JIP-test熒光數(shù)據(jù)及其它生理生態(tài)數(shù)據(jù)主成分綜合分析(PCA)實(shí)例解析
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近年來,快速葉綠素?zé)晒庹T導(dǎo)動(dòng)力學(xué)曲線(OJIP曲線)及其數(shù)據(jù)分析方法JIP-test在植物科學(xué)研究中的應(yīng)用越來越廣泛(BussottiF, et al., 2020; KalajiH M, et al., 2017; Pontes. D, 2019; Tsimilli-michael M, 2020)。
JIP-test提供豐富的參數(shù),PCA進(jìn)行數(shù)據(jù)降維處理,兩者結(jié)合,能夠快速處理并分析大量的實(shí)驗(yàn)數(shù)據(jù),(i)揭示影響實(shí)驗(yàn)的主要參數(shù),并可(ii)聚類不同處理之間的差異,也可用于(iii)大數(shù)據(jù)分析并預(yù)測(cè)植物生長(zhǎng)變化。
近年來,全球范圍內(nèi)短期內(nèi)澇等自然災(zāi)害頻發(fā),并且隨著北半球高緯度地區(qū)秋冬季降水量的增加,這種情況的出現(xiàn)可能會(huì)更加頻繁。
圖1. 主成分分析的向量圖,顯示了低溫對(duì)照和低溫淹水被調(diào)查變量之間的相關(guān)性
光是控制植物生長(zhǎng)發(fā)育的主要因素。
圖2. JIP-test參數(shù)和不同處理的主成分分析(Plant variants: W – white light; WS – white light with shadow; BR – blue and red light; BRS – blue and red light with shadow)
在大規(guī)模生態(tài)調(diào)查中,為了達(dá)成篩選目的和效率,一般使用有限的參數(shù)來對(duì)樣本進(jìn)行快速、簡(jiǎn)單的評(píng)價(jià)和生理分類。
本研究中分析的最大數(shù)據(jù)集源自FunDivEUROPE項(xiàng)目(Functional Significance ofthe Forest Diversity in Europe, European Union, 7th FrameworkProgram)。
圖3. 所選JIP-test參數(shù)的主成分分析
如何實(shí)現(xiàn)對(duì)葉綠素a熒光數(shù)據(jù)(JIP-test參數(shù))、其它生理參數(shù)和基因、蛋白等分子數(shù)據(jù)組成的大數(shù)據(jù)庫進(jìn)行PCA分析?
通常我們可以使用學(xué)術(shù)界常用的商用數(shù)據(jù)分析軟件進(jìn)行PCA分析,如SPSS Statistics(IBM Corp)、Statistica(StatSoft Inc. 2011)和SAS(SAS Enterprise Miner; SAS Institute, Cary, NC)等。
在全球互聯(lián)網(wǎng)化的大趨勢(shì)下,也涌現(xiàn)出一批使用體驗(yàn)更佳、分析更加智能化的在線數(shù)據(jù)分析工具,如SPSSAU(QingSi Technology Ltd 2016-2020)、ClustVis(Metsalu, Tauno et al. 2015)等。
此外以R語言和Python為代表的計(jì)算機(jī)程序設(shè)計(jì)語言可以實(shí)現(xiàn)對(duì)大數(shù)據(jù)的快速智能處理、計(jì)算和制圖,使用R語言和Python對(duì)JIP-test熒光數(shù)據(jù)進(jìn)行PCA數(shù)據(jù)分析也已有非常成熟的語言包進(jìn)行應(yīng)用。
下期文章我們將以IBM SPSS Statistics 26為例詳細(xì)介紹JIP-test熒光參數(shù)PCA分析操作方法,敬請(qǐng)期待!
本文參考文獻(xiàn)
[1] Baeten,L., Verheyen, K., et al. A novel comparative research platform designed to determinethe functional significance of tree species diversity in European forests. Perspect.Plant Ecol. Evol. Syst. 2013, 15 (5), 281–291.
[2] Bussotti F, Gerosa G, Digrado A, et al.Selection of chlorophyll fluorescence parameters as indicators ofphotosynthetic efficiency in large scale plant ecological studies[J].Ecological Indicators, 2020, 108: 105686.
