, The Netherlands
Plant roots are economically very relevant since the distribution pattern of the root system in the soil determines the zone of water and nutrient availability to plants and differences in root and root development is related to crop yields and abilities to escape drought and soil-borne diseases.
The KeyTrack system allows for efficient execution of root research in a high throughput manner. The KeyTrack platform is a robust phenotyping platform in a greenhouse setup. The phenotyping is based on imaging technology and uses the potential of a track that moves all plants fully automated through the greenhouse compartment and scanning areas. The plants grow in individual containers and are photographed at pre-set points in time and from different angles.
The research presented encompasses the creation of an automated root phenotyping protocol and image analysis pipeline. The material used for this research is the tomato LA716 S. pennellii introgression line library created by prof. Dani Zamir. The research described merges the phenotypic data generated with genotypic knowledge, to feed lead discovery and root development in tomato.
The KeyTrack system allows for efficient execution of root research in a high throughput manner. The KeyTrack platform is a robust phenotyping platform in a greenhouse setup. The phenotyping is based on imaging technology and uses the potential of a track that moves all plants fully automated through the greenhouse compartment and scanning areas. The plants grow in individual containers and are photographed at pre-set points in time and from different angles.
The research presented encompasses the creation of an automated root phenotyping protocol and image analysis pipeline. The material used for this research is the tomato LA716 S. pennellii introgression line library created by prof. Dani Zamir. The research described merges the phenotypic data generated with genotypic knowledge, to feed lead discovery and root development in tomato.
Large Scale Phenotyping In Plant Breeding: An Example In Pepper
Fred van Eeuwijk1,2 , Gerie van der Heijden1, , Yu Song3 , Gerrit Polder1 , Anja Dieleman4 , Chris Glasbey3
- 1 Biometris, Wageningen University and Research Centre, P.O. Box 100, 6700 AC Wageningen, The Netherlands
- 2 Centre for Biosystems Genomics, P.O. Box 98, 6700 AB Wageningen, The Netherlands
- 3 BioSS, Kings Buildings, Edinburgh EH9 3JZ, Scotland
- 4 Wageningen UR Greenhouse Horticulture, P.O. Box 644, 6700 AP Wageningen, The Netherlands
The major objective of plant breeding is to develop superior genotypes using genetic, genomic and phenotypic information. More and faster automatic approaches become available to assess huge amounts of genetic and genomic information. In contrast, the collection of phenotypic information is still largely done by manual and visual assessments. An interesting option for large scale phenotyping is by (high throughput) image analysis systems. Within the EU-project SPICY (Smart tools for the Prediction and Improvement of Crop Yield; www.spicyweb.eu), we have developed an imaging platform to record and measure pepper plants while they are growing in the greenhouse. For the analysis of the recorded images two approaches are adopted. The first approach is to measure and count plant parts like leaves, fruits and internodes. For this approach a combination of a range camera and stereovision is used to obtain a 3D reconstruction of the canopy for good segmentation. The other approach is aimed at the extraction of statistical features from the images without trying to segment individual plant parts from a background. The criteria for success in this case are high heritability, i.e., reproducible differences between genotypes, and strong genetic correlation with yield or its components.
The JüLich Plant Phenotyping Center (JPPC) Platform At Forschungszentrum JüLich Gmbh
Kerstin A Nagel , Fiorani Fabio , Ulrich Schurr
Institute of Chemistry and Dynamics of the Geosphere ICG-3 (Phytosphere), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
In recent years, plant phenotyping—from molecules to whole organisms—and the accompanying technological advancements have emerged as crucial assets to basic and applied research in plant biology and agriculture for academia as well as industry. The ability and capacity to phenotype plants using standardized protocols is currently the most important bottleneck to gain knowledge in functional genome research. JPPC (Jülich Plant Phenotyping Center) is at the forefront of cutting-edge research in this field, and in promoting the development of reliable experimental standards and practices. In this presentation we will highlight available applications at the JPPC platform focusing on new developments. Case studies will illustrate how the use of phenotyping infrastructure and sensors technology can be efficiently tied to relevant biological questions. In particular, we will show examples of applications that aim at reproducibly measure parameters of root growth and root system architecture in a range of conditions, from artificial growth media to soil in multiple environments (laboratory, greenhouses, and field). Integration of methods at different scales into “phenotyping chains” gives insight into the mechanisms that cause resource use efficiency in root structure and function, and will improve our understanding of which root phenotypic traits can be transferred from controlled environments to field. These approaches aim at defining to what extent these traits can be transferred from crop to crop in pre-breeding and in agricultural production environments.
Development Of High Throughput Plant Phenotyping Facilities At Aberystwyth
Catherine J Howarth , Alan P Gay , John Draper , Wayne Powell
IBERS Aberystwyth University Gogerddan Aberystwyth SY23 3EB U.K.
