唐娟 望飛勇 張?zhí)m
摘? ? 要:【目的】通過比較砂糖橘和砂糖燈籠橘性狀差異及利用轉(zhuǎn)錄組測序數(shù)據(jù),篩選砂糖橘和砂糖燈籠橘葉、果肉、橘絡(luò)、橘皮之間的差異基因,探究砂糖橘自然變異品種砂糖燈籠橘橘皮、葉中與蠟質(zhì)生物合成相關(guān)的顯著差異基因?!痉椒ā糠謩e取同一生長時(shí)期的砂糖燈籠橘和砂糖橘進(jìn)行觀察記錄,取葉、果肉、橘絡(luò)、橘皮4個(gè)組織樣本,液氮速凍,設(shè)立3個(gè)生物學(xué)重復(fù)進(jìn)行轉(zhuǎn)錄組測序。分析2個(gè)物種間的轉(zhuǎn)錄組測序結(jié)果,尋找關(guān)鍵差異基因?!窘Y(jié)果】通過砂糖燈籠橘與砂糖橘對比,砂糖燈籠橘葉較大、卷曲,邊緣性狀不規(guī)則;果實(shí)偏大,果皮表面布滿溝壑,存在較多點(diǎn)狀突起,同時(shí)葉和果皮部位存在蠟質(zhì)缺失。砂糖燈籠橘葉存在差異基因數(shù)量最多,其次為果肉、皮、橘絡(luò),差異基因主要參與的功能為蛋白結(jié)合、分子結(jié)合、ATP結(jié)合。砂糖燈籠橘葉、果皮分別存在12個(gè)、9個(gè)與蠟質(zhì)生物合成相關(guān)的顯著差異基因,其中包含5個(gè)相同的下調(diào)基因,為CER1、CER3、HHT、P45086A8、P45086A22,這些基因極有可能是導(dǎo)致砂糖燈籠橘表面蠟質(zhì)排布不均的關(guān)鍵基因?!窘Y(jié)論】砂糖橘與砂糖燈籠橘性狀差異明顯,轉(zhuǎn)錄組數(shù)據(jù)顯示葉的差異基因數(shù)量最多,其中葉和果皮中存在5個(gè)表達(dá)趨勢一致的相同蠟質(zhì)合成基因,可能是導(dǎo)致砂糖燈籠橘表面蠟質(zhì)缺失的關(guān)鍵基因。
關(guān)鍵詞:砂糖燈籠橘;砂糖橘;性狀;轉(zhuǎn)錄組;蠟質(zhì)
中圖分類號:S666.2 文獻(xiàn)標(biāo)志碼:A 文章編號:1009-9980(2023)09-1811-12
收稿日期:2023-02-06 接受日期:2023-05-28
基金項(xiàng)目:廣西壯族自治區(qū)科技基地與人才專項(xiàng)(桂科AD20325012)
作者簡介:唐娟,女,助理研究員,研究方向?yàn)楣麡浞N質(zhì)資源收集及育種。Tel:0771-3246396,E-mail:240918087@qq.com
*通信作者 Author for correspondence. Tel:15977480220,E-mail:zhanglan2008@163.com
Transcriptome analysis based on the characteristic difference between Shatang tangerine and Shatang Lantern tangerine
TANG Juan, WANG Feiyong, ZHANG Lan*
(Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China)
Abstract: 【Objective】 In order to investigate the reason for characteristic differences between Shatang tangerine (Citrus reticulat) and Shatang Lantern tangerine, we compared the size of plants, waxy arrangement and transcriptome information. By using transcriptome sequencing data, we screened out the differential genes among the leaves, pulp, tangerine pith and peel of Shatang tangerine and Shatang Lantern tangerine, and explored the significant differential genes related to wax biosynthesis in the peel and leaves. 