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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)。OJIP曲線可以更直觀地表現(xiàn)出差異,JIP-test則提供豐富的參數(shù),由于其測(cè)定方便簡(jiǎn)單,逐漸成為科研工作者們研究光合作用原初光化學(xué)反應(yīng)的有力工具。

在植物科學(xué)實(shí)驗(yàn)中,測(cè)定的實(shí)驗(yàn)數(shù)據(jù)非常多,比如光合作用參數(shù)、植物生長(zhǎng)指標(biāo)、各種酶活性以及分子實(shí)驗(yàn)數(shù)據(jù)等,再加上JIP-test本身提供的幾十種參數(shù),豐富實(shí)驗(yàn)數(shù)據(jù)的同時(shí),也會(huì)給后期的處理帶來很大的工作量。因此,采用準(zhǔn)確的數(shù)據(jù)處理分析方法尤其重要。
主成分分析法(PCA)是數(shù)據(jù)挖掘中常用的一種降維算法。所謂降維,就是把具有相關(guān)性的變量數(shù)目減少,用較少的變量來取代原先變量。在植物科學(xué)研究的實(shí)際應(yīng)用中,各種參數(shù)相互之間會(huì)有影響,通過PCA分析處理后,會(huì)得到有限的幾個(gè)主成分,由其代表實(shí)驗(yàn)參數(shù)就可以說明實(shí)驗(yàn)問題了,也就是所謂的降維(KalajiH M, et al., 2018;Goltsev V, et al., 2012)。

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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。下面通過三篇文章來詳細(xì)介紹二者的結(jié)合應(yīng)用。

1. 解析參數(shù)間的相關(guān)性,篩選出可禁用詞匯解釋問題的參數(shù)(Jurczyk B,2015)

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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。研究結(jié)果表明,淹水溫度是影響植物對(duì)該脅迫反應(yīng)的重要因素。該試驗(yàn)研究了耐寒性不同的四種高羊茅在低溫下對(duì)土壤水分過剩的光合機(jī)構(gòu)響應(yīng),旨在驗(yàn)證Rubisco活性改變引起的葉片水溶性碳水化合物濃度變化是否會(huì)影響土壤水分過剩條件下的光適應(yīng)。

通過研究低溫淹水對(duì)葉綠素 a 熒光參數(shù)、水溶性碳水化合物(WSC)、Rubisco活化酶基因表達(dá)(RcaA)Rubisco活性(RA)的影響,并進(jìn)行PCA主成分分析,以減少需要進(jìn)行詳細(xì)分析的參數(shù)數(shù)量,并篩選出能禁用詞匯解釋問題的參數(shù)。

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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

淹水脅迫會(huì)直接導(dǎo)致植物水下組織供氧不足,缺氧后植物會(huì)加速使用碳儲(chǔ)備進(jìn)而導(dǎo)致碳源供應(yīng)不足。主成分分析證實(shí),由圖1可以看出,淹水脅迫后,被測(cè)變量之間的關(guān)系發(fā)生顯著性改變。在對(duì)照條件時(shí),水溶性碳水化合物與能量傳遞效率相關(guān)參數(shù)(ETo/TRo、ETo/ABS、ETo/RC)有很高的正相關(guān)性,說明WSC的積累在對(duì)照條件下是不受限制的淹水后,WSC與能量耗散效率(DIo/CS、DIo/RC)呈正相關(guān),說明能量轉(zhuǎn)移的干擾可能限制了WSC的濃度。
另一方面,WSC與描述單個(gè)活性反應(yīng)中心效率的參數(shù)高度相關(guān),揭示了類囊體膜可能也因淹水受到損傷。此外,qP和RcaA在對(duì)照植株中的表達(dá)之間的強(qiáng)相關(guān)性可能表明這兩個(gè)性狀的調(diào)控機(jī)制相似,可能與ADP/ATP比值有關(guān)。在淹水條件下,qP和RcaA的表達(dá)不相關(guān),提示另一個(gè)因素可能調(diào)節(jié)RcaA轉(zhuǎn)錄水平。
總的來說低溫淹水后,酶活性劇烈下降,光反應(yīng)階段吸收的光能過剩,維持較高的WSC含量能夠激活光合作用適應(yīng)寒冷的熱耗散機(jī)制,有助于耗散掉過剩光能。
2. 聚類分析不同處理之間的差異(Zhiponova M, 2020)

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光是控制植物生長(zhǎng)發(fā)育的主要因素。光不僅推動(dòng)植物光合作用,光質(zhì)和光照時(shí)間還驅(qū)動(dòng)著植物主要的發(fā)育變化,如光形態(tài)發(fā)生、開花的光周期誘導(dǎo)、向光性、避蔭以及防御等。為了評(píng)估光照條件對(duì)植物生理狀態(tài)的影響,該研究在豌豆植株的早期發(fā)育過程中使用正常白光(W)、白色陰影(WS)、高光強(qiáng)藍(lán)/紅/遠(yuǎn)紅組合光(BR)和低光強(qiáng)藍(lán)/紅/遠(yuǎn)紅組合光(BRS)四種光照射,采用JIP-test來評(píng)估與光吸收和電子傳輸有關(guān)的PSII參數(shù),并通過PCA技術(shù)聚類分析不同光照之間的差異。

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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)

