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Article(id=1256263565850325230, tenantId=1146029695717560320, journalId=1255847803461844995, issueId=1256263559323967535, articleNumber=null, orderNo=null, doi=10.13346/j.mycosystema.250175, pmid=null, cstr=32115.14.j.mycosystema.250175, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1749484800000, receivedDateStr=2025-06-10, revisedDate=null, revisedDateStr=null, acceptedDate=1753891200000, acceptedDateStr=2025-07-31, onlineDate=1777446174347, onlineDateStr=2026-04-29, pubDate=1771689600000, pubDateStr=2026-02-22, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1777446174347, onlineIssueDateStr=2026-04-29, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1777446174347, creator=13701087609, updateTime=1777446174347, updator=13701087609, issue=Issue{id=1256263559323967535, tenantId=1146029695717560320, journalId=1255847803461844995, year='2026', volume='45', issue='2', pageStart='250058', pageEnd='250280', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1777446172791, creator=13701087609, updateTime=1777447435276, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1256268854674710546, tenantId=1146029695717560320, journalId=1255847803461844995, issueId=1256263559323967535, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1256268854678904851, tenantId=1146029695717560320, journalId=1255847803461844995, issueId=1256263559323967535, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=250175, endPage=, ext={EN=ArticleExt(id=1256263567792287993, articleId=1256263565850325230, tenantId=1146029695717560320, journalId=1255847803461844995, language=EN, title=Screening of molecular markers specific for Tilletia controversa based on the whole genome sequence, columnId=1256263562373226548, journalTitle=Mycosystema, columnName=Research paper, runingTitle=null, highlight=null, articleAbstract=

Wheat dwarf smut, caused by Tilletia controversa (TCK), is a dangerous fungal wheat disease that is highly destructive and difficult to eradication, possessing a significant impact. The disease is known as “No. 1 disease of wheat”, and is listed as a quarantine pest by European Plant Protection Organisation (EPPO), Australia, China and other countries/regions and organizations. Due to difficulties for distinguishing TCK from other closely related species such as Tilletia laevis in levels of morphological characteristics and molecular biology, misdiagnosis easily happen in quarantine inspections. In this study, TCK-specific molecular markers were developed at the genomic level, and four candidate genes, namely OG0008430, OG0008601, OG0008603 and OG0008610, were screened. Eight pairs of primers and four probes based on these four candidate genes were designed. Validation of combinations among the primers and probes were verified, and two sets of “triple + single” real-time fluorescence PCR methods were established. This combined method can effectively distinguish target species (TCK) from closely related species, achieving accurate identification of TCK, and it can also be used to distinguish different species within the genus Tilletia.

, correspAuthors=Ruifang GAO, authorNote=null, correspAuthorsNote=
*E-mail:
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由小麦矮腥黑粉菌Tilletia controversa (TCK)引起的小麦矮腥黑穗病是一种危害大、防控难、影响特别大的危险性真菌病害，被称为“小麦一号病”，EPPO、澳大利亚、中国等国家/地区和组织将其列为检疫性病害。小麦矮腥黑粉菌与小麦光腥黑粉菌等近似种在形态学、分子生物学上的区分鉴定较困难，在检疫检查中容易造成误诊。本研究在全基因组水平上开发TCK的特异性分子标记，筛选到4个候选差异基因，即OG0008430、OG0008601、OG0008603、OG0008610，针对这4个基因分别设计了引物和探针，经过组合验证，建立了两组“三重+单重”实时荧光PCR方法，可以有效区分目标种(TCK)和近似种，实现小麦腥黑粉菌的准确鉴定，也可区分腥黑粉菌属的不同种。

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Plant Protection, 33(2): 6-10 (in Chinese), articleTitle=Advances in risk analyses of introduction and establishment of wheat dwarf bunt in China, refAbstract=null), Reference(id=1256263615070483260, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, doi=null, pmid=null, pmcid=null, year=2010, volume=46, issue=3, pageStart=107, pageEnd=115, url=null, language=null, rfNumber=[32], rfOrder=31, authorNames=Zouhar M, Mazáková J, Prokinová E, Váňová M, Ryšánek P, journalName=Plant Protection Science, refType=null, unstructuredReference=Zouhar M, Mazáková J, Prokinová E, Váňová M, Ryšánek P, 2010. Quantification of Tilletia caries and Tilletia controversa mycelium in wheat apical meristem by real-time PCR. Plant Protection Science, 46(3): 107-115, articleTitle=Quantification of Tilletia caries and Tilletia controversa mycelium in wheat apical meristem by real-time PCR., refAbstract=null), Reference(id=1256263615238255424, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, doi=null, pmid=null, pmcid=null, year=2002, volume=32, issue=4, pageStart=312, pageEnd=318, url=null, language=null, rfNumber=[33], rfOrder=32, authorNames=陈克, 姚文国, 章正, 肖悦岩, 严进, 徐岩, 白章红, 陈小帆, 包黎明, journalName=植物病理学报, refType=null, unstructuredReference=陈克, 姚文国, 章正, 肖悦岩, 严进, 徐岩, 白章红, 陈小帆, 包黎明, 2002. 小麦矮腥黑穗病在中国定殖风险分析及区划研究. 植物病理学报, 32(4): 312-318, articleTitle=小麦矮腥黑穗病在中国定殖风险分析及区划研究, refAbstract=null), Reference(id=1256263615380861765, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, doi=null, pmid=null, pmcid=null, year=2007, volume=33, issue=2, pageStart=6, pageEnd=10, url=null, language=null, rfNumber=[34], rfOrder=33, authorNames=周益林, 段霞瑜, 贾文明, 陈万权, 邱焯, journalName=植物保护, refType=null, unstructuredReference=周益林, 段霞瑜, 贾文明, 陈万权, 邱焯, 2007. 小麦矮腥黑穗病(TCK)传入中国及其定殖的风险分析研究进展. 植物保护, 33(2): 6-10, articleTitle=小麦矮腥黑穗病(TCK)传入中国及其定殖的风险分析研究进展, refAbstract=null)], funds=[Fund(id=1256263609852768932, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, awardId=2023HK001, language=EN, fundingSource=Scientific Research Projects of the General Administration of Customs(2023HK001), fundOrder=null, country=null), Fund(id=1256263609966015144, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, awardId=2023HK001, language=CN, fundingSource=海关总署科研项目(2023HK001), fundOrder=null, country=null), Fund(id=1256263610041512618, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, awardId=XZ202201ZY0011N, language=EN, fundingSource=Key Research and Development Projects of the Xizang Autonomous Region Science and Technology Plan(XZ202201ZY0011N), fundOrder=null, country=null), Fund(id=1256263610129593006, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, awardId=XZ202201ZY0011N, language=CN, fundingSource=西藏自治区科技计划项目重点研发计划项目(XZ202201ZY0011N), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1256263577623736651, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, xref=null, ext=[AuthorCompanyExt(id=1256263577682456912, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, companyId=1256263577623736651, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1 Animal and Plant Inspection and Quarantine Technology Center of Shenzhen Customs District of P. R. China, Shenzhen 518045, Guangdong, China), AuthorCompanyExt(id=1256263577690845521, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, companyId=1256263577623736651, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1 深圳海关动植物检验检疫技术中心，广东 深圳 518045)]), AuthorCompany(id=1256263578085110103, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, xref=null, ext=[AuthorCompanyExt(id=1256263578118664536, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, companyId=1256263578085110103, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2 Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China), AuthorCompanyExt(id=1256263578135441753, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, companyId=1256263578085110103, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2 中国科学院微生物研究所，北京 100101)])], figs=[ArticleFig(id=1256263604085600820, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=EN, label=Fig. 1, caption=Multiple real-time fluorescence PCR amplification curve (Combination 1).

A: Triple (OG0008601, OG0008603, OG0008610); B: Single (OG0008430).

