Article(id=1276601512088436948, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1276601397818814642, articleNumber=null, orderNo=null, doi=10.3969/j.issn.1000-2561.2025.01.004, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1722355200000, receivedDateStr=2024-07-31, revisedDate=1724947200000, revisedDateStr=2024-08-30, acceptedDate=null, acceptedDateStr=null, onlineDate=1782295118591, onlineDateStr=2026-06-24, pubDate=1737734400000, pubDateStr=2025-01-25, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1782295118591, onlineIssueDateStr=2026-06-24, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1782295118591, creator=13701087609, updateTime=1782295118591, updator=13701087609, issue=Issue{id=1276601397818814642, tenantId=1146029695717560320, journalId=1235980609244409860, year='2025', volume='46', issue='1', pageStart='1', pageEnd='245', issueExtLink='null', onlineDate='null', pubDate='1737734400000', pubDateStr='2025-01-25', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1782295091347, creator='13701087609', updateTime=1782295207335, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1276601884408418422, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1276601397818814642, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1276601884408418423, tenantId=1146029695717560320, journalId=1235980609244409860, issueId=1276601397818814642, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=35, endPage=43, ext={EN=ArticleExt(id=1276601512335900886, articleId=1276601512088436948, tenantId=1146029695717560320, journalId=1235980609244409860, language=EN, title=Selection and Validation of qRT-PCR Reference Genes in Different Tissues of Nervilia plicata, columnId=1236256430337085821, journalTitle=Chinese Journal of Tropical Crops, columnName=Omics & Biotechnology, runingTitle=null, highlight=null, articleAbstract=

Nervilia plicata is a rare southern Chinese herb. The study on the plant at molecular level is hardly seen. Real-time quantitative PCR (qRT-PCR) has been widely used in plant gene expression analysis, but there is a lack of research on it in N. plicata, which limits the progress of related work. Based on the previous researches, nine candidate reference genes, including Actin, GAPDH, TUA, UBC, UBQ, EF-1α, EF-1β, CYP and RPL, were screened out from the transcriptomic sequencing data. In order to select suitable reference gene in N. plicata, qRT-PCR technique was employed to detect the expression levels of the candidate reference genes in leaf, petiole and corm tissues of the plant. After analyzing the expression levels, the stability and comprehensive analysis of nine genes in different tissues, the most suitable reference gene was obtained. Finally, the most suitable reference gene was validated using NpDFR, Np3GT that related to anthocyanin synthesis. Results showed that the expression stability of EF-1 α and CYP was similar, with the best overall stability. When using either EF-1α or CYP, or the combination of them, as reference, the expression patterns of NpDFR and Np3GT in different tissues were consistent with the transcriptome sequencing results. This indicates that both EF-1 α and CYP can be used as reference genes in N. plicata for qRT-PCR. This study would provide a basis for further research on the molecular mechanism of genes related to the pharmacological effects of N. plicata.

, authors=null, authorsList=Jiayi CHI, Shuxuan LIU, Sishi XIANG, Ruoting ZHAN, Rui HE, authorCompany=null, correspAuthors=Rui HE, authorNote=null, correspAuthorsNote=null, copyrightStatement=null, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, fund=null), CN=ArticleExt(id=1276601514030399722, articleId=1276601512088436948, tenantId=1146029695717560320, journalId=1235980609244409860, language=CN, title=毛叶芋兰不同组织qRT-PCR内参基因选择与验证, columnId=1236256430517440904, journalTitle=热带作物学报, columnName=组学与生物技术, runingTitle=null, highlight=null, articleAbstract=

毛叶芋兰(Nervilia plicata)是一种珍稀南药,目前对其有效成分及其分子调控机理鲜有报道。实时荧光定量PCR(real-time quantitative PCR,qRT-PCR)在植物基因表达分析中得到了广泛应用,但在毛叶芋兰中缺少研究,限制了相关工作的开展。在前期工作基础上,本研究从毛叶芋兰转录组数据库中筛选出ActinGAPDHTUAUBCUBQEF-1αEF-1βCYPRPL共9个常见管家基因,以毛叶芋兰叶片、叶柄和球茎3个组织部位为材料,开展qRT-PCR内参基因的筛选工作。经过9个基因在不同组织的表达水平、稳定性和综合分析,筛选出最适合的内参基因,并选择毛叶芋兰花青素合成途径关键基因NpDFRNp3GT进行验证。结果发现:EF-1αCYP的表达稳定性相近,整体稳定性最好。2个内参基因单独或共同使用时,NpDFRNp3GT在不同组织的表达情况与转录组测序结果基本一致,表明其均可用作qRT-PCR的内参基因。本研究结果为进一步开展毛叶芋兰药效相关基因的分子作用机理研究提供依据。

, authors=

池珈仪(2000—),女,硕士研究生,研究方向:药用植物资源研究及GAP关键技术。

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* 何瑞(HE Rui),E-mail:
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池珈仪(2000—),女,硕士研究生,研究方向:药用植物资源研究及GAP关键技术。

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池珈仪(2000—),女,硕士研究生,研究方向:药用植物资源研究及GAP关键技术。