【Methods】 Four types of tissue samples including leaf, pulp, tangerine pith and peel were taken at the same growth period and frozen in liquid nitrogen immediately for transcriptome sequencing. Three biological replicates were set up for every experiment. Characteristic analysis and toluidine blue staining experiment were observed and recorded by naked eyes. The transcriptome sequencing results between the two samples were analyzed to find out the key differential genes. The change threshold set as the absolute value of log2FC (fold change) was greater than or equal to 1 (FC greater than or equal to 2) and q value was less than 0.05. Besides, we used https://www.omicstudio.cn/index as a tool to analyze difference genes, like GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. 【Results】 Compared with Shatang tangerine, the leaves of Shatang Lantern tangerine were larger and curly, and had irregular edge. The fruit was larger and had a coarse and roughly textured rind. The peel in Shatang Lantern tangerine showed obvious gully, and the surface of the peel was full of dots, like a “l(fā)antern”. After toluidine blue staining, the peel and leave of Shatang Lantern tangerine was covered with dye, indicating that the waxy composition in these parts was loosely distributed. After filtering raw sequencing data of transcriptome, the effective data size was 6.32-8.00 G, respectively. Besides, the effective data accounted for more than 96% of the original data, among which the bases with mass value ≥30 accounted for more than 97% (Q 30%), indicating that the quality of the measured transcriptomic data was good and the results were reliable. When compared with the reference genome of Citrus clementina, the matching rate was 93.32%-95.17%, which could meet the conditions of subsequent bioinformatics analysis. Through comparative analysis of transcriptome data, there were more differential genes in the leave of Shatang Lantern tangerine, followed by pulp, peel and tangerine pith. The main functions of differential genes were protein binding, molecular binding and ATP binding. The number of differential genes ranked in descending order was leaf, pulp, pericarp and tangerine pith, the number of up-regulated genes ranked in descending order was leaf, pulp, pericarp and tangerine pith, which was the same as the number of down-regulated genes. The number of differential genes in leaves were much higher than that of other tissue parts, and the number of down-regulated genes was the largest (3239), followed by the number of up-regulated genes (2443). Tangerine pith had the lowest number of differential genes. 