[3] Goltsev V, Zaharieva I, Chernev P, et al.Drought-induced modifications of photosynthetic electron transport in intactleaves: analysis and use of neural networks as a tool for a rapid non-invasiveestimation[J]. Biochimica et Biophysica Acta (BBA)-Bioenergetics, 2012,1817(8): 1490-1498.
[4] Kalaji H M, Bąba W, Gediga K, et al.Chlorophyll fluorescence as a tool for nutrient status identification inrapeseed plants[J]. Photosynthesis research, 2018, 136(3): 329-343.
[5] Kalaji H M, Schansker G, Brestic M, et al.Frequently asked questions about chlorophyll fluorescence, the sequel[J].Photosynthesis Research, 2017, 132(1): 13-66.
[6] Metsalu, Tauno and Vilo, Jaak. Clustvis: a webtool for visualizing clustering of multivariate data using Principal ComponentAnalysis and heatmap. Nucleic Acids Research, 43(W1): W566–W570, 2015.
[7] Pontes. D, Ontes, M.,Rodriguez, R. and Santiago,E.F. Letter to The Editor. The energy flux theorycelebrates 40 years: toward asystems biology concept? Photosynthetica,2019, vol. 57, iss. 2, p.521-522.
[8] Tsimilli-michael M. Revisiting JIP-test: Aneducative review on concepts, assumptions, approximations, definitions andterminology[J].Photosynthetica,2019,57 (SI): 90-107.
[9] Verheyen, K., Vanhellemont, M., et al. 2016.Contributions of a global network of tree diversity experiments to sustainableforest plantations. Ambio 45, 29–41.
應(yīng)用PCA分析JIP-test熒光數(shù)據(jù)文獻(xiàn)節(jié)選
[1] DimitrovaS, Paunov M, Pavlova B, et al. Special issue in honour of Prof. Reto J.Strasser–Photosynthetic efficiency of two Platanus orientalis L. ecotypesexposed to moderately high temperature-JIP-test analysis[J]. Photosynthetica,2020, 58(SPECIAL ISSUE): 657-670.
[2] BussottiF, Gerosa G, Digrado A, et al. Selection of chlorophyll fluorescence parametersas indicators of photosynthetic efficiency in large scale plant ecologicalstudies[J]. Ecological Indicators, 2020, 108: 105686.
[3] MihaljevićI, Lepeduš H, Šimić D, et al. Photochemical efficiency of photosystem II in twoapple cultivars affected by elevated temperature and excess light in vivo[J].South African Journal of Botany, 2020, 130: 316-326.
[4] Franić M,Jambrović A, Šimić D, et al. Photosynthetic properties of maize hybrids underdifferent environmental conditions probed by the chlorophyll a fluorescence[J].Maydica, 2020, 64(3): 9.
[5] Plich J,Boguszewska-Mańkowska D, Marczewski W. Relations Between PhotosyntheticParameters and Drought-Induced Tuber Yield Decrease in Katahdin-Derived PotatoCultivars[J]. Potato Research, 2020: 1-15.
[6] Vuletic M,Španic V. Special issue in honour of Prof. Reto J. Strasser–Characterization ofphotosynthetic performance during natural leaf senescence in winter wheat:Multivariate analysis as a tool for phenotypic characterization[J]. Photosynthetica2020, 58(2):301-313
[7] Faria-SilvaL, Gallon C Z, Silva D M. Photosynthetic performance is determined byscion/rootstock combination in mango seedling propagation[J]. ScientiaHorticulturae, 2020, 265: 109247.
[8] Banr A,Bruggemann W. Special issue in honour of Prof. Reto J. Strasser–Comparativeanalysis of drought stress response of maize genotypes using chlorophyllfluorescence measurements and leaf relative water content[J]. Photosynthetica,2020, 58(SPECIAL ISSUE): 638-645.
[9] CarreirasJ, Pérez-Romero J A, Mateos-Naranjo E, et al. The effect of heavy metalcontamination pre-conditioning in the heat stress tolerance of native andinvasive Mediterranean halophytes[J]. Ecological Indicators, 2020, 111: 106045.