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Systematic Botany, 2015, 40(2): 413-425., articleTitle=Stuides in Asian Nervilia (Orchidaceae) V: Nervilia futago, a cryptic new species from southwest Japan confirmed by morphological, cytological, and molecular analyses, refAbstract=null), Reference(id=1276601699108258079, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, doi=null, pmid=null, pmcid=null, year=2023, volume=44, issue=11, pageStart=2188, pageEnd=2195, url=null, language=null, rfNumber=[22], rfOrder=29, authorNames=章杨婷, 张燕萍, 黄静妍, 王文君, 童妍, 赵凯, 周育真, journalName=热带作物学报, refType=null, unstructuredReference=章杨婷, 张燕萍, 黄静妍, 王文君, 童妍, 赵凯, 周育真. 一心维纳斯蝴蝶兰花香物质合成相关基因RT-qPCR内参基因筛选[J]. 热带作物学报, 2023, 44(11): 2188-2195., articleTitle=一心维纳斯蝴蝶兰花香物质合成相关基因RT-qPCR内参基因筛选, refAbstract=null), Reference(id=1276601699200532768, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, doi=null, pmid=null, pmcid=null, year=2023, volume=44, issue=11, pageStart=2188, pageEnd=2195, url=null, language=null, rfNumber=[22], rfOrder=30, authorNames=ZHANG Y T, ZHANG Y P, HUANG J Y, WANG W J, TONG Y, ZHAO K, ZHOU Y Z, journalName=Chinese Journal of Tropical Crops, refType=null, unstructuredReference=ZHANG Y T, ZHANG Y P, HUANG J Y, WANG W J, TONG Y, ZHAO K, ZHOU Y Z. Selection of suitable RT-qPCR reference genes for floral scent biosynthesis in Phalaenopsis I-Hsin Venus[J]. Chinese Journal of Tropical Crops, 2023, 44(11): 2188-2195. (in Chinese), articleTitle=Selection of suitable RT-qPCR reference genes for floral scent biosynthesis in Phalaenopsis I-Hsin Venus, refAbstract=null), Reference(id=1276601699301196065, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, doi=null, pmid=null, pmcid=null, year=2023, volume=21, issue=10, pageStart=3282, pageEnd=3289, url=null, language=null, rfNumber=[23], rfOrder=31, authorNames=曹映辉, 郑燕, 张燕萍, 胡美娟, 童妍, 朱尾银, 徐建球, 赵凯, 彭东辉, 周育真, journalName=分子植物育种, refType=null, unstructuredReference=曹映辉, 郑燕, 张燕萍, 胡美娟, 童妍, 朱尾银, 徐建球, 赵凯, 彭东辉, 周育真. 建兰花香物质合成相关基因RT-qPCR内参基因筛选[J]. 分子植物育种, 2023, 21(10): 3282-3289., articleTitle=建兰花香物质合成相关基因RT-qPCR内参基因筛选, refAbstract=null), Reference(id=1276601699380887842, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, doi=null, pmid=null, pmcid=null, year=2023, volume=21, issue=10, pageStart=3282, pageEnd=3289, url=null, language=null, rfNumber=[23], rfOrder=32, authorNames=CAO Y H, ZHENG Y, ZHANG Y P, HU M J, TONG Y, ZHU W Y, XU J Q, ZHAO K, PENG D H, ZHOU Y Z, journalName=Molecular Plant Breeding, refType=null, unstructuredReference=CAO Y H, ZHENG Y, ZHANG Y P, HU M J, TONG Y, ZHU W Y, XU J Q, ZHAO K, PENG D H, ZHOU Y Z. Selection of suitable RT-qPCR reference genes for floral scent biosynthesis in Cymbidium ensifolium[J]. Molecular Plant Breeding, 2023, 21(10): 3282-3289. (in Chinese), articleTitle=Selection of suitable RT-qPCR reference genes for floral scent biosynthesis in Cymbidium ensifolium, refAbstract=null), Reference(id=1276601699494134051, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, doi=null, pmid=null, pmcid=null, year=2006, volume=7, issue=null, pageStart=1, pageEnd=9, url=null, language=null, rfNumber=[24], rfOrder=33, authorNames=SILVER N, BEST S, JIANG J, THEIN S L, journalName=BMC Molecular Biology, refType=null, unstructuredReference=SILVER N, BEST S, JIANG J, THEIN S L. Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR[J]. BMC Molecular Biology, 2006, 7: 1-9., articleTitle=Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR, refAbstract=null)], funds=[Fund(id=1276601695090114817, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, awardId=2022-NJS-00-002; 粤财农[2022]184号, language=CN, fundingSource=2022年省级乡村振兴战略专项资金种业振兴项目“广东省南药种业创新园项目”(2022-NJS-00-002; 粤财农[2022]184号), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1276601685531295943, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, xref=null, ext=[AuthorCompanyExt(id=1276601685539684552, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, companyId=1276601685531295943, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine / Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou University of Chinese Medicine / School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China), AuthorCompanyExt(id=1276601685548073161, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, companyId=1276601685531295943, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=广州中医药大学中药资源科学与工程研究中心/广州中医药大学岭南中药资源教育部重点实验室/广州中医药大学中药学院,广东广州 510006)])], figs=[ArticleFig(id=1276601691717894379, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=EN, label=Fig. 1, caption=Electrophoresis of PCR amplification products of nine candidate reference genes, figureFileSmall=qxkRxPnMafE4KUz7ys3VFA==, figureFileBig=eDLXg5s/Y3jxlIuVUG62ng==, tableContent=null), ArticleFig(id=1276601691793391852, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=CN, label=图1, caption=9个候选内参基因普通PCR产物电泳检测

M: DL500 DNA marker; 1: Actin; 2: GAPDH; 3: TUA; 4: UBC; 5: UBQ; 6: EF-; 7: EF-; 8: CYP; 9: RPL.