【Conclusion】 These results indicated that the differences between Shatang tangerine and Shatang Lantern tangerine were mainly reflected in leaves, pulp and peel, which was consistent with the results observed by naked eyes. According to the differences in wax distribution of the two cultivars, the genes involved in the keratin, suberin and waxy biosynthesis pathway (map00073) were analyzed. There were 12 and 9 different genes related to wax biosynthesis in the leaf and peel of Shatang Lantern tangerine, respectively, including 5 identical down-regulated genes, named as CER1, CER3, HHT, cytochrome P45086A8 and cytochrome P45086A22. These genes were highly likely to be the key genes causing uneven waxy distribution on the surface of Shatang Lantern tangerine. Most of the differential genes were down-regulated except FACR2 in pericarp and cytochrome P45086B1 and cytochrome P45096A1 in leaf. Therefore, the characteristics of Shatang tangerine and Shatang Lantern tangerine were significantly different including morphology and waxy distribution. The transcriptome data showed that the number of differentially expressed genes was largest in the leaves, and there were five identical wax synthesis genes with the same expression trend in the middle leaves and the peel, which may be the key genes leading to the loss of wax on the surface of Shatang Lantern tangerine.
Key words: Shatang Lantern tangerine; Shatang tangerine; Character; Transcriptome; Wax
砂糖燈籠橘(Shatang Lantern tangerine)為砂糖橘[1]的自然變異品種,其表皮布滿溝壑,酷似燈籠,故而得名。砂糖燈籠橘產(chǎn)地為廣西,形態(tài)獨(dú)特美觀,口感較砂糖橘好,糖度高,深受廣大消費(fèi)群體歡迎。對該變異進(jìn)行品質(zhì)相關(guān)研究具有重要意義。