[10] BlackhallV, Orioli G A, Colavita M G. JIP-test parameters to study apple peelphotosystem II behavior under high solar radiation stress during fruitdevelopment[J]. Photosynthetica 2020, 58(2):314-322
[11] SwoczynaT, Latocha P. Monitoring seasonal damage of photosynthetic apparatus in maturestreet trees exposed to road-side salinity caused by heavy traffic[J]. Photosynthetica58 (SI): 388-399, 2020
[12] Gast A,Romermann C, Bucher S F. Seasonal variation and trade-off between frostresistance and photosynthetic performance in woody species[J]. Photosynthetica2020, 58(2):331-340
[13] WiewióraB, Żurek G, Rybka K, et al. The origin of Epichloë endophyte-perennial ryegrasssymbionts modify plant reactions to elevated concentration of Pb2+, Cd2+ andCu2+ ions in soil[J]. BMC Plant Biology,2020.
[14] Samborska-SkutnikI A, Kalaji H M, Sieczko L, et al. Special issue in honour of Prof. Reto J.Strasser–Structural and functional response of photosynthetic apparatus ofradish plants to iron deficiency[J]. Photosynthetica 2020, 58(2):205-213
[15] Janka E,Umetani I, Sposob M, et al. Special issue in honour of Prof. Reto J.Strasser–Photosynthesis response of microalgae (Tetradesmus wisconsinensis) todifferent inorganic carbon sources probed with chlorophyll fluorescenceanalysis[J].Photosynthetica 2020, 58(2):236-244
[16] Galic V,MAZUR M, ŠIMIĆ D, et al. Special issue in honour of Prof. Reto J.Strasser–Plant biomass in salt-stressed young maize plants can be modelledwithphotosynthetic performance[J]. Photosynthetica 2020, 58(2):194-204
[17] ZhiponovaM, Paunov M, Anev S, et al. JIP-test as a tool for early diagnostics of plantgrowth and flowering upon selected light recipe[J]. Photosynthetica 58 (SI):399-408, 2020
[18] Arslan Ö,Nalcaiyi A S B, Erdal Ş Ç, et al. Analysis of drought response of sunflowerinbred lines by chlorophyll a fluorescence induction kinetics[J]. Photosynthetica2020, 58(2):348-357
[19] SwoczynaT, Łata B, Stasiak A, et al. JIP-test in assessing sensitivity to nitrogendeficiency in two cultivars of Actinidia arguta (Siebold et Zucc.) Planch. exMiq[J]. Photosynthetica, 2019, 57(2): 646-658.
[20] SamborskaI A, Kalaji H M, Sieczko L, et al. Can just one-second measurement ofchlorophyll a fluorescence be used to predict sulphur deficiency in radish(Raphanus sativus L. sativus) plants[J]. Current Plant Biology, 2019, 19:100096.
[21] Galić V,Mazur M, Šimić D, et al. Plant biomass in salt-stressed young maize plants canbe modelled with photosynthetic performance[J]. Photosynthetica, 2019, 57:9-19.
[22] Faria-SilvaL, Gallon C Z, Filgueiras P R, et al. Irrigation improves plant vitality inspecific stages of mango tree development according to photosyntheticefficiency[J]. Photosynthetica, 2019, 57(3): 820-829.
[23] PietriniF, Carnevale M, Beni C, et al. Effect of Different Copper Levels on Growth andMorpho-Physiological Parameters in Giant Reed (Arundo donax L.) inSemi-Hydroponic Mesocosm Experiment[J]. Water, 2019, 11(9): 1837.
[24] Xie Y,Sun X, Feng Q, et al. Comparative physiological and metabolomic analyses revealmechanisms of Aspergillus aculeatus-mediated abiotic stress tolerance in tallfescue[J]. Plant Physiology and Biochemistry, 2019, 142: 342-350.
[25] RusinowskiS, Szada-Borzyszkowska A, Zieleźnik-Rusinowska P, et al. How autochthonousmicroorganisms influence physiological status of Zea mays L. cultivated onheavy metal contaminated soils [J]. Environmental Science and PollutionResearch, 2019, 26(5): 4746-4763.