, figureFileSmall=qxkRxPnMafE4KUz7ys3VFA==, figureFileBig=eDLXg5s/Y3jxlIuVUG62ng==, tableContent=null), ArticleFig(id=1276601691902443757, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=EN, label=Fig. 2, caption=Melting curves of nine candidate reference genes

–d(RFU)/dT indicates the change in fluorescence intensity for every 1 ℃ change in temperature.

, figureFileSmall=afpVleVme0gc3a9K6xvEhg==, figureFileBig=vHZK5b6o0Bv9hQUqkV7Itw==, tableContent=null), ArticleFig(id=1276601691973746926, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=CN, label=图2, caption=9个候选内参基因熔解曲线

–d(RFU)/dT表示温度每变化1℃荧光强度的变化值。

, figureFileSmall=afpVleVme0gc3a9K6xvEhg==, figureFileBig=vHZK5b6o0Bv9hQUqkV7Itw==, tableContent=null), ArticleFig(id=1276601692045050095, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=EN, label=Fig. 3, caption=Ct values distribution of nine candidate reference genes

The line inside the box indicates median, the upper and lower edges of the box indicate the third quartile and the first quartiles respectively, and the horizontal line above and below the box indicates the maximum and minimum limits respectively.

, figureFileSmall=ig/DWyy4eWxvaldVj9rkmQ==, figureFileBig=6w7ow7+2e2+cU4hnn2QIqA==, tableContent=null), ArticleFig(id=1276601692103770352, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=CN, label=图3, caption=9个候选内参基因Ct值分布

箱体中的横线表示中位数,箱体的上、下边线分别表示第三四分位数、第一四分位数,箱体上、下方横线分别表示上限、下限。

, figureFileSmall=ig/DWyy4eWxvaldVj9rkmQ==, figureFileBig=6w7ow7+2e2+cU4hnn2QIqA==, tableContent=null), ArticleFig(id=1276601693781491953, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=EN, label=Fig. 4, caption=∆Ct values distribution of paired candidate reference genes, figureFileSmall=G6sed7nmH5sAcN5GeZoufg==, figureFileBig=u61xZN2gs28yz+uX13rdsw==, tableContent=null), ArticleFig(id=1276601693848600818, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=CN, label=图4, caption=配对候选内参基因∆Ct值分布, figureFileSmall=G6sed7nmH5sAcN5GeZoufg==, figureFileBig=u61xZN2gs28yz+uX13rdsw==, tableContent=null), ArticleFig(id=1276601693940875507, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=EN, label=Fig. 5, caption=Average expression stability M and stability values of nine candidate reference genes analyzed by geNorm and NormFinder respectively, figureFileSmall=4JzsMDMIQwLu6F/l+tW7Nw==, figureFileBig=YWrrpKIcok6HjRreSNNU6g==, tableContent=null), ArticleFig(id=1276601694012178676, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=CN, label=图5, caption=geNorm与NormFinder软件分别计算9个候选内参基因表达M值与SV, figureFileSmall=4JzsMDMIQwLu6F/l+tW7Nw==, figureFileBig=YWrrpKIcok6HjRreSNNU6g==, tableContent=null), ArticleFig(id=1276601694083481845, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=EN, label=Fig. 6, caption=Pairwise variation values calculated by geNorm, figureFileSmall=APQU88UDUjEx03UYIL12cg==, figureFileBig=51WqkMsRI68aermrfZbAow==, tableContent=null), ArticleFig(id=1276601694163173622, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=CN, label=图6, caption=geNorm软件计算配对变异值, figureFileSmall=APQU88UDUjEx03UYIL12cg==, figureFileBig=51WqkMsRI68aermrfZbAow==, tableContent=null), ArticleFig(id=1276601694226088183, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=EN, label=Fig. 7, caption=CV and SD of nine candidate reference genes calculated by BestKeeper, figureFileSmall=3derO61x0PfHaJncwzlbYg==, figureFileBig=/qeK+BIO2PKKbpyDlMge6w==, tableContent=null), ArticleFig(id=1276601694289002744, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=CN, label=图7, caption=BestKeeper软件计算9个候选内参基因CV与SD, figureFileSmall=3derO61x0PfHaJncwzlbYg==, figureFileBig=/qeK+BIO2PKKbpyDlMge6w==, tableContent=null), ArticleFig(id=1276601694351917305, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=EN, label=Fig. 8, caption=Comprehensive analysis by RefFinder, figureFileSmall=5/gV+YxpNT9keHK8VHd+bA==, figureFileBig=yrVNVgb7HzBgKlBPbtm15w==, tableContent=null), ArticleFig(id=1276601694423220474, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=CN, label=图8, caption=RefFinder程序综合分析, figureFileSmall=5/gV+YxpNT9keHK8VHd+bA==, figureFileBig=yrVNVgb7HzBgKlBPbtm15w==, tableContent=null), ArticleFig(id=1276601694490329339, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=EN, label=Fig. 9, caption=Relative expression levels of NpDFR and Np3GT normalized by different reference genes in N. plicata, figureFileSmall=Jq9IM1h0rldMftsgbRJJIg==, figureFileBig=PjR/0BgztCTEmmPwV6bdNA==, tableContent=null), ArticleFig(id=1276601694570021116, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=CN, label=图9, caption=毛叶芋兰不同内参基因对NpDFRNp3GT基因在叶片、球茎中表达水平验证, figureFileSmall=Jq9IM1h0rldMftsgbRJJIg==, figureFileBig=PjR/0BgztCTEmmPwV6bdNA==, tableContent=null), ArticleFig(id=1276601694729404669, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=EN, label=Tab. 1, caption=