, figureFileSmall=7q+OUoljnE7AZ9dYn9JYVg==, figureFileBig=CwolSkOqMIOdInAC8r63ig==, tableContent=null), ArticleFig(id=1256263604542779960, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=CN, label=图1, caption=多重实时荧光PCR扩增曲线(组合一)

A：三重(OG0008601、OG0008603、OG0008610)；B：单重(OG0008430)

, figureFileSmall=7q+OUoljnE7AZ9dYn9JYVg==, figureFileBig=CwolSkOqMIOdInAC8r63ig==, tableContent=null), ArticleFig(id=1256263605276783170, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=EN, label=Fig. 2, caption=Multiple real-time fluorescence PCR amplification curve (Combination 2).

A: Triple (OG0008430, OG0008603, OG0008610); B: Single (OG0008601).

, figureFileSmall=WDWKy4dXAVNmbvdxyopAsQ==, figureFileBig=uzOmtCNrFd7udZUx7PxXYw==, tableContent=null), ArticleFig(id=1256263605394223686, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=CN, label=图2, caption=多重实时荧光PCR扩增曲线(组合二)

A：三重(OG0008430、OG0008603、OG0008610)；B：单重(OG0008601)

, figureFileSmall=WDWKy4dXAVNmbvdxyopAsQ==, figureFileBig=uzOmtCNrFd7udZUx7PxXYw==, tableContent=null), ArticleFig(id=1256263605708796491, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=EN, label=Table 1, caption=

Information of isolates of Tilletia species used for whole genomic analysis

, figureFileSmall=null, figureFileBig=null, tableContent=
序号
Serial number		 中文名
Chinese name		 拉丁名
Scientific name		 菌系
Isolate code		 全基因组数据来源
Source of genome data
1 小麦矮腥黑粉菌 T. controversa TCK-79 自测(This study)
2 小麦矮腥黑粉菌 T. controversa TCK-XJ 自测(This study)
3 小麦光腥黑粉菌 T. foetida TFO-XJ 自测(This study)
4 小麦矮腥黑粉菌 T. controversa OR GenBank (GCA_905071765.1)
5 小麦光腥黑粉菌 T. laevis ATCC 42080 GenBank (GCA_009428275.1)
6 小麦光腥黑粉菌 T. laevis DAOMC 238040 GenBank (GCA_009428285.1)
7 小麦光腥黑粉菌 T. laevis L-19 GenBank (GCA_905071715.1)
8 小麦光腥黑粉菌 T. laevis LLFL GenBank (GCA_905071755.1)
9 黑麦草腥黑粉菌 T. walkeri DAOMC 238049 GenBank (GCA_009428295.1)
10 黑麦草腥黑粉菌 T. walkeri DAOMC 236422 GenBank (GCA_001645055.2)
11 印度腥黑粉菌 T. indica DAOMC 236408 GenBank (GCA_009428345.1)
12 印度腥黑粉菌 T. indica DAOMC 236416 GenBank (GCA_001645015.2)
13 印度腥黑粉菌 T. indica DAOMC 236414 GenBank (GCA_009428365.1)
14 小麦网腥黑粉菌 T. caries DAOMC 238032 GenBank (GCA_001645005.2)
15 小麦网腥黑粉菌 T. caries AI GenBank (GCA_905068135.1)
16 小麦网腥黑粉菌 T. caries AA11 GenBank (GCA_905072865.1)
17 小麦网腥黑粉菌 T. caries AZH3 GenBank (GCA_905071745.1)
18 小麦网腥黑粉菌 T. caries AO GenBank (GCA_905071735.1)
19 小麦矮腥黑粉菌 T. controversa DAOMC 236426 GenBank (GCA_001645045.2)
20 小麦矮腥黑粉菌 T. controversa DAOMC 238052 GenBank (GCA_009428265.1)
21 小麦矮腥黑粉菌 T. controversa OA2 GenBank (GCA_905071725.1)
22 小麦矮腥黑粉菌 T. controversa OL14 GenBank (GCA_905071785.1)
23 小麦矮腥黑粉菌 T. controversa OW GenBank (GCA_905071705.1)
24 小麦矮腥黑粉菌 T. controversa OV GenBank (GCA_905071775.1)
25 稻粒腥黑粉菌 T. horrida TX6 GenBank (GCA_030462715.1)
26 稻粒腥黑粉菌 T. horrida TX7 GenBank (GCA_030504495.1)
27 稻粒腥黑粉菌 T. horrida TX5 GenBank (GCA_030462695.1)
28 稻粒腥黑粉菌 T. horrida TX3 GenBank (GCA_030462655.1)
29 稻粒腥黑粉菌 T. horrida TX1 GenBank (GCA_030462675.1)
30 稻粒腥黑粉菌 T. horrida TX2 GenBank (GCA_030462665.1)
31 稻粒腥黑粉菌 T. horrida TX4 GenBank (GCA_030462685.1)
), ArticleFig(id=1256263606107255376, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=CN, label=表1, caption=

用于全基因组分析的Tilletia菌株信息

, figureFileSmall=null, figureFileBig=null, tableContent=
序号
Serial number		 中文名
Chinese name		 拉丁名
Scientific name		 菌系
Isolate code		 全基因组数据来源
Source of genome data
1 小麦矮腥黑粉菌 T. controversa TCK-79 自测(This study)
2 小麦矮腥黑粉菌 T. controversa TCK-XJ 自测(This study)
3 小麦光腥黑粉菌 T. foetida TFO-XJ 自测(This study)
4 小麦矮腥黑粉菌 T. controversa OR GenBank (GCA_905071765.1)
5 小麦光腥黑粉菌 T. laevis ATCC 42080 GenBank (GCA_009428275.1)
6 小麦光腥黑粉菌 T. laevis DAOMC 238040 GenBank (GCA_009428285.1)
7 小麦光腥黑粉菌 T. laevis L-19 GenBank (GCA_905071715.1)
8 小麦光腥黑粉菌 T. laevis LLFL GenBank (GCA_905071755.1)
9 黑麦草腥黑粉菌 T. walkeri DAOMC 238049 GenBank (GCA_009428295.1)
10 黑麦草腥黑粉菌 T. walkeri DAOMC 236422 GenBank (GCA_001645055.2)
11 印度腥黑粉菌 T. indica DAOMC 236408 GenBank (GCA_009428345.1)
12 印度腥黑粉菌 T. indica DAOMC 236416 GenBank (GCA_001645015.2)
13 印度腥黑粉菌 T. indica DAOMC 236414 GenBank (GCA_009428365.1)
14 小麦网腥黑粉菌 T. caries DAOMC 238032 GenBank (GCA_001645005.2)
15 小麦网腥黑粉菌 T. caries AI GenBank (GCA_905068135.1)
16 小麦网腥黑粉菌 T. caries AA11 GenBank (GCA_905072865.1)
17 小麦网腥黑粉菌 T. caries AZH3 GenBank (GCA_905071745.1)
18 小麦网腥黑粉菌 T. caries AO GenBank (GCA_905071735.1)
19 小麦矮腥黑粉菌 T. controversa DAOMC 236426 GenBank (GCA_001645045.2)
20 小麦矮腥黑粉菌 T. controversa DAOMC 238052 GenBank (GCA_009428265.1)
21 小麦矮腥黑粉菌 T. controversa OA2 GenBank (GCA_905071725.1)
22 小麦矮腥黑粉菌 T. controversa OL14 GenBank (GCA_905071785.1)
23 小麦矮腥黑粉菌 T. controversa OW GenBank (GCA_905071705.1)
24 小麦矮腥黑粉菌 T. controversa OV GenBank (GCA_905071775.1)
25 稻粒腥黑粉菌 T. horrida TX6 GenBank (GCA_030462715.1)
26 稻粒腥黑粉菌 T. horrida TX7 GenBank (GCA_030504495.1)
27 稻粒腥黑粉菌 T. horrida TX5 GenBank (GCA_030462695.1)
28 稻粒腥黑粉菌 T. horrida TX3 GenBank (GCA_030462655.1)
29 稻粒腥黑粉菌 T. horrida TX1 GenBank (GCA_030462675.1)
30 稻粒腥黑粉菌 T. horrida TX2 GenBank (GCA_030462665.1)
31 稻粒腥黑粉菌 T. horrida TX4 GenBank (GCA_030462685.1)
), ArticleFig(id=1256263606275027540, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=EN, label=Table 2, caption=