對(duì)獲得的JIP-test參數(shù)進(jìn)行主成分分析表明,盡管不同處理之間存在重疊,但它們對(duì)光合機(jī)構(gòu)的影響差異還是很容易區(qū)分的。
PC1根據(jù)PSII活性分離出不同的處理,較低的值表示更高的PSII性能(低光吸收、高光化學(xué)和電子傳輸效率);PC2則對(duì)應(yīng)PSI活性,較高的值表明PSI性能較高。
W處理表現(xiàn)出PSI和PSII的禁用詞匯綜合性能;WS處理表現(xiàn)出PSI和PSII的禁用詞匯綜合性能;BR處理表現(xiàn)出受損的PSII和完整的PSI活性;BRS處理表現(xiàn)出低PSI和完整的PSII性能。
結(jié)合其他生理數(shù)據(jù)和主成分分析可以揭示光合作用與開花的關(guān)系。具有高PSII表現(xiàn)(-PC1)的W和BRS處理在其發(fā)育后期發(fā)育出相同數(shù)量的花,而具有抑制PSII活性(+PC1)的WS和BR植株發(fā)育后期沒有開花。
研究結(jié)果表明,PIABS在PC1上最相關(guān),可作為預(yù)測(cè)豌豆開花數(shù)量的最準(zhǔn)確指標(biāo)。
3. 通過PCA技術(shù)對(duì)大樣本試驗(yàn)進(jìn)行數(shù)據(jù)分析(Bussotti F, 2020)

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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。人們提出了許多形態(tài)、化學(xué)和生理指標(biāo)來評(píng)價(jià)生態(tài)系統(tǒng)中的植物狀況。其中,葉綠素的瞬時(shí)熒光分析(JIP-test)被認(rèn)為特別適用于大型生態(tài)調(diào)查,并能在短時(shí)間內(nèi)篩選出許多樣品。

JIP-test提供了五十多個(gè)參數(shù)來評(píng)估植物光合機(jī)構(gòu)的光化學(xué)性質(zhì)和功能,這些參數(shù)可以描述光化學(xué)過程在能量吸收、俘獲和電子傳輸方面的不同階段。
該研究采用主成分分析法(PCA)對(duì)過去在野外條件(森林、人工林和牧場(chǎng))和實(shí)驗(yàn)室條件中獲得的43987個(gè)測(cè)量數(shù)據(jù)進(jìn)行分析,目的是探討JIP-test參數(shù)之間的關(guān)系,以選擇最合適的參數(shù)來捕捉植物光合效率的變異性及其對(duì)逆境的響應(yīng)。

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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)。此項(xiàng)目中分析了整個(gè)歐洲的森林生態(tài)系統(tǒng),從地中海到歐洲北部地區(qū),涵蓋了豐富的差異樹種組成。其中包括天然高大森林(In Italy, Spain, Romania,Poland,Finland, Baeten et al., 2013)和人工林場(chǎng)(In Finland and Germany, seeVerheyen et al.,2016)。

通過PCA技術(shù)分析發(fā)現(xiàn),所選的JIP-test參數(shù)形成了三個(gè)很好分離的簇。其中兩個(gè)位于PC1(Cluster 1&2)上,一個(gè)(Cluster 3)位于PC2上。每一組參數(shù)描述了不同的生理過程:光能捕獲和光化學(xué)階段(Cluster 1)、耗散(Cluster 2)和熱階段(Cluster 3)。基于PCA分析,該研究認(rèn)為樣品的整體光合性能可以用PITOT來表示,或者用Fv/Fm和ΔVIP共同來表示。

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圖3. 所選JIP-test參數(shù)的主成分分析

在大多數(shù)情況下,植物的光合性能可用Fv/Fm和ΔVIP來描述。經(jīng)過驗(yàn)證,F(xiàn)v/Fm和ΔVIP能夠有效地代表各種調(diào)查(野外和實(shí)驗(yàn)室)、氣候和時(shí)間跨度、植物物種和功能群(針葉樹和闊葉樹物種、草本植物)中樣本的變異性。因此,可用于探索性調(diào)查,以篩選大樣本植物的光合性能,以及它們對(duì)不同生態(tài)條件的適應(yīng)性。
在林業(yè)或生態(tài)學(xué)調(diào)查方面,以JIP-test為代表的植被葉綠素?zé)晒馓匦缘拇笠?guī)模野外調(diào)查對(duì)驗(yàn)證無人機(jī)或衛(wèi)星遙感觀測(cè)結(jié)果具有重要意義,遙感觀測(cè)數(shù)據(jù)和野外實(shí)地調(diào)查數(shù)據(jù)之間的銜接將是今后生態(tài)學(xué)研究的一個(gè)重要領(lǐng)域(Bussotti F, 2020)!
總述
以上實(shí)例說明,PCA分析與JIP-test結(jié)合應(yīng)用越來越廣泛,大大提高了數(shù)據(jù)分析效率,能夠快速判斷實(shí)驗(yàn)處理后的主要變化,并分析主要影響因素,從而對(duì)實(shí)驗(yàn)材料進(jìn)行預(yù)判。近年來,PCA在植物科學(xué)研究中的應(yīng)用呈上升趨勢(shì),相信科研工作者們會(huì)開發(fā)出更多更好的應(yīng)用方向。

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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!

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