依靠目前RNA-Seq技術(shù)獲得的轉(zhuǎn)錄組數(shù)據(jù)在植物功能基因挖掘、植物性狀分析、輔助植物育種方面已獲得較多成果。如葛卉等[2]通過對金枝黃花柳親本及回交子代進(jìn)行轉(zhuǎn)錄組測序,發(fā)現(xiàn)兩者葉綠素合成酶相關(guān)基因表達(dá)量出現(xiàn)差異,從而使代謝通路發(fā)生變化,進(jìn)而導(dǎo)致枝條顏色存在明顯差異。蔡宇等[3]通過建立溝葉結(jié)縷草的Illumina高通量測序平臺,以野生型和多穗突變體為樣本進(jìn)行轉(zhuǎn)錄組測序,挖掘與花序發(fā)育相關(guān)的重要基因,結(jié)合WGCNA分析認(rèn)為EHD1、MADS14為影響花序發(fā)生的關(guān)鍵基因,為溝葉結(jié)縷草的植物育種提供了關(guān)鍵的技術(shù)支撐。轉(zhuǎn)錄組數(shù)據(jù)結(jié)合植物形狀分析往往能提供更多的參考證據(jù),如鄭雪夢等[4]通過對京欣3號、甜王2種硬度不同的西瓜進(jìn)行轉(zhuǎn)錄組數(shù)據(jù)測序,分析后發(fā)現(xiàn)硬度較大的甜王與碳水化合物代謝、脂質(zhì)代謝途徑相關(guān)的基因與京欣3號具有顯著性差異,通過生物信息學(xué)分析為品種篩選提供了參考依據(jù)。通過對草莓白肉突變體小白及親本草莓紅顏的轉(zhuǎn)錄組測序,范小青等[5]發(fā)現(xiàn)小白草莓中存在參與苯丙素、類黃酮、黃酮、黃酮醇生物合成途徑的差異基因,這些基因與花青素代謝具有密切的關(guān)聯(lián),該研究為草莓花色苷形成提供了理論依據(jù),也為白草莓的育種提供了一定的支持。劉戀等[6]針對同一遺傳背景下的3個(gè)金柑品種的果皮性狀差異,選取了同一時(shí)期的滑皮金柑、融安金柑、脆蜜金柑的果皮進(jìn)行轉(zhuǎn)錄組測序,發(fā)現(xiàn)融安金柑在苯丙烷生物合成途徑中的關(guān)鍵基因的表達(dá)與其他兩者存在明顯差異,并且木質(zhì)素合成相關(guān)基因的表達(dá)量明顯降低,進(jìn)而果皮表現(xiàn)出韌性差、易失水的特征。由此可見,通過轉(zhuǎn)錄組測序技術(shù)可以從分子水平上對植物性狀進(jìn)行探究,可以挖掘重要的特征基因,有助于更好地利用基因工程技術(shù)實(shí)現(xiàn)品種的高產(chǎn)及優(yōu)質(zhì)生產(chǎn),對植物育種的發(fā)展具有顯著意義。
柑橘類物種果實(shí)表面布滿蠟質(zhì),是植物抵御外界病蟲害的第一層保護(hù)屏障,同時(shí)有研究發(fā)現(xiàn),蠟質(zhì)對果實(shí)保水、延緩衰老及貯藏保鮮等具有重要作用[7],目前果實(shí)蠟質(zhì)生物合成途徑已經(jīng)基本被解析清楚,蠟質(zhì)排布及蠟質(zhì)含量對于植物的品質(zhì)極其重要[8-9]。同時(shí),干旱、鹽脅迫等環(huán)境對于植物表面蠟質(zhì)生物合成也極其重要,呂慧等[10]通過測定不同土壤含水量、不同鈉鹽環(huán)境下生長的辣椒轉(zhuǎn)錄組數(shù)據(jù),發(fā)現(xiàn)干旱、鹽脅迫主要影響苯丙烷的生物合成途徑,適度的脅迫會(huì)使辣椒素積累更多。Tanaka等[11]利用甲苯胺藍(lán)染液對擬南芥葉片進(jìn)行染色,發(fā)現(xiàn)對于表面蠟質(zhì)缺失或排列分布不均的擬南芥葉片,甲苯胺藍(lán)能夠快速將其染色,大大加快了蠟質(zhì)分布的檢測速度,因此該方法廣泛應(yīng)用于植物中。
目前砂糖燈籠橘相關(guān)的研究報(bào)道較少,筆者以同一產(chǎn)地、同一生長時(shí)期的砂糖橘、砂糖燈籠橘為研究材料,對其表型進(jìn)行觀察對比,同時(shí)取葉、果實(shí)、橘絡(luò)、果肉4個(gè)組織部位分別進(jìn)行轉(zhuǎn)錄組測序,進(jìn)行對比分析,重點(diǎn)關(guān)注與蠟質(zhì)生物合成相關(guān)的關(guān)鍵基因,研究結(jié)果可為探究砂糖燈籠橘表型特異性原因及蠟質(zhì)生物合成的變化提供分子水平上的理論支持及參考。
1 材料和方法
1.1 試驗(yàn)材料
砂糖燈籠橘及砂糖橘(Citrus reticulata ‘Shiyue Ju)產(chǎn)地均為廣西,砂糖燈籠橘樣本為自然變異品種,均為3年生植株,采收于2021年10月下旬。選擇成熟程度相近、大小相仿的果實(shí),按照果肉、橘絡(luò)、果皮、葉4個(gè)部位進(jìn)行分離,果肉保留囊衣,果皮保留白皮層,分別取3株砂糖燈籠橘、砂糖橘植物,設(shè)立3個(gè)生物學(xué)重復(fù),用錫箔紙包裹,依次編號,迅速放置于液氮速凍,將樣本送至杭州聯(lián)川生物技術(shù)股份有限公司進(jìn)行轉(zhuǎn)錄組測序。對測序得到的原始數(shù)據(jù)進(jìn)行質(zhì)控、差異基因分析及篩選。
1.2 性狀分析
分別取相同生長發(fā)育時(shí)期的砂糖燈籠橘及砂糖橘果實(shí)、葉,對其表觀形態(tài)進(jìn)行觀察記錄,比較性狀差異。
1.3 蠟質(zhì)排布分析