Tilletia species materials used for T. controversa specificity validation

, figureFileSmall=null, figureFileBig=null, tableContent=
序号
Serial Number		 编号
Isolate		 拉丁名
Scientific name		 中文名
Chinese name
1 ATCC42079 Tilletia controversa 小麦矮腥黑粉菌
2 TCK-XJ T. controversa 小麦矮腥黑粉菌
3 CBS121955 T. walkeri 黑麦草腥黑粉菌
4 CBS121956-1 T. walkeri 黑麦草腥黑粉菌
5 CBS121956-2 T. walkeri 黑麦草腥黑粉菌
6 5114 T. indica 印度腥黑粉菌
7 ATCC42080 T. foetida 小麦光腥黑粉菌
8 CBS121950 T. laevis 小麦光腥黑粉菌
9 CBS32432 T. laevis 小麦光腥黑粉菌
10 CBS324.32 T. laevis 小麦光腥黑粉菌
11 CBS121949 T. laevis 小麦光腥黑粉菌
12 TFO-XJ T. laevis 小麦光腥黑粉菌
13 CBS122992 T. fusca var. fusca 禾草腥黑粉菌
14 ATCC90926 T. fusca var. fusca 禾草腥黑粉菌
15 CBS121948 T. brevifaciens /
16 CBS122991 T. goloskokovii /
17 CBS122995 T. goloskokovii /
18 CBS123001-1 T. bromi 雀麦腥黑粉菌
19 CBS123001-2 T. bromi 雀麦腥黑粉菌
20 CBS119.19-1 T. tritici 小麦网腥黑粉菌
21 CBS119.19-2 T. tritici 小麦网腥黑粉菌
22 CBS121954 T. vankyi /
23 CBS372.36 T. caries 小麦网腥黑粉菌
24 CBS366.36 T. caries 小麦网腥黑粉菌
25 CBS371.36 T. caries 小麦网腥黑粉菌
26 CBS121951 T. caries 小麦网腥黑粉菌
27 CBS373.36 T. caries 小麦网腥黑粉菌
28 CBS370.36 T. caries 小麦网腥黑粉菌
29 CBS160.85 T. caries 小麦网腥黑粉菌
30 CBS372.36 T. caries 小麦网腥黑粉菌
31 CBS368.36 T. caries 小麦网腥黑粉菌
32 CBS374.36 T. caries 小麦网腥黑粉菌
33 CBS369.36 T. caries 小麦网腥黑粉菌
34 CBS375.31 T. caries 小麦网腥黑粉菌
35 ATCC90927 T. fusca var. bromitectorum 禾草腥黑粉菌
36 CBS277.28 T. horrida 稻粒腥黑粉菌
37 CBS122087 T. secalis 黑麦草腥黑粉菌
), ArticleFig(id=1256263606556045913, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=CN, label=表2, caption=

用于小麦矮腥黑粉菌特异性验证的Tilletia属菌株材料

, figureFileSmall=null, figureFileBig=null, tableContent=
序号
Serial Number		 编号
Isolate		 拉丁名
Scientific name		 中文名
Chinese name
1 ATCC42079 Tilletia controversa 小麦矮腥黑粉菌
2 TCK-XJ T. controversa 小麦矮腥黑粉菌
3 CBS121955 T. walkeri 黑麦草腥黑粉菌
4 CBS121956-1 T. walkeri 黑麦草腥黑粉菌
5 CBS121956-2 T. walkeri 黑麦草腥黑粉菌
6 5114 T. indica 印度腥黑粉菌
7 ATCC42080 T. foetida 小麦光腥黑粉菌
8 CBS121950 T. laevis 小麦光腥黑粉菌
9 CBS32432 T. laevis 小麦光腥黑粉菌
10 CBS324.32 T. laevis 小麦光腥黑粉菌
11 CBS121949 T. laevis 小麦光腥黑粉菌
12 TFO-XJ T. laevis 小麦光腥黑粉菌
13 CBS122992 T. fusca var. fusca 禾草腥黑粉菌
14 ATCC90926 T. fusca var. fusca 禾草腥黑粉菌
15 CBS121948 T. brevifaciens /
16 CBS122991 T. goloskokovii /
17 CBS122995 T. goloskokovii /
18 CBS123001-1 T. bromi 雀麦腥黑粉菌
19 CBS123001-2 T. bromi 雀麦腥黑粉菌
20 CBS119.19-1 T. tritici 小麦网腥黑粉菌
21 CBS119.19-2 T. tritici 小麦网腥黑粉菌
22 CBS121954 T. vankyi /
23 CBS372.36 T. caries 小麦网腥黑粉菌
24 CBS366.36 T. caries 小麦网腥黑粉菌
25 CBS371.36 T. caries 小麦网腥黑粉菌
26 CBS121951 T. caries 小麦网腥黑粉菌
27 CBS373.36 T. caries 小麦网腥黑粉菌
28 CBS370.36 T. caries 小麦网腥黑粉菌
29 CBS160.85 T. caries 小麦网腥黑粉菌
30 CBS372.36 T. caries 小麦网腥黑粉菌
31 CBS368.36 T. caries 小麦网腥黑粉菌
32 CBS374.36 T. caries 小麦网腥黑粉菌
33 CBS369.36 T. caries 小麦网腥黑粉菌
34 CBS375.31 T. caries 小麦网腥黑粉菌
35 ATCC90927 T. fusca var. bromitectorum 禾草腥黑粉菌
36 CBS277.28 T. horrida 稻粒腥黑粉菌
37 CBS122087 T. secalis 黑麦草腥黑粉菌
), ArticleFig(id=1256263606874813020, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=EN, label=Table 3, caption=

Primer characteristics and PCR reaction conditions

, figureFileSmall=null, figureFileBig=null, tableContent=
基因
Gene		 引物
Primer		 引物长度
Length of
primer/bp		 Tm/℃ GC/% 片段长度
Length of
fragment/bp		 退火温度
Annealing
temperature/℃		 循环数
Number
of cycles
OG0008430 primer-8430-1F 19 56.3 57.9 121 52 32
primer-8430-1R 19 56 57.9
primer-8430-2F 19 56.4 57.9 264 54 33
primer-8430-2R 20 56.1 55
OG0008601 primer-8601-1F 22 55.9 50 262 54 35
primer-8601-1R 20 56.1 55
primer-8601-2F 20 55.8 60 127 54 35
primer-8601-2R 20 56.1 55
OG0008603 primer-8603-1F 21 55.9 57.1 265 54 36
primer-8603-1R 20 55.7 55
primer-8603-2F 21 56.5 52.4 266 54 36
primer-8603-2R 19 55.9 57.9
OG0008610 primer-8610-1F 19 56.1 57.9 180 52 35
primer-8610-1R 21 56.2 57.1
primer-8610-2F 19 55.6 52.6 177 54 35
primer-8610-2R 20 55.9 55
), ArticleFig(id=1256263607134859875, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=CN, label=表3, caption=