[26] Fusaro L,Salvatori E, Mereu S, et al. Photosynthetic traits as indicators forphenotyping urban and peri-urban forests: A case study in the metropolitan cityof Rome[J]. Ecological indicators, 2019, 103: 301-311.
[27] Pérez-RomeroJ A, Duarte B, Barcia-Piedras J M, et al. Investigating the physiologicalmechanisms underlying Salicornia ramosissima response to atmospheric CO2enrichment under coexistence of prolonged soil flooding and saline excess[J].Plant physiology and biochemistry, 2019, 135: 149-159.
[28] de SouzaLopes J, da Costa K C P, Fernandes V S, et al. Functional traits associated tophotosynthetic plasticity of young Brazil nut (Bertholletia excelsa) plants[J].Flora, 2019, 258: 151446.
[29] Bąba W,Kompała-Bąba A, Zabochnicka-Świątek M, et al. Discovering trends inphotosynthesis using modern analytical tools: More than 100 reasons to usechlorophyll fluorescence[J]. 2019.Photosynthetica 57(2):668-679
[30] Yang T Y,Cai L Y, Qi Y P, et al. BioMed Research International Increasing NutrientSolution pH Alleviated Aluminum-induced Inhibition of Growth and Impairment ofPhotosynthetic Electron Transport Chain in Citrus sinensis Seedlings[J]. BioMedResearch International,2019
[31] Çicek N,Kalaji H M, Ekmekci Y. Probing the photosynthetic efficiency of some Europeanand Anatolian Scots pine populations under UV-B radiation using polyphasicchlorophyll a fluorescence transient[J]. Photosynthetica 2020, 58(2):468-478
[32] Kalaji HM, Račková L, Paganová V, et al. Can chlorophyll-a fluorescence parameters beused as bio-indicators to distinguish between drought and salinity stress inTilia cordata Mill [J]. Environmental and Experimental Botany, 2018, 152:149-157.
[33] SamborskaI A, Kalaji H M, Sieczko L, et al. Structural and functional disorder in thephotosynthetic apparatus of radish plants under magnesium deficiency[J].Functional Plant Biology, 2018, 45(6): 668-679.
[34] Boguszewska‐Mańkowska D, Pieczyński M, Wyrzykowska A, et al. Divergent strategies displayed bypotato (Solanum tuberosum L.) cultivars to cope with soil drought[J]. Journalof agronomy and crop science, 2018, 204(1): 13-30.
[35] Kalaji HM, Bąba W, Gediga K, et al. Chlorophyll fluorescence as a tool for nutrientstatus identification in rapeseed plants[J]. Photosynthesis research, 2018, 136(3):329-343.
[36] Duarte B,Cabrita M T, Vidal T, et al. Phytoplankton community-level bio-opticalassessment in a naturally mercury contaminated Antarctic ecosystem (DeceptionIsland) [J]. Marine environmental research, 2018, 140: 412-421.
[37] Arslan Ö,Eyidoğan F, Ekmekçi Y. Freezing tolerance of chickpea: biochemical andmolecular changes at vegetative stage[J]. Biologia Plantarum, 2018, 62(1):140-148.
[38] DigradoA, Bachy A, Mozaffar A, et al. Long‐term measurements of chlorophyll a fluorescence using the JIP‐test show that combined abiotic stressesinfluence the photosynthetic performance of the perennial ryegrass (Loliumperenne) in a managed temperate grassland[J]. Physiologia plantarum, 2017,161(3): 355-371.
[39] MarcińskaI, Czyczyło-Mysza I, Skrzypek E, et al. Application of photochemical parametersand several indices based on phenotypical traits to assess intraspecificvariation of oat (Avena sativa L.) tolerance to drought[J]. Acta PhysiologiaePlantarum, 2017, 39(7): 153.
[40] DigradoA, Gourlez de la Motte L, Bachy A, et al. Long-term field study of theinfluence of the photosynthetic performance of temperate grassland species onecosystem CO2 exchange fluxes at the ecosystem-scale[J]. Gembloux Agro-biotech,2017.