Primer sequences for nine candidate reference genes

, figureFileSmall=null, figureFileBig=null, tableContent=
基因Gene引物序列(5′–3′)Primer sequence (5′–3′)片段长度Product length/bp
ActinF: ATGGTTAAGGCTGGTT
R: TTAGATTGGGCTTCGTCA
139
GAPDHF: ACGCAATCACTGCCACTC
R: TCCCTCAGACTCTTCCTTTAT
270
TUAF: GTTCAGCATCAACCGACTC
R: ACCACAGCATCCACCTTT
140
UBCF: GGAAGAGGTTGATGAGGGAC
R: ACAGTTGGCGGCTTATTT
193
UBQF: GGCTCCAATTCTGTAATCC
R: TTTGCCAGTGAGGGTCTT
291
EF-1αF: GCGGAGATCCTGACCAAG
R: CGTCTGCCTCATATCCCTGA
210
EF-1βF: ATGGCTATCTCCTTCACAA
R: GTTACAGCGGCATAAACT
131
CYPF: CTGGCGGTGAGTCTATTT
R: CTGTGACCCATTCGTGTT
116
RPLF: GCGTTCACCGCAAGCACA
R: GGGACCAGTAACCAGAAGCAA
147
), ArticleFig(id=1276601694813290750, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=CN, label=表1, caption=

9个候选内参基因引物序列

, figureFileSmall=null, figureFileBig=null, tableContent=
基因Gene引物序列(5′–3′)Primer sequence (5′–3′)片段长度Product length/bp
ActinF: ATGGTTAAGGCTGGTT
R: TTAGATTGGGCTTCGTCA
139
GAPDHF: ACGCAATCACTGCCACTC
R: TCCCTCAGACTCTTCCTTTAT
270
TUAF: GTTCAGCATCAACCGACTC
R: ACCACAGCATCCACCTTT
140
UBCF: GGAAGAGGTTGATGAGGGAC
R: ACAGTTGGCGGCTTATTT
193
UBQF: GGCTCCAATTCTGTAATCC
R: TTTGCCAGTGAGGGTCTT
291
EF-1αF: GCGGAGATCCTGACCAAG
R: CGTCTGCCTCATATCCCTGA
210
EF-1βF: ATGGCTATCTCCTTCACAA
R: GTTACAGCGGCATAAACT
131
CYPF: CTGGCGGTGAGTCTATTT
R: CTGTGACCCATTCGTGTT
116
RPLF: GCGTTCACCGCAAGCACA
R: GGGACCAGTAACCAGAAGCAA
147
), ArticleFig(id=1276601694876205311, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=EN, label=Tab. 2, caption=

Amplification efficiency of nine candidate reference genes

, figureFileSmall=null, figureFileBig=null, tableContent=
基因Gene扩增效率E/%斜率K相关系数R2
Actin120.60–2.90710.9949
GAPDH100.10–3.31920.9932
TUA99.58–3.33200.9959
UBC93.72–3.48230.9944
UBQ91.36–3.54810.9906
EF-1α99.64–3.33060.9908
EF-1β91.96–3.53090.9917
CYP91.21–3.55240.9932
RPL97.49–3.38360.9969
), ArticleFig(id=1276601694934925568, tenantId=1146029695717560320, journalId=1235980609244409860, articleId=1276601512088436948, language=CN, label=表2, caption=

9个候选内参基因扩增效率

, figureFileSmall=null, figureFileBig=null, tableContent=
基因Gene扩增效率E/%斜率K相关系数R2
Actin120.60–2.90710.9949
GAPDH100.10–3.31920.9932
TUA99.58–3.33200.9959
UBC93.72–3.48230.9944
UBQ91.36–3.54810.9906
EF-1α99.64–3.33060.9908
EF-1β91.96–3.53090.9917
CYP91.21–3.55240.9932
RPL97.49–3.38360.9969
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毛叶芋兰不同组织qRT-PCR内参基因选择与验证
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池珈仪 , 刘舒璇 , 向思诗 , 詹若挺 , 何瑞 *
热带作物学报 | 组学与生物技术 2025,46(1): 35-43
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热带作物学报 |组学与生物技术 2025 , 46 (1) : 35 -43
毛叶芋兰不同组织qRT-PCR内参基因选择与验证
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池珈仪, 刘舒璇, 向思诗, 詹若挺, 何瑞*
作者信息
  • 广州中医药大学中药资源科学与工程研究中心/广州中医药大学岭南中药资源教育部重点实验室/广州中医药大学中药学院,广东广州 510006
通讯作者:
* 何瑞(HE Rui),E-mail:
Selection and Validation of qRT-PCR Reference Genes in Different Tissues of Nervilia plicata
Jiayi CHI, Shuxuan LIU, Sishi XIANG, Ruoting ZHAN, Rui HE*
Affiliations
  • Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine / Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou University of Chinese Medicine / School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
出版时间: 2025-01-25 doi: 10.3969/j.issn.1000-2561.2025.01.004
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毛叶芋兰(Nervilia plicata)是一种珍稀南药,目前对其有效成分及其分子调控机理鲜有报道。实时荧光定量PCR(real-time quantitative PCR,qRT-PCR)在植物基因表达分析中得到了广泛应用,但在毛叶芋兰中缺少研究,限制了相关工作的开展。在前期工作基础上,本研究从毛叶芋兰转录组数据库中筛选出ActinGAPDHTUAUBCUBQEF-1αEF-1βCYPRPL共9个常见管家基因,以毛叶芋兰叶片、叶柄和球茎3个组织部位为材料,开展qRT-PCR内参基因的筛选工作。经过9个基因在不同组织的表达水平、稳定性和综合分析,筛选出最适合的内参基因,并选择毛叶芋兰花青素合成途径关键基因NpDFRNp3GT进行验证。结果发现:EF-1αCYP的表达稳定性相近,整体稳定性最好。2个内参基因单独或共同使用时,NpDFRNp3GT在不同组织的表达情况与转录组测序结果基本一致,表明其均可用作qRT-PCR的内参基因。本研究结果为进一步开展毛叶芋兰药效相关基因的分子作用机理研究提供依据。