引物特征和PCR反应条件

, figureFileSmall=null, figureFileBig=null, tableContent=
基因
Gene		 引物
Primer		 引物长度
Length of
primer/bp		 Tm/℃ GC/% 片段长度
Length of
fragment/bp		 退火温度
Annealing
temperature/℃		 循环数
Number
of cycles
OG0008430 primer-8430-1F 19 56.3 57.9 121 52 32
primer-8430-1R 19 56 57.9
primer-8430-2F 19 56.4 57.9 264 54 33
primer-8430-2R 20 56.1 55
OG0008601 primer-8601-1F 22 55.9 50 262 54 35
primer-8601-1R 20 56.1 55
primer-8601-2F 20 55.8 60 127 54 35
primer-8601-2R 20 56.1 55
OG0008603 primer-8603-1F 21 55.9 57.1 265 54 36
primer-8603-1R 20 55.7 55
primer-8603-2F 21 56.5 52.4 266 54 36
primer-8603-2R 19 55.9 57.9
OG0008610 primer-8610-1F 19 56.1 57.9 180 52 35
primer-8610-1R 21 56.2 57.1
primer-8610-2F 19 55.6 52.6 177 54 35
primer-8610-2R 20 55.9 55
), ArticleFig(id=1256263607344575080, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=EN, label=Table 4, caption=

Homologous genes preliminarily screened

, figureFileSmall=null, figureFileBig=null, tableContent=
同源基因
Orthogroup		 GCA_
001645045		 GCA_
009428265		 GCA_
905071705		 GCA_
905071725		 GCA_
905071765		 GCA_
905071775		 GCA_
905071785
OG0007373 1 1 4 1 3 2 2
OG0008089 2 2 1 2 1 1 1
OG0008411 1 1 1 1 2 1 1
OG0008418 1 1 1 1 1 2 1
OG0008429 1 1 1 1 2 1 1
OG0008430 1 1 1 1 2 1 1
OG0008581 1 1 1 1 1 1 1
OG0008593 1 1 1 1 1 1 1
OG0008596 1 1 1 1 1 1 1
OG0008601 1 1 1 1 1 1 1
OG0008602 1 1 1 1 1 1 1
OG0008603 1 1 1 1 1 1 1
OG0008608 1 1 1 1 1 1 1
OG0008610 1 1 1 1 1 1 1
OG0008612 1 1 1 1 1 1 1
), ArticleFig(id=1256263607466209901, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=CN, label=表4, caption=

初步筛选获得的同源基因

, figureFileSmall=null, figureFileBig=null, tableContent=
同源基因
Orthogroup		 GCA_
001645045		 GCA_
009428265		 GCA_
905071705		 GCA_
905071725		 GCA_
905071765		 GCA_
905071775		 GCA_
905071785
OG0007373 1 1 4 1 3 2 2
OG0008089 2 2 1 2 1 1 1
OG0008411 1 1 1 1 2 1 1
OG0008418 1 1 1 1 1 2 1
OG0008429 1 1 1 1 2 1 1
OG0008430 1 1 1 1 2 1 1
OG0008581 1 1 1 1 1 1 1
OG0008593 1 1 1 1 1 1 1
OG0008596 1 1 1 1 1 1 1
OG0008601 1 1 1 1 1 1 1
OG0008602 1 1 1 1 1 1 1
OG0008603 1 1 1 1 1 1 1
OG0008608 1 1 1 1 1 1 1
OG0008610 1 1 1 1 1 1 1
OG0008612 1 1 1 1 1 1 1
), ArticleFig(id=1256263607831114354, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=EN, label=Table 5, caption=

The identification efficiency of species of the genus Tilletia based on amplification with screened genes

, figureFileSmall=null, figureFileBig=null, tableContent=
样本编号
Sample		 拉丁名
Scientific name		 筛选的基因
Genes screened
OG0008430 OG0008601 OG0008603 OG0008610
TCK-79 Tilletia contorversa √ √ √ √
TCK-XJ T. contorversa √ √ √ √
CBS121956 T. walkeri - - - √
CBS121956 T. walkeri - - - -
CBS121955 T. walkeri - - - -
CBS32432 T. laevis - √ - -
CBS324.32 T. laevis - - - -
CBS121949 T. laevis - - - √
TFO-XJ T. laevis - - - -
TFe-XJ T. laevis - - - √
CBS366.36 T. caries √ - - √
CBS371.36 T. caries - - - -
CBS121951 T. caries - - - -
CBS373.36 T. caries - - - √
CBS370.36 T. caries - - - √
CBS160.85 T. caries - - - √
CBS372.36 T. caries - - - -
CBS368.36 T. caries - - - -
CBS374.36 T. caries - - - -
CBS369.36 T. caries - - - √
CBS385.36 T. caries - - - -
CBS122995 T. goloskokovii √ - √ √
CBS122991 T. goloskokovii - - √ √
ATCC90927 T. bromitectorum - - √ √
CBS277.28 T. horrida √ - √ -
CBS121954 T. vankyi - - - -
CBS122087 T. secalis √ - √ √
ATCC42080 T. foetida √ - √ √
ATCC90926 T. fusca √ - √ √
CBS121948 T. brevifaciens √ - - √
CBS123001 T. bromi - - - -
CBS119.19 T. tritici - - - -
), ArticleFig(id=1256263608049218166, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=CN, label=表5, caption=

筛选的基因扩增后对Tilletia属的种水平区分鉴定效率

, figureFileSmall=null, figureFileBig=null, tableContent=
样本编号
Sample		 拉丁名
Scientific name		 筛选的基因
Genes screened
OG0008430 OG0008601 OG0008603 OG0008610
TCK-79 Tilletia contorversa √ √ √ √
TCK-XJ T. contorversa √ √ √ √
CBS121956 T. walkeri - - - √
CBS121956 T. walkeri - - - -
CBS121955 T. walkeri - - - -
CBS32432 T. laevis - √ - -
CBS324.32 T. laevis - - - -
CBS121949 T. laevis - - - √
TFO-XJ T. laevis - - - -
TFe-XJ T. laevis - - - √
CBS366.36 T. caries √ - - √
CBS371.36 T. caries - - - -
CBS121951 T. caries - - - -
CBS373.36 T. caries - - - √
CBS370.36 T. caries - - - √
CBS160.85 T. caries - - - √
CBS372.36 T. caries - - - -
CBS368.36 T. caries - - - -
CBS374.36 T. caries - - - -
CBS369.36 T. caries - - - √
CBS385.36 T. caries - - - -
CBS122995 T. goloskokovii √ - √ √
CBS122991 T. goloskokovii - - √ √
ATCC90927 T. bromitectorum - - √ √
CBS277.28 T. horrida √ - √ -
CBS121954 T. vankyi - - - -
CBS122087 T. secalis √ - √ √
ATCC42080 T. foetida √ - √ √
ATCC90926 T. fusca √ - √ √
CBS121948 T. brevifaciens √ - - √
CBS123001 T. bromi - - - -
CBS119.19 T. tritici - - - -
), ArticleFig(id=1256263608250544764, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=EN, label=Table 6, caption=

Information of primer and probe sequences of candidate gene fragments

, figureFileSmall=null, figureFileBig=null, tableContent=
基因编号
Gene code		 引物名称
Primer		 引物序列
Primer sequence (5′→3′)		 探针
Probe		 探针序列
Probe sequence
OG0008430 primer-8430-1F TGATGACGCTCCAGCCAGA primer-8430-1PF 5′-FAM-TCTTCGACCACTGGAGAGTCA-3′-MGB
primer-8430-1R GCCATGACGACGGACGAAT
primer-8430-2F GCCGTCGCTGTTGTCTTGA primer-8430-2PR 5′-JOE-CCACCGACGACCTGACGCTCT-3′-BHQ1
primer-8430-2R AGCCTTGCGGAAGTCATACG
OG0008601 primer-8601-1F CCTGTGAATGAACTTGGCTGAC primer-8601-1PF 5′-HEX-CTCCGAACACGACCCTCAACG-3′-MGB
primer-8601-1R GTTGGCGTAGATGGCACTCA
primer-8601-2F GTTCACTCCGACCGAGAAGG primer-8601-2PF 5′-JOE-AGTCTTGGTCGGTCAGGGCAT-3′-BHQ1
primer-8601-2R GTTGGCGTAGATGGCACTCA
OG0008603 primer-8603-1F CTACCACCACACCACCTCTTC primer-8603-1PF 5′-FAM-ACTCAAGGCAAGGTTGGGACA-3′-BHQ1
primer-8603-1R GTCCGCTTGGTCGTAGTTGA
primer-8603-2F TACCACCACACCACCTCTTCA primer-8603-2PF 5′-JOE-AGGTTGGGACAAAGCTATCGG-3′-BHQ1
primer-8603-2R AGGTCCGCTTGGTCGTAGT
OG0008610 primer-8610-1F AGGCGGTAAGTGCGTTGTC primer-8610-1PR 5′-ROX-ATGATGTAGCGTTGCTCCAGG-3′-BHQ2
primer-8610-1R AGACTTGAGGACGAGGAGGAG
primer-8610-2F AAGGCGGTAAGTGCGTTGT primer-8610-2PR 5′-CY-5-TGTAGCGTTGCTCCAGGGTGT-3′-BHQ2
primer-8610-2R TTGAGGACGAGGAGGAGCAT
), ArticleFig(id=1256263608477037182, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=CN, label=表6, caption=