[41] Yang X Q,Zhang Q S, Zhang D, et al. Light intensity dependent photosynthetic electrontransport in eelgrass (Zostera marina L.) [J]. Plant Physiology andBiochemistry, 2017, 113: 168-176.
[42] SemerciA, Semerci H, Çalişkan B, et al. Morphological and physiological responses todrought stress of European provenances of Scots pine[J]. European Journal ofForest Research, 2017, 136(1): 91-104.
[43] MajewskaM L, Rola K, Zubek S. The growth and phosphorus acquisition of invasive plantsRudbeckia laciniata and Solidago gigantea are enhanced by arbuscularmycorrhizal fungi[J]. Mycorrhiza, 2017, 27(2): 83-94.
[44] Kalaji HM, Schansker G, Brestic M, et al. Frequently asked questions about chlorophyllfluorescence, the sequel[J]. Photosynthesis Research, 2017, 132(1): 13-66.
[45] DąbrowskiP, Baczewska A H, Pawluśkiewicz B, et al. Prompt chlorophyll a fluorescence asa rapid tool for diagnostic changes in PSII structure inhibited by salt stressin Perennial ryegrass[J]. Journal of Photochemistry and Photobiology B:Biology, 2016, 157: 22-31.
[46] Kalaji HM, Jajoo A, Oukarroum A, et al. Chlorophyll a fluorescence as a tool to monitorphysiological status of plants under abiotic stress conditions[J]. Actaphysiologiae plantarum, 2016, 38(4): 102.
[47] PollastriniM, Holland V, Brüggemann W, et al. Taxonomic and ecological relevance of thechlorophyll a fluorescence signature of tree species in mixed Europeanforests[J]. New Phytologist, 2016, 212(1): 51-65.
[48] Canton GC, Bertolazi A A, Cogo A J D, et al. Biochemical and ecophysiological responsesto manganese stress by ectomycorrhizal fungus Pisolithus tinctorius and inassociation with Eucalyptus grandis[J]. Mycorrhiza, 2016, 26(5): 475-487.
[49] JurczykB, Rapacz M, Pociecha E, et al. Changes in carbohydrates triggered by lowtemperature waterlogging modify photosynthetic acclimation to cold in Festucapratensis[J]. Environmental and experimental botany, 2016, 122: 60-67.
[50] Bąba W,Kalaji H M, Kompała-Bąba A, et al. Acclimatization of photosynthetic apparatusof tor grass (Brachypodium pinnatum) during expansion[J]. PloS one, 2016,11(6).
[51] Ogar A,Sobczyk Ł, Turnau K. Effect of combined microbes on plant tolerance to Zn–Pbcontaminations[J]. Environmental Science and Pollution Research, 2015, 22(23):19142-19156.
[52] Østrem L,Rapacz M, Larsen A, et al. Influences of growth cessation and photoacclimationon winter survival of non-native Lolium–Festuca grasses in high-latituderegions[J]. Environmental and Experimental Botany, 2015, 111: 21-31.
[53] Fusaro L,Salvatori E, Mereu S, et al. Urban and peri-urban forests in the metropolitanarea of Rome: Ecophysiological response of Quercus ilex L. in two greeninfrastructures in an ecosystem services perspective[J]. Urban Forestry &Urban Greening, 2015, 14(4): 1147-1156.
[54] Tyrka M,Rapacz M, Fiust A, et al. Quantitative trait loci mapping of freezing toleranceand photosynthetic acclimation to cold in winter two‐and six‐rowed barley[J]. Plant Breeding, 2015, 134(3): 271-282.
[55] Kalaji HM, Oukarroum A, Alexandrov V, et al. Identification of nutrient deficiency inmaize and tomato plants by in vivo chlorophyll a fluorescence measurements[J].Plant physiology and biochemistry, 2014, 81: 16-25.
[56] GiovenzanaV, Beghi R, Buratti S, et al. Monitoring of fresh-cut Valerianella locustaLaterr. shelf life by electronic nose and VIS–NIR spectroscopy[J]. Talanta,2014, 120: 368-375.