毛叶芋兰  /  内参基因  /  实时荧光定量PCR  /  表达稳定性

Nervilia plicata is a rare southern Chinese herb. The study on the plant at molecular level is hardly seen. Real-time quantitative PCR (qRT-PCR) has been widely used in plant gene expression analysis, but there is a lack of research on it in N. plicata, which limits the progress of related work. Based on the previous researches, nine candidate reference genes, including Actin, GAPDH, TUA, UBC, UBQ, EF-1α, EF-1β, CYP and RPL, were screened out from the transcriptomic sequencing data. In order to select suitable reference gene in N. plicata, qRT-PCR technique was employed to detect the expression levels of the candidate reference genes in leaf, petiole and corm tissues of the plant. After analyzing the expression levels, the stability and comprehensive analysis of nine genes in different tissues, the most suitable reference gene was obtained. Finally, the most suitable reference gene was validated using NpDFR, Np3GT that related to anthocyanin synthesis. Results showed that the expression stability of EF-1 α and CYP was similar, with the best overall stability. When using either EF-1α or CYP, or the combination of them, as reference, the expression patterns of NpDFR and Np3GT in different tissues were consistent with the transcriptome sequencing results. This indicates that both EF-1 α and CYP can be used as reference genes in N. plicata for qRT-PCR. This study would provide a basis for further research on the molecular mechanism of genes related to the pharmacological effects of N. plicata.