对候选基因片段设计的引物探针序列信息

, figureFileSmall=null, figureFileBig=null, tableContent=
基因编号
Gene code		 引物名称
Primer		 引物序列
Primer sequence (5′→3′)		 探针
Probe		 探针序列
Probe sequence
OG0008430 primer-8430-1F TGATGACGCTCCAGCCAGA primer-8430-1PF 5′-FAM-TCTTCGACCACTGGAGAGTCA-3′-MGB
primer-8430-1R GCCATGACGACGGACGAAT
primer-8430-2F GCCGTCGCTGTTGTCTTGA primer-8430-2PR 5′-JOE-CCACCGACGACCTGACGCTCT-3′-BHQ1
primer-8430-2R AGCCTTGCGGAAGTCATACG
OG0008601 primer-8601-1F CCTGTGAATGAACTTGGCTGAC primer-8601-1PF 5′-HEX-CTCCGAACACGACCCTCAACG-3′-MGB
primer-8601-1R GTTGGCGTAGATGGCACTCA
primer-8601-2F GTTCACTCCGACCGAGAAGG primer-8601-2PF 5′-JOE-AGTCTTGGTCGGTCAGGGCAT-3′-BHQ1
primer-8601-2R GTTGGCGTAGATGGCACTCA
OG0008603 primer-8603-1F CTACCACCACACCACCTCTTC primer-8603-1PF 5′-FAM-ACTCAAGGCAAGGTTGGGACA-3′-BHQ1
primer-8603-1R GTCCGCTTGGTCGTAGTTGA
primer-8603-2F TACCACCACACCACCTCTTCA primer-8603-2PF 5′-JOE-AGGTTGGGACAAAGCTATCGG-3′-BHQ1
primer-8603-2R AGGTCCGCTTGGTCGTAGT
OG0008610 primer-8610-1F AGGCGGTAAGTGCGTTGTC primer-8610-1PR 5′-ROX-ATGATGTAGCGTTGCTCCAGG-3′-BHQ2
primer-8610-1R AGACTTGAGGACGAGGAGGAG
primer-8610-2F AAGGCGGTAAGTGCGTTGT primer-8610-2PR 5′-CY-5-TGTAGCGTTGCTCCAGGGTGT-3′-BHQ2
primer-8610-2R TTGAGGACGAGGAGGAGCAT
), ArticleFig(id=1256263608686752387, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=EN, label=Table 7, caption=

Combination and results of multiple qPCR (Combination 1)

, figureFileSmall=null, figureFileBig=null, tableContent=
组合
Combination		 引物名称
Primer		 探针
Probe		 供试菌
Species		 检测
Test
(8601-2)		 Ct值
Ct
value		 检测
Test
(8603-1)		 Ct值
Ct
value		 检测
Test
(8610-1)		 Ct值
Ct
value
三重
Triple
(OG0008601,
OG0008603,
OG0008610)		 primer-8601-2F primer-8601-2PF Tilletia walkeri - 33.39 - 34.23 - 29.12
primer-8601-2R T. goloskokovii √ 28.61 √ 29.11 √ 27.92
primer-8603-1F primer-8603-1PF T. bromitectorum - 34.13 √ 32.19 √ 28.59
primer-8603-1R T. secalis √ 32.28 √ 32.59 √ 28.66
primer-8610-1F primer-8610-1PR T. caries - 35.06 - 35.33 - 29.29
primer-8610-1R T. caries - 34.7 - - - 28.9
T. contorversa √ 30.76 √ 31.52 √ 28.28
CK - - - - - -
单重
Single
(OG0008430)		 primer-8430-2F primer-8430-2PR T. secalis - -
primer-8430-2R T. goloskokovii - -
T. foetida √ 33.53
T. caries - -
T. fusca √ 33
T. caries - -
T. contorversa √ 34.69
- - -
), ArticleFig(id=1256263608938410633, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=CN, label=表7, caption=

多重qPCR组合及其检测结果(组合一)

, figureFileSmall=null, figureFileBig=null, tableContent=
组合
Combination		 引物名称
Primer		 探针
Probe		 供试菌
Species		 检测
Test
(8601-2)		 Ct值
Ct
value		 检测
Test
(8603-1)		 Ct值
Ct
value		 检测
Test
(8610-1)		 Ct值
Ct
value
三重
Triple
(OG0008601,
OG0008603,
OG0008610)		 primer-8601-2F primer-8601-2PF Tilletia walkeri - 33.39 - 34.23 - 29.12
primer-8601-2R T. goloskokovii √ 28.61 √ 29.11 √ 27.92
primer-8603-1F primer-8603-1PF T. bromitectorum - 34.13 √ 32.19 √ 28.59
primer-8603-1R T. secalis √ 32.28 √ 32.59 √ 28.66
primer-8610-1F primer-8610-1PR T. caries - 35.06 - 35.33 - 29.29
primer-8610-1R T. caries - 34.7 - - - 28.9
T. contorversa √ 30.76 √ 31.52 √ 28.28
CK - - - - - -
单重
Single
(OG0008430)		 primer-8430-2F primer-8430-2PR T. secalis - -
primer-8430-2R T. goloskokovii - -
T. foetida √ 33.53
T. caries - -
T. fusca √ 33
T. caries - -
T. contorversa √ 34.69
- - -
), ArticleFig(id=1256263609122960017, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=EN, label=Table 8, caption=

Combination and results of multiple qPCR (Combination 2)

, figureFileSmall=null, figureFileBig=null, tableContent=
引物名称
Primer		 探针
Probe		 供试菌
Species		 检测
Test
(8430-1)		 Ct值
Ct
value		 检测试
Test
(8603-1)		 Ct值
Ct
value		 检测
Test
(8610-2)		 Ct值
Ct
value
三重
Triple
(OG0008430,
OG0008603,
OG0008610)		 primer-8430-1F primer-8430-1PF Tilletia caries √ 26.29 - - √ 24.42
primer-8430-1R T. bromitectorum - 27.61 √ 28.13 √ 27.5
primer-8603-1F primer-8603-1PF T. foetida √ 26.94 √ 28.29 √ 27.84
primer-8603-1R T. caries - 27.96 - - - 29.02
primer-8610-2F primer-8610-2PR T. caries - 27.5 - - √ 27.47
primer-8610-2R T. caries - 27.5 - - √ 28.37
T. contorversa √ 26.83 √ 27.97 √ 27.92
CK - - - - - -
单重
Single
(OG0008601)		 primer-8601-1F primer-8601-1PF T. laevis √ 33.5
primer-8601-1R T. caries - -
T. secalis √ 32.66
T. foetida - 35.78
T. fusca - 36.15
T. caries - 35.55
T. contorversa √ 29.97
- - -
), ArticleFig(id=1256263609391395479, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=CN, label=表8, caption=