分別取砂糖燈籠橘、砂糖橘的橘皮、葉,置于甲苯胺藍(lán)染色液(1%)中浸泡2~4 h,清水沖洗0.5 h,比較染色部位的差異。
1.4 轉(zhuǎn)錄組數(shù)據(jù)分析
委托聯(lián)川生物技術(shù)公司對樣品進(jìn)行RNA提取及轉(zhuǎn)錄組測序。
通過Cutadapt等[12]將含接頭、polyA、polyG的reads、N>5%的reads、低質(zhì)量reads等去除,獲得有效數(shù)據(jù)。以柑橘屬克里曼丁橘(Citrus ‘Clementina)參考基因組數(shù)據(jù)為參照,使用HISAT2(https://ccb.jhu.edu/software/hisat2)[13-15]進(jìn)行比對,使用StringTie軟件(https://ccb.jhu.edu/software/hisat2)[14,16-17] 對轉(zhuǎn)錄本進(jìn)行組裝并用FPKM[15,18]定量。分別對砂糖燈籠橘、砂糖橘4個(gè)組織部位的轉(zhuǎn)錄組數(shù)據(jù)進(jìn)行比較分析。針對物種間性狀差異,篩選可能引起表型差異的關(guān)鍵基因。使用R包edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html)對樣本之間的差異基因進(jìn)行分析,設(shè)定變化閾值為log2FC(fold change)絕對值≥1(差異倍數(shù)FC≥2),同時(shí)q值<0.05作為篩選兩者差異基因的標(biāo)準(zhǔn)。對篩選得到的差異基因進(jìn)行統(tǒng)計(jì)分析,利用聯(lián)川生物云平臺(https://www.omicstudio.cn/index)的在線繪圖工具繪制GO富集分析[19-20]、KEGG通路富集分析[21]圖。
2 結(jié)果與分析
2.1 砂糖燈籠橘、砂糖橘的性狀特征
對同一時(shí)期的砂糖燈籠橘、砂糖橘葉及成熟果實(shí)外觀形態(tài)進(jìn)行觀察比對(圖1),發(fā)現(xiàn)砂糖燈籠橘葉卷曲程度比砂糖橘明顯,砂糖燈籠橘葉偏大,且葉邊緣呈現(xiàn)不規(guī)則形態(tài),而砂糖橘邊緣較平滑;砂糖燈籠橘果實(shí)較砂糖橘偏大,且果皮呈現(xiàn)明顯的溝壑,果皮表面布滿點(diǎn)狀突起,形似“燈籠”。
2.2 砂糖燈籠橘、砂糖橘蠟質(zhì)分布
如圖2所示,甲苯胺藍(lán)染料能對植物表面蠟質(zhì)排布不均勻的地方進(jìn)行染色,通過對砂糖燈籠橘、砂糖橘果皮及葉的染色實(shí)驗(yàn),發(fā)現(xiàn)蠟質(zhì)分布不均勻且主要存在于果臍附近,砂糖橘整個(gè)外果皮能被均勻染色,而砂糖燈籠橘僅果實(shí)表面突起的位置極易被染色,這部分蠟質(zhì)缺失現(xiàn)象較明顯,說明在自然變異過程中,砂糖燈籠橘中存在的某些與蠟質(zhì)生物合成相關(guān)基因在轉(zhuǎn)錄水平表達(dá)量發(fā)生變化,進(jìn)而導(dǎo)致這種現(xiàn)象發(fā)生。
2.3 砂糖燈籠橘、砂糖橘轉(zhuǎn)錄組測序質(zhì)量評估
將高通量測序后的原始數(shù)據(jù)去除接頭、未識別數(shù)據(jù)等獲得有效數(shù)據(jù)。通過基因組比對,對各基因的表達(dá)量進(jìn)行分析。
經(jīng)過過濾后有效數(shù)據(jù)大小為6.32~8.00 G,從表1中可以看出,有效數(shù)據(jù)占原始數(shù)據(jù)的比例均為96%以上,而其中質(zhì)量值≥30的堿基所占的比例(Q 30%)皆大于97%,說明測得的轉(zhuǎn)錄組數(shù)據(jù)質(zhì)量較好、結(jié)果真實(shí)可信。與克里曼丁橘參考基因組進(jìn)行比對,其匹配率為93.32%~95.17%,能夠滿足后續(xù)生物信息學(xué)分析的條件。
2.4 砂糖燈籠橘、砂糖橘差異表達(dá)基因分析
分別對砂糖燈籠橘、砂糖橘中提取得到的有效基因進(jìn)行統(tǒng)計(jì)分析,對葉、果肉、橘絡(luò)、果皮4個(gè)組織部位的差異基因進(jìn)行比較(圖3)。發(fā)現(xiàn)差異基因數(shù)量總數(shù)排列為葉>果肉>果皮>橘絡(luò),上調(diào)基因數(shù)量排列為葉>果肉>果皮>橘絡(luò),下調(diào)基因數(shù)量排列為葉>果肉>果皮>橘絡(luò);砂糖燈籠橘葉的上、下調(diào)差異基因數(shù)量遠(yuǎn)高于其他組織部位,下調(diào)基因的數(shù)量最多,為3239個(gè),其次是上調(diào)基因的數(shù)量,為2443個(gè);橘絡(luò)的差異基因數(shù)量最少。這些結(jié)果說明砂糖燈籠橘、砂糖橘的差異主要體現(xiàn)在葉、果肉、果皮這3個(gè)部位,這與肉眼觀察到的結(jié)果一致。