Nervilia plicata  /  reference gene  /  qRT-PCR  /  expression stability
池珈仪, 刘舒璇, 向思诗, 詹若挺, 何瑞. 毛叶芋兰不同组织qRT-PCR内参基因选择与验证. 热带作物学报, 2025 , 46 (1) : 35 -43 . DOI: 10.3969/j.issn.1000-2561.2025.01.004
Jiayi CHI, Shuxuan LIU, Sishi XIANG, Ruoting ZHAN, Rui HE. Selection and Validation of qRT-PCR Reference Genes in Different Tissues of Nervilia plicata[J]. Chinese Journal of Tropical Crops, 2025 , 46 (1) : 35 -43 . DOI: 10.3969/j.issn.1000-2561.2025.01.004
实时荧光定量PCR(real-time quantitative PCR,qRT-PCR)是将聚合酶链式反应和荧光染料相结合的检测技术,能以较高的灵敏度和特异度实时监测模板扩增的反应进程[1],是定量分析样品中核酸分子的最常用的分子生物学技术之一[2]。因其快速简便,结果准确性高,qRT-PCR技术被普遍应用于生命科学及其相关领域,具有广泛应用价值。常用于基因表达分析、突变检测、物种鉴定等[3]
qRT-PCR结果的准确可靠性可能受到如RNA质量、逆转录、引物的特异性和实验者操作精准性等的影响[4]。为了避免这些因素的影响,准确反映目的基因的表达水平,在qRT-PCR过程中使用一个或多个合适的基因进行标准化至关重要[5]。这种能用于标准化qRT-PCR数据的基因即为内参基因(reference gene),一般为管家基因。管家基因如GAPDHActin18S rRNAtubulinEF-1αubiquitin等在各组织和细胞中的表达都相对稳定,可用作基因相对表达分析检测的参考。然而,内参基因的表达水平也会因物种差异、生物生长发育阶段的变化或实验条件的不同而发生变化,因此在特定条件下,必须对所选取的内参基因进行表达稳定性的验证[6]。geNorm、NormFinder和Bestkeeper为目前评估内参基因稳定性的3种主流软件[7-8]
毛叶芋兰[Nervilia plicata(Andr.)Schitr.]是兰科芋兰属珍稀药用植物。《中国植物志》[9-10]中记载该植物具利肺止咳、益肾、解毒止痛之功效,其主要药效化学成分为黄酮类物质[10]。目前针对毛叶芋兰的研究非常少,基本只有关于其物种鉴定和化学成分研究的报道,缺少对其有效成分及其分子调控机理的研究。qRT-PCR技术在植物基因表达分析中被广泛应用,但在毛叶芋兰中也缺乏相关研究,尚未见其内参基因筛选的报道,这限制了相关工作的进一步开展。
本研究以毛叶芋兰的叶、叶柄、球茎3个部位为材料,从前期获得的转录组数据库中选取9个常见管家基因(ActinGAPDHTUAUBCUBQEF-1αEF-1βCYPRPL)作为候选内参基因,利用qRT-PCR检测它们在3个不同部位的表达情况,结合∆Ct法分析,采用geNorm、NormFinder和Bestkeeper软件以及RefFinder程序分析并筛选出毛叶芋兰不同组织部位表达最稳定的内参基因,为进一步采用分子生物学技术研究毛叶芋兰及其他兰科植物奠定基础。
本研究所用植物材料种植于广州中医药大学中药学院资源中心植物培养室,经相关参考文献并结合《中国植物志》[9-11]中形态描述及其来源地等鉴定为毛叶芋兰(Nervilia plicata)。选择叶片完全伸展的3株毛叶芋兰植株,于2023年8月采集叶片、叶柄和球茎,用DEPC水将采摘的样本清洗干净,立即液氮速冻,转移并保存于–80 ℃备用。
使用RNA提取试剂盒(CW2598S,CWBIO)按说明书提取毛叶芋兰的RNA,1.0%琼脂糖凝胶电泳检测所获RNA的完整性;使用反转录试剂盒(R223,Vazyme)将检验合格的RNA样品反转录成cDNA,储存于–20 ℃冰箱备用。
参考已发表的近缘物种内参基因序列,对已完成测序的毛叶芋兰不同组织部位的转录组数据(未发表)进行本地蛋白序列blast,结合从数据库中筛选出的注释为9个基因的所有转录本,进一步以每千个碱基的转录每百万映射读取的碎片(FPKM值)>100且变异系数(coefficient of variation,CV)最小为筛选标准,获得9个候选内参基因,根据其各自核苷酸序列采用Primer Premier 5.0软件设计对应引物(表1)。
以反转录后得到的总cDNA原液为模板,使用Premix Taq(TaKaRa TaqTM version 2.0 plus dye)(RR902Q)进行普通PCR扩增,反应体系:Premix Taq(TaKaRa TaqTMversion 2.0 plus dye)12.5 μL,上游引物0.5 μL,下游引物0.5 μL,添加ddH2O至25 μL,PCR反应程序参照试剂盒说明书设置。所设计的引物其特异性通过3.0%琼脂糖凝胶电泳初步检测,并在qRT-PCR后观察熔解曲线进一步确认。
使用伯乐CFX96 real-time PCR定量分析仪和Biosharp universal SYBR qPCR Master Mix(BL697A)试剂盒进行实时荧光定量PCR检测。参照说明书配制反应体系:cDNA模板1 μL(以cDNA原液5倍稀释液为模板),上游引物0.4 μL,下游引物0.4 μL,2×universal SYBR green master mix 10 μL,ddH2O 8.2 μL。参照说明书设置2步法qRT-PCR反应程序。
将毛叶芋兰的叶、叶柄、球茎的cDNA等量混匀成1份总cDNA模板,依次稀释50、51、52、53、54倍共5个浓度梯度,进行qRT-PCR检测。使用Excel软件,以5个稀释倍数的对数为横坐标、其对应的Ct值为纵坐标进行线性拟合,得到标准曲线及其斜率(K),利用公式E=(10–1/K–1)×100%计算[12],得到各内参引物的扩增效率(E)。
以毛叶芋兰各样品cDNA的5倍稀释液为模板,对各候选内参基因进行qRT-PCR检测,反应体系和程序同1.2.4,每个样品进行3次技术重复。