多重qPCR组合及其检测结果(组合二)

, figureFileSmall=null, figureFileBig=null, tableContent=
引物名称
Primer		 探针
Probe		 供试菌
Species		 检测
Test
(8430-1)		 Ct值
Ct
value		 检测试
Test
(8603-1)		 Ct值
Ct
value		 检测
Test
(8610-2)		 Ct值
Ct
value
三重
Triple
(OG0008430,
OG0008603,
OG0008610)		 primer-8430-1F primer-8430-1PF Tilletia caries √ 26.29 - - √ 24.42
primer-8430-1R T. bromitectorum - 27.61 √ 28.13 √ 27.5
primer-8603-1F primer-8603-1PF T. foetida √ 26.94 √ 28.29 √ 27.84
primer-8603-1R T. caries - 27.96 - - - 29.02
primer-8610-2F primer-8610-2PR T. caries - 27.5 - - √ 27.47
primer-8610-2R T. caries - 27.5 - - √ 28.37
T. contorversa √ 26.83 √ 27.97 √ 27.92
CK - - - - - -
单重
Single
(OG0008601)		 primer-8601-1F primer-8601-1PF T. laevis √ 33.5
primer-8601-1R T. caries - -
T. secalis √ 32.66
T. foetida - 35.78
T. fusca - 36.15
T. caries - 35.55
T. contorversa √ 29.97
- - -
), ArticleFig(id=1256263609534001818, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=EN, label=Table 9, caption=

Validation of four pairs of primers for Tilletia species based on amplification

, figureFileSmall=null, figureFileBig=null, tableContent=
样本名称
Sample		 基因代码
Gene code		 比对结果
Blast results
Max score Total score Query cover E value Per. Ident. Acc. Len. Accession
Tilletia controversa OG0008601 309 309 16% 1E-88 100 167 Query_321797
T. indica OG0008430 / / / / / / /
T. foetida OG0008430 68 68 10% 5E-17 95.24 45 Query_6580459
T. vankyi OG0008430 80.5 80.5 10% 1E-20 100 50 Query_309859
T. walkeri OG0008601 / / / / / / /
T. bromi OG0008601 311 311 16% 3E-89 99.42 171 Query_512181
T. goloskokovii OG0008603 322 322 34% 8E-93 98.37 188 Query_5118639
T. laevis OG0008610 / / / / / / /
T. tritici OG0008610 / / / / / / /
), ArticleFig(id=1256263609689191069, tenantId=1146029695717560320, journalId=1255847803461844995, articleId=1256263565850325230, language=CN, label=表9, caption=

筛选的4对引物对Tilletia属的种的扩增序列验证准确性

, figureFileSmall=null, figureFileBig=null, tableContent=
样本名称
Sample		 基因代码
Gene code		 比对结果
Blast results
Max score Total score Query cover E value Per. Ident. Acc. Len. Accession
Tilletia controversa OG0008601 309 309 16% 1E-88 100 167 Query_321797
T. indica OG0008430 / / / / / / /
T. foetida OG0008430 68 68 10% 5E-17 95.24 45 Query_6580459
T. vankyi OG0008430 80.5 80.5 10% 1E-20 100 50 Query_309859
T. walkeri OG0008601 / / / / / / /
T. bromi OG0008601 311 311 16% 3E-89 99.42 171 Query_512181
T. goloskokovii OG0008603 322 322 34% 8E-93 98.37 188 Query_5118639
T. laevis OG0008610 / / / / / / /
T. tritici OG0008610 / / / / / / /
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基于全基因组开发小麦矮腥黑粉菌特异性分子标记
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高瑞芳 1, * , 赵鹏 2 , 汤怡静 1 , 刘宵宵 1 , 徐欣宇 1 , 郑铭森 1
菌物学报 | 研究论文 2026,45(2): 250175
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菌物学报 | 研究论文 2026, 45(2): 250175
基于全基因组开发小麦矮腥黑粉菌特异性分子标记
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高瑞芳1, * , 赵鹏2, 汤怡静1, 刘宵宵1, 徐欣宇1, 郑铭森1
作者信息
  • 1 深圳海关动植物检验检疫技术中心，广东 深圳 518045
  • 2 中国科学院微生物研究所，北京 100101
Screening of molecular markers specific for Tilletia controversa based on the whole genome sequence
Ruifang GAO1, * , Peng ZHAO2, Yijing TANG1, Xiaoxiao LIU1, Xinyu XU1, Mingsen ZHENG1
Affiliations
  • 1 Animal and Plant Inspection and Quarantine Technology Center of Shenzhen Customs District of P. R. China, Shenzhen 518045, Guangdong, China
  • 2 Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
出版时间: 2026-02-22 doi: 10.13346/j.mycosystema.250175
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摘要
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由小麦矮腥黑粉菌Tilletia controversa (TCK)引起的小麦矮腥黑穗病是一种危害大、防控难、影响特别大的危险性真菌病害，被称为“小麦一号病”，EPPO、澳大利亚、中国等国家/地区和组织将其列为检疫性病害。小麦矮腥黑粉菌与小麦光腥黑粉菌等近似种在形态学、分子生物学上的区分鉴定较困难，在检疫检查中容易造成误诊。本研究在全基因组水平上开发TCK的特异性分子标记，筛选到4个候选差异基因，即OG0008430、OG0008601、OG0008603、OG0008610，针对这4个基因分别设计了引物和探针，经过组合验证，建立了两组“三重+单重”实时荧光PCR方法，可以有效区分目标种(TCK)和近似种，实现小麦腥黑粉菌的准确鉴定，也可区分腥黑粉菌属的不同种。

小麦矮腥黑粉菌  /  多重实时荧光PCR  /  分子标记  /  全基因组  /  检测方法

Wheat dwarf smut, caused by Tilletia controversa (TCK), is a dangerous fungal wheat disease that is highly destructive and difficult to eradication, possessing a significant impact. The disease is known as “No. 1 disease of wheat”, and is listed as a quarantine pest by European Plant Protection Organisation (EPPO), Australia, China and other countries/regions and organizations. Due to difficulties for distinguishing TCK from other closely related species such as Tilletia laevis in levels of morphological characteristics and molecular biology, misdiagnosis easily happen in quarantine inspections. In this study, TCK-specific molecular markers were developed at the genomic level, and four candidate genes, namely OG0008430, OG0008601, OG0008603 and OG0008610, were screened. Eight pairs of primers and four probes based on these four candidate genes were designed. Validation of combinations among the primers and probes were verified, and two sets of “triple + single” real-time fluorescence PCR methods were established. This combined method can effectively distinguish target species (TCK) from closely related species, achieving accurate identification of TCK, and it can also be used to distinguish different species within the genus Tilletia.