同時(shí),對不同組織的差異基因分別進(jìn)行GO、KEGG分析。結(jié)果發(fā)現(xiàn),葉內(nèi)顯著差異基因主要參與的KEGG通路包括植物-病原互作、核糖體、ABC轉(zhuǎn)運(yùn)蛋白、半乳糖代謝、磷酸肌醇代謝。GO分析顯示,差異基因主要參與的生物學(xué)過程為抗逆、生物反應(yīng)、DNA復(fù)制的轉(zhuǎn)錄調(diào)控;差異基因主要位于細(xì)胞核、質(zhì)膜、膜整體組件;參與的分子功能為蛋白結(jié)合、分子結(jié)合、ATP結(jié)合。果肉顯著差異基因參與的KEGG通路主要為植物激素信號傳導(dǎo)、類苯基丙烷生物合成、淀粉和蔗糖代謝、黃酮類生物合成、半乳糖代謝。GO分析顯示其參與的生物學(xué)過程包括DNA復(fù)制的轉(zhuǎn)錄調(diào)控、DNA復(fù)制的轉(zhuǎn)錄、生物反應(yīng);這些基因的分子功能為蛋白結(jié)合、分子結(jié)合、ATP結(jié)合;與葉子GO分析結(jié)果相同的是,果肉的差異基因同樣位于細(xì)胞核、質(zhì)膜、膜整體組件。對果皮的顯著差異基因進(jìn)行KEGG分析后,發(fā)現(xiàn)其參與的通路主要為類苯基丙烷生物合成、光合作用、黃酮類生物合成、芪類、雙苯庚烷及姜辣素生物合成、光合生物體的固碳作用。GO分析結(jié)果顯示,果皮差異基因參與的生物學(xué)過程、基因定位及分子功能與果肉完全一致,但從具體的基因功能來看,果肉組織的差異基因主要在細(xì)胞壁、胞外區(qū)、質(zhì)膜部位參與作用,其主要功能為DNA結(jié)合轉(zhuǎn)錄因子活性;而果皮的差異基因主要位于細(xì)胞膜、葉綠體類囊體及膜,其功能主要為氧化還原酶活性、參與次生代謝生物合成過程。對橘絡(luò)的顯著差異基因進(jìn)行KEGG分析后發(fā)現(xiàn),其主要參與類苯基丙烷的生物合成、黃酮類生物合成、過氧物酶體、芪類、雙苯庚烷、姜辣素的生物合成,氨基糖、核苷酸糖的代謝。GO分析顯示橘絡(luò)中的大部分差異基因功能為黃酮類生物合成、黃酮類糖脂化、木質(zhì)素生物合成、氧化還原酶、植物型次生細(xì)胞壁生物合成等。橘絡(luò)差異基因的生物學(xué)過程包括DNA復(fù)制的轉(zhuǎn)錄調(diào)控、生物反應(yīng)、氧化還原過程;這些基因主要位于細(xì)胞核、質(zhì)膜、膜整體組件;其分子功能為蛋白結(jié)合、DNA結(jié)合轉(zhuǎn)錄因子活性、分子結(jié)合。
砂糖燈籠橘果皮在外觀形態(tài)上與砂糖橘明顯不同,為了對其差異性狀進(jìn)行更深入的解析,篩選果皮內(nèi)p<0.01的顯著差異基因,進(jìn)行富集分析。
砂糖燈籠橘果皮上調(diào)基因共669個(gè),從GO富集結(jié)果(圖4)可以看出,大部分差異基因?yàn)樯锓磻?yīng)類,其次是分子功能,差異數(shù)量最多的基因其功能為氧化還原作用、次生代謝產(chǎn)物合成及DNA復(fù)制。從通路富集結(jié)果可以看出,差異數(shù)量最多的基因與苯丙素生物合成相關(guān),其次是黃酮類生物合成、芥子油苷生物合成。
砂糖燈籠橘果皮下調(diào)基因共775個(gè),超過一半的差異基因?yàn)榧?xì)胞組分1類,主要與細(xì)胞膜、細(xì)胞器膜有關(guān)。在生物反應(yīng)1類中,差異基因主要參與了氧化還原反應(yīng)、水楊酸響應(yīng)及DNA復(fù)制。從KEGG通路分析可知,差異基因參與了光反應(yīng)、苯丙素的生物合成、半乳糖代謝等過程(圖5)。值得注意的是,砂糖燈籠橘中與角質(zhì)層、蠟質(zhì)合成相關(guān)基因的表達(dá)量呈現(xiàn)明顯變化,這可能是砂糖燈籠橘呈現(xiàn)出表型差異的重要原因。
2.5 砂糖燈籠橘、砂糖橘調(diào)控蠟質(zhì)生物合成相關(guān)基因篩選
根據(jù)前期的甲苯胺藍(lán)染色實(shí)驗(yàn)結(jié)果,初步推測砂糖燈籠橘、砂糖橘在蠟質(zhì)生物合成基因表達(dá)上存在著明顯的差異,因此重點(diǎn)對果皮和葉的蠟質(zhì)生物合成相關(guān)基因進(jìn)行統(tǒng)計(jì)分析。初步篩選砂糖橘、砂糖燈籠橘果皮差異基因中參與到角質(zhì)、軟木脂、蠟質(zhì)生物合成途徑(map00073)的基因,共得到40個(gè)基因。以log2FC的絕對值≥1且q值<0.05作為標(biāo)準(zhǔn)篩選具有顯著性差異的基因,得到了9個(gè)基因,分別為LOC18055362 (CER3 isoform X1)、LOC18038381(FACR2)、LOC18048646(cytochrome P45086A22)、LOC18035687(HHT)、LOC18049733(CER1 isoform?X2)、LOC18046005(cytochrome P45086A8)、LOC-18039129(CER1)、LOC18039665(hypothetical protein CICLE_v10013412mg)、LOC18044180(TAT),除FACR2基因上調(diào)外,其余基因表達(dá)量均降低。