[57] Żurek G,Rybka K, Pogrzeba M, et al. Chlorophyll a fluorescence in evaluation of theeffect of heavy metal soil contamination on perennial grasses[J]. Plos one,2014, 9(3).
[58] SalvatoriE, Fusaro L, Gottardini E, et al. Plant stress analysis: Application of prompt,delayed chlorophyll fluorescence and 820 nm modulated reflectance. Insightsfrom independent experiments[J]. Plant physiology and biochemistry, 2014, 85:105-113.
[59] Zurek G,Rybka K, Pogrzeba M, et al. Chlorophyll a Fluorescence in Evaluation of theEffect of Heavy Metal Soil Contamination[J]. Plos one,2014.
[60] BlumenthalJ, Megherbi D B, Lussier R. Unsupervised machine learning via Hidden MarkovModels for accurate clustering of plant stress levels based on imagedchlorophyll fluorescence profiles & their rate of change in time[C]//2014IEEE International Conference on Computational Intelligence and VirtualEnvironments for Measurement Systems and Applications (CIVEMSA). IEEE, 2014:76-81.
[61] VanHeerden P D R. Differential acclimation capacity to frost in sugarcanevarieties grown under field conditions[J]. Plant Growth Regulation, 2014,72(2): 181-187.
[62] PotgieterC, De Beer M, Claassens S. The effect of canola (Brassica napus) as abiofumigant on soil microbial communities and plant vitality: a pot study[J].South African Journal of Plant and Soil, 2013, 30(4): 191-201.
[63] BresticM, Zivcak M. PSII fluorescence techniques for measurement of drought and hightemperature stress signal in crop plants: protocols andapplications[M]//Molecular stress physiology of plants. Springer, India, 2013:87-131.
[64] GoltsevV, Zaharieva I, Chernev P, et al. Drought-induced modifications ofphotosynthetic electron transport in intact leaves: analysis and use of neuralnetworks as a tool for a rapid non-invasive estimation[J]. Biochimica etBiophysica Acta (BBA)-Bioenergetics, 2012, 1817(8): 1490-1498.
[65] Jones MO, Piron-Prunier F, Marcel F, et al. Characterisation of alleles of tomatolight signalling genes generated by TILLING[J]. Phytochemistry, 2012, 79:78-86.
[66] GoltsevV, Zaharieva I, Chernev P, et al. Drought-induced modifications ofphotosynthetic electron transport in intact leaves: analysis and use of neuralnetworks as a tool for a rapid non-invasive estimation[J]. Biochimica etBiophysica Acta (BBA)-Bioenergetics, 2012, 1817(8): 1490-1498.
[67] MaboetaM, van Rensburg L. Vermicomposting of Industrial Organic Wastes and itsApplication in Mine Rehabilitation Strategies–An Overview from a South AfricanPerspective[J].2012
[68] Wagg S,Mills G, Hayes F, et al. OZONE AND DROUGHT STRESS INTERACTIONS IN BEAN ANDGRASSLAND SPECIES[J]. Programme &, 2011: 33.
[69] PollastriniM, Desotgiu R, Cascio C, et al. Growth and physiological responses to ozone andmild drought stress of tree species with different ecological requirements[J].Trees, 2010, 24(4): 695-704.
[70] Torres-RomeroD, King-Diaz B, Strasser R J, et al. Friedelane triterpenes from Celastrusvulcanicola as photosynthetic inhibitors[J]. Journal of agricultural and foodchemistry, 2010, 58(20): 10847-10854.
[71] Kirova M,Ceppi G, Chernev P, et al. Using artificial neural networks for plant taxonomicdetermination based on chlorophyll fluorescence induction curves[J].Biotechnology & Biotechnological Equipment, 2009, 23(sup1): 941-945.
[72] Pérez-MéndezA, Maldonado-Rodríguez R, Torres-Rivas E, et al. Pisum sativum classificationbased on a methodological approach for pattern recognition using discriminantanalysis and neural networks[J]. stress, 2005, 8(17): 18.
[73] Soja G,Soja A. Recognizing the sources of stress in wheat and bean by usingchlorophyll fluorescence induction parameters as inputs for neural networkmodels[J]. PHYTON-HORN-, 2005, 45(3): 157.
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