Tilletia controversa  /  multiple real-time fluorescence PCR  /  molecular marker  /  genome  /  detection method
高瑞芳, 赵鹏, 汤怡静, 刘宵宵, 徐欣宇, 郑铭森. 基于全基因组开发小麦矮腥黑粉菌特异性分子标记. 菌物学报, 2026 , 45 (2) : 250175 - . DOI: 10.13346/j.mycosystema.250175
Ruifang GAO, Peng ZHAO, Yijing TANG, Xiaoxiao LIU, Xinyu XU, Mingsen ZHENG. Screening of molecular markers specific for Tilletia controversa based on the whole genome sequence[J]. Mycosystema, 2026 , 45 (2) : 250175 - . DOI: 10.13346/j.mycosystema.250175
正文
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小麦Triticum aestivum L.是世界上最重要的主食作物之一。小麦矮腥黑穗病是小麦的一种经济毁灭性疾病，通过种子和土壤传播的疾病，经常危害冬季长期积雪地区的冬小麦(Muhae-Ud- Din et al. 2020a)。积雪较多促进小麦矮腥黑粉菌生长。土壤冻结前的长期寒冷、稳定湿润条件，适合冬孢子萌发和侵染。冬孢子具有很强的抗逆性，在有利的环境条件下，病原菌可以存活长达10年(Helback 1959；Trione 1982；Goates & Peterson 1999)。此病害会导致小麦产量减少，在严重发生条件下，损失可能达到70%-80%，甚至完全绝收(Parlak 1981)。释放三甲胺产生腐烂鱼腥味，也导致面粉质量下降(Parlak 1981；Chen et al. 2016)。该病害是小麦上危害大、防控难、影响特别大的一种危险性真菌病害，被称为“小麦一号病”(Mathre 1996)。该病害首次于1847年在捷克被发现，目前在欧洲、美洲、亚洲和非洲等31个国家均有分布(Gassner & Niemann 1954；Dewey 1975；Trione 1982；Grey 1986)。该病害大流行可使小麦减产75%以上，甚至绝产(Trione 1982；Trione et al. 1989)。其致病菌小麦矮腥黑粉菌Tilletia controversa J.G. Kühn寄主多达80余种，其繁殖体冬孢子可在土壤中存活长达10年以上，传播途径多样、抗逆性强，一旦传入则难以根除，欧洲地中海植物保护组织(EPPO)及泛非植物保护委员会(IAPPC)、澳大利亚、土耳其、捷克等区域性植物保护组织及国家均将其列入检疫性病害名录。我国于1966年将该病菌列为对外检疫性病菌(农业农村部与商务部联合发布《进口植物检疫对象名单》)，之后多次修订名录，仍将该病菌保留在检疫性有害生物名录至今。
检疫性有害生物的准确鉴定是植物检疫的技术基础，直接影响植物检疫链条。进口小麦中常有雀麦、黑麦草、早熟禾等其他禾本科杂草种子，这些杂草种子是小麦矮腥黑粉菌近似种的寄主，如小麦光腥黑粉菌T. laevis、雀麦腥黑粉菌T. bromi、禾草腥黑粉菌T. fusca var. bromi- tectorum，而小麦矮腥黑粉菌与这些同属不同种的形态特征相似，在检疫过程中容易造成误判(Wilcoxson & Saari 1996；Carris et al. 2006)。为了寻找准确、快速、简便的检测方法，几十年来，国内外学者对T. controversa及其近似种的比较形态学、自发荧光显微学、萌发生物学、血清学、生化技术等方面进行了大量研究。基于分子生物学技术的研究最多，以此建立了实时荧光PCR、数字PCR、MALDI-TOF MS等(Pimentel et al. 2000；Gao et al. 2010；Liu et al. 2020；Muhae-Ud-Din et al. 2020b；Chen et al. 2021)，但是，这些方法在特异性、适用性等方面都相对有限。有些方法不能准确区分T. controversa和其他种(Josefsen & Christiansen 2002；Kochanová et al. 2004；Mulholland & Mcewan 2010；Zouhar et al. 2010；Pieczul et al. 2018)；有些方法仅针对有限数量的样本有效(Liu et al. 2009)。由于常用于系统发育分析的基因组区域缺乏多态性(Mulholland & Mcewan 2010；Jayawardena et al. 2019)，因此，必须探索其他DNA区域以开发特异性分析。现有的国标《植物检疫-小麦矮腥黑穗病菌检疫鉴定方法》(GB/T 18085-2000)在应用时存在依靠检测人员的经验、耗时长、常规分子鉴定区分能力有限等不足，然而，植物检疫需要建立准确、快速的检测方法，形成相应检测鉴定的标准。因此，需要建立精准、快速、高灵敏性的检测鉴定方法。本研究通过比较全基因组分析筛选同源基因，设计引物验证同源基因的特异性，建立多基因联合筛选，以有效区分该病菌与其近似种。建立多重实时荧光PCR方法，适合用于口岸检测，提高小麦检疫通关效率，防止小麦矮腥黑粉菌随小麦原粮贸易和种质资源交流而扩散传播到其他地区的风险，保障我国小麦生产和贸易安全，为解决贸易争端提供检疫检测技术手段。
1 材料与方法
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1.1 供试材料
进行比较全基因组分析的Tilletia属全基因组数据共31份，3份为自测全基因组，28份来自GenBank组装注释的全基因组，其中T. controversa共有7份全基因组数据(表1)。3份自测全基因组为2个T. controversa (编号为TCK-79和TCK-XJ)，1个T. laevis (编号TFO-XJ)。
1.2 基因片段筛选分析
使用OrthoFinder (version 2.5.4)的序列相似性，对供试病菌的蛋白序列进行同源序列聚类，初步筛选出T. contorversa特有的蛋白序列，依次确定其对应的核酸序列，使用MUSCLE (v3.8.31)进行核酸序列的多序列比对，筛选出一致性100%的核酸序列片段。
1.3 序列片段验证
将筛选的序列片段比对到GenBank数据库中，根据提交的全基因组信息筛选出核酸序列的编码序列(coding domain sequence, CDS)，通过NCBI在线BLASTX比对到NR数据库，CDS片段序列及其蛋白序列分别比对到转录组数据分析获得的基因序列上。
1.4 基因引物探针设计
对筛选出的核酸序列补充其全基因组中上下游各100 bp，使用Oligo 7 (MDL Information Systems)、Primer 6 (PREMIER Biosoft)、NCBI 提供的在线工具Primer-BLAST (整合了Primer 3和Blast工具的功能)对片段进行引物设计。
1.5 基因特异性验证
1.5.1 PCR扩增
对供试样本进行PCR扩增，验证目标基因的区分度，用于特异性验证的菌种材料见表2，制备DNA用于验证模板。PCR扩增体系为50 μL，其中Taq Mix 25.0 μL、引物(10 pmol/μL) 2.0 μL、DNA模板(100 ng/μL) 1.0 μL，补充ddH2O至50 μL。扩增条件为：94 ℃ 5 min；94 ℃ 30 s，退火30 s，72 ℃ 30 s；72 ℃ 8 min。引物特征、退火温度、循环数见表3。
1.5.2 Sanger测序
扩增产物送美格基因进行测序，验证扩增产物是否为目标基因。使用软件MEGA 7 (Mega Limited)进行比对排序。
1.5.3 全基因组测序比对
对供试菌系T. controversa TCK-XJ、T. foetida TFO-XJ和T. secalis CBS122087进行全基因组测序，构建文库后采用Illumina平台进行PE150测序(美格基因)，与T. controversa全基因组比对相似性。
1.6 多重实时荧光PCR体系优化
针对PCR扩增引物，设计相应荧光探针进行测试，开发多重荧光PCR检验体系，进行组合优化。明确检测目标数量为四重PCR或“三重+单重”PCR。使用Bioer 9600荧光定量PCR仪(FQD-96A，博日科技)，根据仪器支持的荧光通道，匹配出所有可行的组合方案。删除光谱重叠组合及本身发荧光的基团组合，根据Ct值，结合普通PCR扩增结果为参照，判断样本有效扩增性。单探针对照验证单独运行各探针，检查基团是否有效扩增。混合模板测试验证用阳性TCK模板验证多通道同时检测的准确性，是否与普通PCR结果一致。
2 结果与分析
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2.1 比较全基因组分析筛选同源基因片段