There is a need to develop high throughput plant phenomics to bridge the phenotype-genotype gap that will lead to the improvements in crop performance necessary to feed the growing world population. The facility under development at Aberystwyth will be based around automated non-destructive image analysis using a Scanalyzer 3-D HTS system developed by LemnaTec running in a new glasshouse complex. Detailed consultations with potential users have provided the specifications for the system. A central advantage of the approach is that it is inherently non-destructive, allowing repeated measurements to be made on individual plants in a pre-programmed sequence through time with minimal operator intervention. The system is designed to cope with small plants such as forage grasses, forage legumes, Brachypodium and Arabidopsis, and with larger plants such as oats, wheat, barley, maize and Miscanthus. The plant phenomics facility will be closely linked to both chemical phenotyping and genotyping facilities in Aberystwyth along with field trials. Use of the facility will accelerate the selection of appropriate germplasm for breeding varieties which will perform robustly under the conditions predicted for the UK and beyond in the future. Furthermore, it will provide a focus for trans-disciplinary research to facilitate the discovery of the genetic and environmental bases for variation in complex traits that underpin the major global challenges for food and energy security, water utilization and adaptation to a changing climate.
DROPS: An EU-Funded Project To Improve Crop Performance Under Drought Conditions
Francois Tardieu1 , Alain Charcosset2 , Xavier Draye3 , Graeme Hammer4 , Bjorn Usadel5 , Roberto Tuberosa6
- 1 INRA, UMR 759 LEPSE, 2 place Viala, 34060 Montpellier, France
- 2 INRA, Station de Génétique Végétale, Ferme du Moulon, 91190 Gif-sur-Yvette, France
- 3 Crop Physiology and Plant Breeding, Université catholique de Louvain, Croix du Sud 2/11, 1348 Louvain-la-Neuve, Belgium
- 4 Agricultural Production Systems Research Unit, The University of Queensland, Brisbane, Qld 4072, Australia
- 5 Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
- 6 DISTA, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
DROPS (DROught-tolerant yielding PlantS) is an EU-funded project (2010-2015) that will develop novel methods and strategies to improve crop performance under drought conditions. An interdisciplinary approach based on phenotyping under controlled and field conditions will generate data that will be used for ecophysiological modeling to predict crop performance under fluctuating water regimes. QTL discovery for traits of importance under drought conditions will produce additional data for modeling crop performance based on QTL effects. The project will target root architecture, transpiration efficiency, vegetative growth maintenance and seed abortion in maize and durum wheat. DROPS will:
Develop new screens under controlled and field conditions that will consider indicators which are (i) highly heritable and measurable in a high-throughput fashion in phenotyping platforms, (ii) based on metabolite concentration, sensitivity parameters of models or hormonal balance, (iii) genetically related to target traits and able to predict genotype performance in the field via simulation and/or statistical models;
Explore the natural variation of the target traits by (i) linking the target traits to physiological pathways, genes or genomic regions, (ii) assessing the effects of a large allelic diversity for the four target traits via association genetics;
Support crop improvement strategies by developing methods for estimating the comparative advantages of relevant alleles and traits in fields with contrasting drought scenarios. This will be achieved via field experiments and by developing new crop models able to estimate the effects of alleles on crop growth, yield and water-use efficiency.
Develop new screens under controlled and field conditions that will consider indicators which are (i) highly heritable and measurable in a high-throughput fashion in phenotyping platforms, (ii) based on metabolite concentration, sensitivity parameters of models or hormonal balance, (iii) genetically related to target traits and able to predict genotype performance in the field via simulation and/or statistical models;
Explore the natural variation of the target traits by (i) linking the target traits to physiological pathways, genes or genomic regions, (ii) assessing the effects of a large allelic diversity for the four target traits via association genetics;
Support crop improvement strategies by developing methods for estimating the comparative advantages of relevant alleles and traits in fields with contrasting drought scenarios. This will be achieved via field experiments and by developing new crop models able to estimate the effects of alleles on crop growth, yield and water-use efficiency.
A Platform For High Throughput Phenotyping Of Plant/Plant And Plant/Microorganisms Interactions.
Christophe SALON , Christian JEUDY , Celine BERNARD , Richard THOMPSON , Vivienne GIANINAZZI-PEARSON , Xavier REBOUD , Philippe LEMANCEAU , Jacques CANEILL
UMR Agroecology, National Institute of Agronomical Research (INRA), 17 rue Sully, BP86510, 21065 Dijon Cedex
To overcome crop yields stagnation due to increased occurrence of biotic and abiotic stresses, innovative methods have to be developed to produce high-quality food for the increasing world population while preserving/enhancing the quality of the environment. The High Throughput Plant Phenotyping Platform (PPHD), located in Dijon, France (http://www.dijon.inra.fr/), provides searchers with an infrastructure able to apply well-characterized biotic and abiotic constraints to several hundreds of genotypes (and so thousands of plants) and to accurately measure a series of functional traits. It allows establishing/testing causal relationships between genetic markers and phenotypes related to plant performance under a range of environmental conditions, including those forecasted by models of climate change.