首先对各候选内参基因的表达水平进行分析,将每组qRT-PCR获得的各部位所有Ct值绘制成箱线图。稳定性分析是使用∆Ct法对原始数据进行计算,同时将原始数据输入到BestKeeper软件进行分析。各内参基因的相对表达量通过2–ΔΔCt法计算获得,将数据转化后,再分别输入到geNorm和NormFinder软件进行分析,最后使用RefFinder在线程序对所有结果进行综合评估,筛选出在毛叶芋兰不同组织中表达最稳定的内参基因。
通过综合评估筛选的最优的2个基因被选作为内参基因。利用qRT-PCR检测毛叶芋兰叶片与球茎中(转录组未测叶柄)花青素代谢途径关键酶基因NpDFRNp3GT的表达情况,结合转录组数据,验证这2个最优内参基因的表达稳定性。
使用超微量分光光度计(型号:Nanodrop Lite)检测提取获得的RNA的浓度和纯度,各样品浓度为69.0~133.7 ng/μL,A260/A280值均在2.0~2.2范围,说明其纯度较好,电泳检测均具有28S RNA、18S RNA 2个条带,且未出现弥散现象,满足后续试验的要求。
按照1.2.2方法,从毛叶芋兰转录组数据库中筛选出9个候选内参基因Actin、GAPDH、TUA、UBC、UBQ、EF-1α、EF-1β、CYP、RPL,其普通PCR产物经电泳检测,结果显示清晰单一的条带,各内参基因扩增出116~291 bp符合预期大小的特异性片段(图1),表明设计的引物可用于后续qRT-PCR分析。
进一步验证所设计引物的特异性并分析其扩增效率,9个候选内参基因的熔解曲线均呈现出清晰的单一峰值特征,说明无引物二聚体形成或非特异性扩增,熔解曲线的Tm值均在80~85 ℃之间(图2);按1.2.4方法在Excel中计算得到标准曲线的相关系数(R2)介于0.9906~0.9969之间,线性关系良好,扩增效率(E)介于91.21%~120.60%之间(表2),9个内参基因的引物均符合后续分析要求。
Ct值代表内参基因的表达水平,基因的Ct值若较低,则通常指示其具有较高的表达水平,反之则表达水平较低。毛叶芋兰的3个组织部位中9个候选内参基因的Ct值范围为20.686~26.470,其中平均Ct值最大与最小的基因分别是RPL(25.631)和EF-1α(22.342),说明RPL表达丰度最低,EF-1α最高9个候选内参基因在表达丰度上的排序为:EF-1α>GAPDH>UBC>CYP>UBQ>EF-1β>TUA>Actin>RPL
Ct值的波动反映稳定性,波动越小表示基因表达越稳定。将Ct值绘制成箱线图,以初步评估各候选内参基因表达水平的离散程度。其中GAPDH的箱线最长,说明其表达丰度变异性最大,稳定性最差,而EF-1β箱线最短,其Ct值为23.072~23.710,波动小(图3)。从表达丰度来看EF-1β基因可能是毛叶芋兰不同组织中较为稳定的内参基因。
将候选内参基因两两配对,计算对应的各样本中配对的2个内参基因的∆Ct值(图4),再算出配对的2个内参基因于所有样本间∆Ct值的标准偏差(standard deviation,SD),最后分别得到9个候选内参基因∆Ct值的平均标准偏差(SD mean)。
TUACYP分别与其他8个基因进行比较时,它们与较小偏离量相关(SD mean分别为0.359和0.363),因此这2个基因的变异性较小。但将GAPDHEF-分别与其他8个基因进行比较时,偏差(SD mean分别为0.725和0.744)明显增加,表明其变异大。EF-1αActinUBQUBCRPL都显示出中等水平的偏差(SD mean分别为0.371、0.372、0.419、0.564和0.593)。SD mean越小预示着基因越稳定,由此可见最稳定的基因为TUA,最不稳定的基因为EF-
结果显示9个候选内参基因表达稳定M值均在1.5以下,说明它们的稳定性均较好,9个候选基因都可以用作毛叶芋兰的内参基因(图5)。9个候选内参基因的稳定性由geNorm软件分析排序依次为EF-1α=CYP(0.092)>TUA(0.120)>Actin(0.141)>UBQ(0.189)>UBC(0.279)>RPL(0.360)>GAPDH(0.432)>EF-1β(0.501)。
geNorm软件对输入的数据进行二次自动分析,分析内参基因平均稳定性的变化水平,通过计算配对变异值(Vn/Vn+1)来预测最佳内参基因的个数。在本研究中,配对变异分析结果显示(图6),所有配对变异值均小于0.15,即从图中最稳定的2个基因(最左边)开始,V2/V3<0.15,表明在毛叶芋兰各组织样品中使用2个内参基因可以达到理想的校正效果,综合第一次分析结果,geNorm软件的结论是可选择EF-1αCYP 2个基因作为毛叶芋兰的内参基因。
NormFinder软件的分析与geNorm相似,其分析所得结果稳定值(stability value,SV)越低的候选基因,则表示拥有更高的内参基因稳定性。
在该软件分析中,候选内参基因稳定性依次为TUA(0.181)>CYP(0.208)>EF-1α(0.220)>UBQ(0.255)>UBC(0.278)>Actin(0.285)>GAPDH(0.762)>RPL(0.786)>EF-1β(1.999),与geNorm软件分析的结果排名趋势相似(图5)。其中TUACYPEF-1α的SV最小,说明这3个基因稳定性最高,TUA被NormFinder软件选为最优内参基因。
BestKeeper通过计算CV与SD,来反映内参基因的稳定性。当CV与SD的值都较低时,则说明该基因具有更高的稳定性。其中SD的默认阈值为1.0,当SD低于1.0时则认为该基因表达稳定。分析结果显示,在毛叶芋兰不同组织中,GAPDH的SD(1.14)高于默认阈值,提示不宜作为此物种的内参基因,其余8个基因的SD均小于默认阈值,说明它们的表达也均较为稳定;其中EF-1β的CV与SD都最低,稳定性最好(图7)。
使用RefFinder在线分析网站进行综合评估。结果显示(图8),各内参基因在不同组织中的表达稳定性综合排序由高到低依次为EF-1αCYPTUAUBQUBCActinEF-1βRPLGAPDH。其中EF-1αCYP的表达稳定性相近,整体稳定性最好,适合作为毛叶芋兰的内参基因;而稳定性最差的是GAPDH,提示该基因不适合作为毛叶芋兰荧光定量PCR的内参基因。
单独使用和组合使用综合排名最靠前的2个内参基因EF-1αCYP,对毛叶芋兰的叶片和球茎2个组织部位中花青素代谢途径关键基因NpDFRNp3GT的表达差异进行分析,并与转录组数据进行比较,验证所选的这2个内参基因的稳定性。结果显示,单独或者组合使用EF-1αCYP作为内参基因时,同一目的基因在不同器官中的表达情况相同,即2个目的基因在毛叶芋兰叶片中的相对表达均高于在球茎中的表达,这与转录组所测得的这2个目的基因在2个器官中FPKM值的大小是一致的(图9)。说明单独或者组合使用EF-1αCYP作为qRT-PCR的内参基因都能够较准确得出毛叶芋兰各部位中各基因的相对表达量。