對葉片參與蠟質(zhì)生物合成途徑的差異基因進(jìn)行篩選,獲得了40個(gè)差異基因,以log2FC的絕對值≥1且q值<0.05為原則篩選其中的顯著差異基因,共獲得12個(gè)基因,分別為LOC18055362 (CER3 isoform X1)、LOC18049733(CER1 isoform X2)、LOC18037666(alkane hydroxylase MAH1-like)、LOC18037897(cyto-
chrome P45096A1)、LOC18049734(CER1)、LOC180-35687(HHT)、LOC18052048(omega-hydroxypalmitate O-feruloyl transferase)、LOC18034580(hypothetical protein CUMW_152270)、LOC18046005(cytochrome P45086A8)、LOC18048646(cytochrome P45086A22)、LOC18044337(cytochrome P45086B1)和LOC18036471(ERF011)。砂糖燈籠橘葉的上調(diào)基因?yàn)長OC18037897、LOC18044337,其余基因皆下調(diào)。
對葉片、果皮篩選與蠟質(zhì)合成相關(guān)的顯著差異基因繪制韋恩圖(圖6),其中2個(gè)組織部位存在5個(gè)相同的基因,分別為LOC18055362、LOC18048646、LOC18035687、LOC18049733、LOC18046005,與砂糖橘相比,這些基因呈現(xiàn)明顯的下調(diào),提示這些基因可能與砂糖燈籠橘蠟質(zhì)的生物合成密切相關(guān);同時(shí),葉中獨(dú)立存在7個(gè)與蠟質(zhì)合成相關(guān)的顯著差異基因,果皮中存在4個(gè)與蠟質(zhì)合成相關(guān)的顯著差異基因,說明不同組織部位與蠟質(zhì)生物合成相關(guān)基因的表達(dá)存在獨(dú)特性。
3 討 論
植物自然突變體[22]是植物在生長發(fā)育過程中,其基因組內(nèi)某些基因突變,從而導(dǎo)致其出現(xiàn)性狀或代謝物成分變化從而形成的新的個(gè)體。對于突變體的研究通常是從植物的表型、遺傳物質(zhì)角度出發(fā),與野生型植株進(jìn)行性狀及轉(zhuǎn)錄組數(shù)據(jù)的比較分析,找到突變的分子機(jī)制。
基于的Illumina的測序技術(shù)[23-24]已被證明轉(zhuǎn)錄組學(xué)適用于植物基因注釋、基因表達(dá)分析以及通路研究。本研究中,以自然突變的砂糖燈籠橘、其同源砂糖橘為樣本進(jìn)行二代轉(zhuǎn)錄組測序,篩選后發(fā)現(xiàn)不同組織部位差異基因數(shù)量各不相同,趨勢為葉>果肉>果皮>橘絡(luò)。經(jīng)過GO分析后發(fā)現(xiàn),葉、果皮、橘絡(luò)的差異基因主要位于細(xì)胞核、質(zhì)膜、膜整體組件,果肉組織中的差異基因主要分布于細(xì)胞壁、胞外區(qū)、質(zhì)膜部位。注意到果肉中顯著差異基因參與的KEGG通路主要為植物激素信號傳導(dǎo)、類苯基丙烷類生物合成、黃酮類生物合成等。根據(jù)文獻(xiàn)報(bào)道,柑橘果肉中的乙烯、赤霉素、脫落酸、吲哚乙酸、玉米素等內(nèi)源性激素[25]對于果實(shí)的甜度、成熟落果[26]、色澤[27]等特征至關(guān)重要。而苯丙烷類及黃酮類生物合成基因主要參與到植物的生長發(fā)育及抗逆等生物功能,許多MYB類轉(zhuǎn)錄因子可以調(diào)控苯丙烷類[28]、黃酮類化合物生物[29-30]合成中相關(guān)基因的表達(dá),進(jìn)而增強(qiáng)植物的抗逆性。因此果肉中篩選得到的差異基因極有可能對砂糖燈籠橘的果實(shí)甜度及生長發(fā)育至關(guān)重要。在對差異基因數(shù)量最多的葉子轉(zhuǎn)錄組數(shù)據(jù)分析后發(fā)現(xiàn),其差異基因主要參與到植物-病原互作、半乳糖代謝、轉(zhuǎn)運(yùn)蛋白運(yùn)輸?shù)冗^程。柑橘類果皮富含多種化學(xué)成分[31-32],在食品、醫(yī)藥方面具有巨大的應(yīng)用潛力,同時(shí),果皮作為柑橘抵抗自然環(huán)境、病蟲害的第一道防線[33],其組成結(jié)構(gòu)極其重要,轉(zhuǎn)錄組數(shù)據(jù)顯示,果皮中的差異基因主要參與到抗逆、轉(zhuǎn)錄調(diào)控、生物反應(yīng)等過程。柑橘橘絡(luò)中富含多種類黃酮類化合物,如橙皮苷、槲皮素[34],GO分析顯示,砂糖燈籠橘橘絡(luò)差異基因主要參與到黃酮類化合物的生物合成及糖脂化作用,對抵抗外界惡劣環(huán)境、生長發(fā)育具有重要意義。