PPHD is constituted of a building (hosting activities related to plant material preparation, plant growth and post growth analysis) with S2 modular greenhouses and climatic chambers. These are equipped with conveyors belts to homogenize plant growth conditions and automatically bring plant units to the phenotyping cabinets. Phenotyping is based on image analysis (visible light, near infrared and fluorescence) which allows characterizing non destructively and automatically i) a large variety of plant species and specifically designed high throughput rhizotrons ii) seeds or microorganisms, plantlets. Because of its specificity consisting in the high throughput study of plant/plant and plant(pathogene-symbiotic)micro organisms interactions at the shoot level and more specifically the root level, PPHD constitutes a major infrastructure for identifying determinants of plant adaptation to new cropping systems displaying enhanced agro ecological services.
PPHD is constituted of a building (hosting activities related to plant material preparation, plant growth and post growth analysis) with S2 modular greenhouses and climatic chambers. These are equipped with conveyors belts to homogenize plant growth conditions and automatically bring plant units to the phenotyping cabinets. Phenotyping is based on image analysis (visible light, near infrared and fluorescence) which allows characterizing non destructively and automatically i) a large variety of plant species and specifically designed high throughput rhizotrons ii) seeds or microorganisms, plantlets. Because of its specificity consisting in the high throughput study of plant/plant and plant(pathogene-symbiotic)micro organisms interactions at the shoot level and more specifically the root level, PPHD constitutes a major infrastructure for identifying determinants of plant adaptation to new cropping systems displaying enhanced agro ecological services.
——Scientific image processing since 1998
LemnaTec公司位于德國亞琛市，于1998年5月由8位不同學(xué)科背景的合作者共同成立。公司一直延續(xù)著“結(jié)合多學(xué)科能力”的理念，因此，LemnaTec 科研團(tuán)隊(duì)由不同學(xué)科背景的專家組成，主要包括生物學(xué)家、物理學(xué)家、化學(xué)家、生物信息學(xué)家、生態(tài)毒理學(xué)家以及硬件軟件工程師等等。他們?yōu)橹参锉硇徒M學(xué)研究、高通量掃描（植物、種苗、昆蟲以及其他生物）、自動化評估（生態(tài)毒理學(xué)效應(yīng)等）提供了完美的解決方案。植物表型數(shù)字化圖像通過Scanalyzer 3D和Scanalyzer HTS系統(tǒng)及時獲取，利用高級的圖像處理系統(tǒng)和整合的數(shù)據(jù)分析功能，能對任何一個可見的參數(shù)（如顏色、形狀、大小和結(jié)構(gòu)等）進(jìn)行測定和深入的分析。LemnaTec的目標(biāo)：超越人眼，具體化分析生物學(xué)性狀！
——It is a Green Gene Revolution
KeyGene作為世界知名的生物公司，長期致力于作物產(chǎn)量、品質(zhì)和健康狀況的研究，并在多種作物上探索和發(fā)掘了大量的遺傳變異。20多年來，KeyGene利用其尖端的分子育種技術(shù)和農(nóng)作物性狀改良平臺，竭誠地為無數(shù)的育種公司提供技術(shù)支持，極大地推動了作物改良的進(jìn)程。為了進(jìn)一步的提供更加優(yōu)質(zhì)的服務(wù)，KeyGene公司放眼于未來，決定大力發(fā)展高通量植物表型鑒定技術(shù)，有效推動基因連鎖控制的復(fù)雜性狀的篩選和鑒定，更好的為遺傳育種工作服務(wù)。KeyGene總部位于荷蘭瓦赫寧根市，在美國馬里蘭州羅克維爾市設(shè)有分公司，與中國上海生命科學(xué)研究院設(shè)有合作實(shí)驗(yàn)室。
——服務(wù)于中國的植物表型組學(xué)研究
上海澤泉科技有限公司作為的植物科學(xué)與農(nóng)業(yè)科學(xué)產(chǎn)品與系統(tǒng)解決方案提供商，是德國LemnaTec公司在中國的唯一合作伙伴。澤泉科技攜手澤泉開放實(shí)驗(yàn)室專業(yè)的技術(shù)服務(wù)團(tuán)隊(duì)，致力于為作物育種、植物功能基因組學(xué)、植物表型組學(xué)等領(lǐng)域的客戶提供完善的產(chǎn)品與系統(tǒng)解決方案。