合适的内参基因对于分析目标基因表达情况的准确性和可靠性非常重要。β-tubulin可作为毛唇芋兰(Nervilia plicata)qRT-PCR的校正内参基因[13]。适于铁皮石斛(Dendrobium officinale)不同组织的内参基因为EF-1α或18S rRNA[14],其中前者在铁皮石斛叶色突变体中被验证为稳定且可靠[15];而在其原球茎时期的所有样本中,传统的管家基因表达稳定性均较差,研究筛选得到的内参基因组合不是常用的管家基因,而是ASS+APH1L[15-16];蕙兰(Cymbidium faberi)中可以选用ACTUBQ3GAPDH作为其所有时期所有器官的内参基因使用,但单独分析某器官或者某生长期的目标基因表达情况时,采用其中2个内参基因进行归一化处理能得到更为准确的数据[17];蝴蝶兰(Phalaenopsis spp.)的整个发育阶段各组织的最适内参基因是ACT[18],而低温胁迫条件下,PhPP2Aa基因最适合作为目的基因转录水平研究的内参基因[19]。内参基因的稳定性因物种及其组织部位、生长发育阶段和胁迫条件的不同而有所变化,因此应该为研究的特定的物种或新的试验条件选择最稳定的参考基因[20]
球茎是毛叶芋兰的繁殖器官,其主要为圆球或椭圆形,球茎上长有细弱的匍匐茎或根状茎,每个球茎上每年只长1~2片叶,极少见开花。且芋兰属植物即便开花也多为先开花,花落后才长出叶子,仅有个别物种可以同时见到花和叶子[21]。本研究所种植的毛叶芋兰均未能观察到开花者,且植物材料个体少而小、根和根茎细小,也无法获得足够质量的根和根茎,故选取叶片、叶柄和球茎作为研究材料。前期研究发现β-tubulinTUB)可用作近源物种毛唇芋兰的qRT-PCR研究中的内参基因[13],但本研究前期发现该基因在毛叶芋兰中表达水平较低(以51倍总cDNA稀释液作为模板时Ct值最小值为27.820),制作标准曲线试验中以53倍总cDNA稀释液作为模板时已无法检测到相应Ct值,因此未选择该内参基因进行后续分析。
经稳定性分析,发现Bestkeeper筛选出排行第一位的基因为EF-1β,而使用其他3种方法所得结果中EF-1β排在最后一位,Bestkeeper与其他分析方法所得结果不一样的情况在其他植物的内参基因筛选研究中也报道过[22-23]。不同软件的统计学算法不同,结果亦不同:Bestkeeper是将测得的所有Ct值直接输入软件中,计算目的基因的组内差异,比较不同基因的CV与SD并进行稳定性排序,稳定性与其在各样品中Ct值的离散程度密切相关,Ct值的变化范围越小,则基因的稳定性通常越高。∆Ct法也是对原始数据直接计算,比较每个样本中“成对基因”的相对表达量,若ΔCt有波动,说明其中1个或2个基因都是可变的,可引入更多的基因继续比较,综合比较哪个基因的变异性更小[24]。从图4可见若引入EF-1β,其他与之匹配的组合∆Ct值的波动幅度增大。geNorm和NormFinder与前2个方法不同的是,首先都要将Ct值转化成相对定量数据,再输入到各软件自动寻找各候选基因在不同样本中的最高Ct值,再将所有测得的各基因的Ct值减去所找到的最高Ct值,最后计算表达水平比率,结合组内和组间的差异进行分析。可见对所有软件得出的结果需要进行综合评估,结合并验证,才能筛选到最适合的内参基因。
本研究利用qRT-PCR技术,使用∆Ct法初步分析,并结合3种常用软件geNorm、NormFinder、Bestkeeper与RefFinder程序,综合评估能用于标准化qRT-PCR数据的9个候选内参基因(ActinGAPDHTUAUBCUBQEF-1αEF-1βCYPRPL)在毛叶芋兰不同组织部位的稳定性,结果表明9个内参基因综合排序为EF-1α>CYP>TUA>UBQ>UBC>Actin>EF-1β>RPL>GAPDH。其中单独或联合使用EF-1αCYP作为内参基因,NpDFRNp3GT在不同组织的表达情况与转录组测序结果基本一致。EF-1αCYP皆可作为毛叶芋兰qRT-PCR的内参基因,用于不同组织间基因表达的差异性分析试验。
  • 2022年省级乡村振兴战略专项资金种业振兴项目“广东省南药种业创新园项目”(2022-NJS-00-002; 粤财农[2022]184号)
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2025年第46卷第1期
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doi: 10.3969/j.issn.1000-2561.2025.01.004
  • 接收时间:2024-07-31
  • 首发时间:2026-06-24
  • 出版时间:2025-01-25
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  • 收稿日期:2024-07-31
  • 修回日期:2024-08-30
基金
2022年省级乡村振兴战略专项资金种业振兴项目“广东省南药种业创新园项目”(2022-NJS-00-002; 粤财农[2022]184号)
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    广州中医药大学中药资源科学与工程研究中心/广州中医药大学岭南中药资源教育部重点实验室/广州中医药大学中药学院,广东广州 510006

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* 何瑞(HE Rui),E-mail:
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2种不同金属材料的力学参数

Family
属数
Number of
genus
种数
Number of
species
占总种数比例
Percentage of
total species (%)

Genus
种数
Number of
species
占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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