通過甲苯胺藍(lán)染液染色實(shí)驗(yàn),發(fā)現(xiàn)砂糖燈籠橘葉片、果皮表面存在蠟質(zhì)缺失的現(xiàn)象。植物表面的蠟質(zhì)是由脂肪酸及其衍生物混合構(gòu)成的一道屏障[35],主要用于抵抗外界輻射、抵抗氣溫脅迫、防止病蟲害危害及水分散失[36-37]。根據(jù)轉(zhuǎn)錄組差異基因篩選的數(shù)據(jù),砂糖燈籠橘果皮中存在9個(gè)與蠟質(zhì)生物合成相關(guān)的差異基因,葉片中存在12個(gè)差異基因,果皮中只有FACR2為上調(diào)基因,其余基因表達(dá)量皆下調(diào)。FACR2為柑橘的脂肪酰輔酶A還原酶2異構(gòu)體X2,參與到蠟質(zhì)生物合成的第一步,即還原酶蛋白編碼。目前對于該基因的具體功能未見報(bào)道,但對小麥中超長鏈脂肪酰輔酶A還原酶TaFAR的研究[38]表明,F(xiàn)AR能夠促進(jìn)葉片表皮蠟質(zhì)晶體的合成,存在正向調(diào)控的作用。因此可以推測柑橘中的FACR2基因極有可能正向調(diào)節(jié)蠟質(zhì)晶體的合成,但由于砂糖燈籠橘體內(nèi)飽和脂肪酸底物不足,即使其表達(dá)量高,也很難轉(zhuǎn)化為脂肪醇。葉片中存在2個(gè)與蠟質(zhì)合成相關(guān)的上調(diào)基因,皆為細(xì)胞色素P450酶。CYP450為單加氧酶,廣泛參與植物中多種次生代謝產(chǎn)物的生物合成[39-40],其可能參與到砂糖燈籠橘蠟質(zhì)合成相關(guān)化合物的代謝通路中。葉片、果皮與蠟質(zhì)生物合成相關(guān)的差異基因韋恩圖顯示2個(gè)組織樣本中存在5個(gè)共同基因,分別為CER1、CER3、HHT、細(xì)胞色素P45086A8、細(xì)胞色素P45086A22,表達(dá)量皆顯著下調(diào)。CER1、CER3為擬南芥烷烴合成酶同源基因[41-42]。擬南芥中CER3等基因[43]可以參與到花粉內(nèi)油脂類化合物合成與轉(zhuǎn)運(yùn);小麥中的CER1[42]能夠調(diào)控其表面蠟質(zhì)合成,正向調(diào)控韌皮部防衛(wèi)反應(yīng)及應(yīng)對麥長管蚜的抗性。因此CER系列基因?qū)τ谡{(diào)控砂糖燈籠橘表面果皮、葉片蠟質(zhì)成分的合成和積累起著至關(guān)重要的作用,其下調(diào)可能會(huì)直接導(dǎo)致砂糖燈籠橘蠟質(zhì)缺失。HHT編碼阿魏酸輔酶A轉(zhuǎn)移酶,從而參與木脂素生物合成?;诨ɑú窀邷丨h(huán)境下的表達(dá)譜篩選到與蠟質(zhì)合成相關(guān)基因KcHHT,能夠明顯提升花花柴蠟質(zhì)合成,進(jìn)而增強(qiáng)其抗逆作用[44],因此可以推測出篩選到的砂糖燈籠橘中HHT基因也能夠直接參與到蠟質(zhì)生物合成,其表達(dá)量降低也會(huì)導(dǎo)致砂糖燈籠橘表面蠟質(zhì)缺失。目前砂糖燈籠橘中篩選的蠟質(zhì)合成相關(guān)基因的功能研究尚未見報(bào)道,后續(xù)對這些基因進(jìn)行具體深入的研究有助于砂糖燈籠橘的定向優(yōu)質(zhì)育種。
4 結(jié) 論
砂糖燈籠橘為砂糖橘自然變異品種,其葉大且葉片邊緣不規(guī)則;果實(shí)較砂糖橘大,果皮有明顯溝壑,表面布滿點(diǎn)狀突起,形似“燈籠”。甲苯胺藍(lán)染色說明葉片、果實(shí)表面蠟質(zhì)排布不均。轉(zhuǎn)錄組測序發(fā)現(xiàn)葉片差異基因數(shù)量最多,其次為果肉、果皮、橘絡(luò)。篩選葉片、果皮中與蠟質(zhì)生物合成相關(guān)的顯著差異基因,發(fā)現(xiàn)葉片中存在12個(gè),果皮中存在9個(gè),且有5個(gè)共同的顯著下調(diào)基因,分別為CER1、CER3、HHT、細(xì)胞色素P45086A8、細(xì)胞色素P45086A22,這些基因可能是砂糖燈籠橘表面蠟質(zhì)生物合成的關(guān)鍵基因。進(jìn)一步對這些基因的功能進(jìn)行深入挖掘,可以為定向培育優(yōu)質(zhì)的砂糖燈籠橘種質(zhì)資源提供理論依據(jù)。
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