检索T. controversa全基因组信息共7条，其数据编号信息如下：GCA_001645045、GCA_ 009428265、GCA_905071705、GCA_905071725、GCA_905071765、GCA_905071775、GCA_ 905071785，其中GCA_905071765为目标菌TCK的参考基因组(Ref)。使用OrthoFinder软件聚类共获得12 587个基因簇，其中在目标菌中存在基因拷贝，同时，在同属的其他种中不存在拷贝的基因簇共15条(表4)。根据核酸序列比对结果，去除序列差异较大的基因簇，保留在7条全基因组中至少5条全基因组中序列完全一致的基因片段，共筛选到8个同源序列片段。核酸序列中的CDS片段在线比对到NR数据库的结果显示，除目标菌的蛋白序列能够有较好比对结果外，其他种部分也有比对结果，为了保证特异性，避免扩增假阳性，需去除此类序列，最终保留的序列片段作为候选的特异性片段，共有4条，分别为OG0008430、OG0008601、OG0008603、OG0008610。对37个Tilletia属的种进行PCR扩增和Sanger测序验证，结果显示其中4个全基因组合可对Tilletia属的种进行区分鉴定(表5)。针对T. controversa，需要对这4个基因进行同时扩增，才可与近似种区分。因此，针对此4个候选基因设计引物探针，建立检测方法。
2.2 候选基因引物探针设计
针对OG0008430、OG0008601、OG0008603、OG0008610这4个基因及保留的上下游碱基，采用默认条件进行引物设计，获取引物信息， 4个基因共设计了8对引物(表6)。结合普通PCR结果，设计荧光探针，优化建立的实时荧光PCR反应体系为20 μL，其中2×qPCR Mix 10.0 μL、引物(10 pmol/μL) 0.4 μL、荧光探针0.2 μL、DNA 模板(100 ng/μL) 4.0 μL，补充ddH2O至20 μL。反应条件为95 ℃ 30 s；95 ℃ 10 s，58 ℃ 20 s，72 ℃ 30 s，共40个循环；95 ℃ 15 s，60 ℃ 1 min，72 ℃ 15 s，梯度温度0.5 ℃，梯度恒温时间20 s。
2.3 多重实时荧光PCR方法的建立
为了提高检测方法的效率，建立多重实时荧光PCR，反应体系及扩增程序见表7。在多重qPCR中针对不同靶标菌的检测，选用不同光谱波长范围的荧光基团。虽然，许多荧光光谱相似的荧光基团的最大发射波长不同，但是，在其附近的波段内，仍然会相互重叠。因此，需要排除掉可能存在的发射光谱之间相互干扰的荧光基团组合，选取部分样本对其余多组探针组合进行测试，最终获得一组组合方式，能够将多对引物探针同时进行扩增，并且扩增结果与普通PCR结果一致。经过多次组合检测测试，形成“三重+单重”的实时荧光PCR方式，可有效区分目标种和其他种，组合方式共有2种(表7，表8)，一种为“三重(OG0008601、OG0008603、OG0008610)+单重(OG0008430)”，另一种为“三重(OG0008430、OG0008603、OG0008610)+单重(OG0008601)”。
2.4 特异性验证
所有样本有Ct值即判定为有效扩增。TCK- XJ为阳性对照，CK为阴性对照，当阴性对照无Ct值，样本有Ct值即判定为有效扩增(图1，图2)。试验结果表明，探针primer-8601-2PF、primer-8603-1PF、primer-8610-1PR三重qPCR组合，以及primer-8430-1PF、primer-8603-1PF、primer-8610-2PR三重qPCR组合可以有效进行扩增，扩增结果与普通PCR扩增结果一致，满足Tilletia属大部分种的区分鉴定。对于这两种多重qPCR无法有效区分的Tilletia属的种，针对探针primer-8430-2PR、primer-8601-1PF进行单独PCR扩增。针对8条探针的两组“三重qPCR+单重qPCR”组合，可将Tilletia属的全部供试种进行有效区分。两组“三重+单重”扩增结果需同时满足4个目的片段均为阳性，则可对T. controversa和近似种进行区分。
2.5 准确性验证
通过扩增后测序进行序列比对来验证扩增结果的准确性和建立结果的可靠性。4个基因片段对Tilletia属内各个种可以实现准确的鉴定和区分，各基因对相应种的BLAST比对结果(表9)表明在全基因组水平筛选的基因可以实现准确的种水平上的鉴定。
3 讨论
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小麦矮腥黑粉菌对我国影响的风险评估研究认为，在新疆维吾尔自治区北部、西藏、四川、河南、山东和淮河流域等主要的冬小麦种植区具有非常高的风险(陈克等 2002；周益林等 2007)。因此，对小麦矮腥黑粉菌的检疫一直以来都是国际粮食贸易谈判的焦点，也是国际大小麦粮食贸易会谈和双边植物检疫协定关注的重要内容。T. controversa的准确鉴定直接关系到对疫区划定、议定书条款签订、检疫政策制定、指定口岸能力考核、实验室检疫、除害处理效果评价、后续监管等。T. controversa鉴定方法最早于1961年3月获准试行，1963年冬，又获准在上海、天津、广州、青岛等口岸扩大试行。1973年在北美小麦中首次检出后，经历了近30年的实践摸索，检疫鉴定方法不断完善，于2000年发布并实施国家标准GB/T 18085-2000《植物检疫 小麦矮化腥黑穗病菌检疫鉴定方法》。然而，自2000年开始使用该标准，针对未发现菌瘿只看到零星冬孢子等情形如何鉴定，未给出规定，在口岸检疫中寻找菌瘿却需要大量的人力物力。标准中还缺少分子生物学检测方法，而采用传统的形态学、荧光特性、萌发特性等鉴定方法耗时长，影响货物快速通关，这种低效率的检测手段对企业利益、码头安全都是很大的挑战。
关于T. controversa精准快速鉴定方法的制定是粮食检疫现实所需，但一直以来都是难点。利用常规基因对T. controversa及近似种区分，但区分的近似种数量有限，特异性和准确度有待提高。近年来，有研究从全基因组水平筛选基因片段用于区分鉴定近似种，取得了一些进展(Sharifnabi et al. 2018；Liu et al. 2020；Chen et al. 2021；Forster et al. 2022)。Nguyen et al. (2019)分析了T. controversa等5个Tilletia属的种的10个菌系的全基因组，设计了不同种的特异性引物探针，但对小麦或者没有菌瘿时的单个孢子的鉴定效力未作讨论。Sedaghatjoo et al. (2021)比较了该属6个种的21个菌系的全基因组，以识别出在所有T. controversa分离物中特异且保守的DNA区域，开发了环介导等温扩增技术(loop-mediated isothermal amplification, LAMP)检测方法，但是，对T. trabutii产生假阳性信号，特异性为97.7%。Sedaghatjoo et al. (2022)对T. controversa和T. cares、T. laevis的全基因组分析认为3个物种的全基因组非常相似，使用241个单拷贝基因可以进行区分。本研究基于前人对T. controversa在基因组水平筛选特异标记基因的经验，在全基因组水平通过比较全基因组的方法，利用同源基因进化分析得出OG0008430、OG0008601、OG0008603、OG0008610这4个基因可以有效区分T. controversa及其他近似种，验证了4个基因联合使用对T. controversa鉴定的特异性和准确性，弥补了利用常规方法通过一个基因对T. controversa鉴定在准确性上的不足。
4 结论
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本研究在全基因组水平通过比较全基因组的方法，利用同源基因进化分析得出OG0008430等4个基因可以有效区分小麦矮腥黑粉菌及其他近似种，设计了8对引物探针并建立了两组“三重+单重”组合实时荧光PCR检测方法，该方法耗时短、可精准快速地对Tilletia属的种进行有效区分，可直接应用于进口小麦的原粮检疫。进一步，可针对未发现菌瘿的单个冬孢子或者少量冬孢子开展鉴定效力的测试验证，从理论上可明显提高检测效率和有效性。
作者贡献
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高瑞芳：论文构思及撰写；赵鹏：分子生物学分析；汤怡静：样品整理及试验；刘宵宵：引物探针的筛选和优化；徐欣宇：试验、表格制作、图片绘制；郑铭森：数据处理。
利益冲突声明
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该研究不存在任何潜在利益冲突的商业或财务关系。
基金
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  • 海关总署科研项目(2023HK001)
  • 西藏自治区科技计划项目重点研发计划项目(XZ202201ZY0011N)
文献
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doi: 10.13346/j.mycosystema.250175
  • 接收时间：2025-06-10
  • 首发时间：2026-04-29
  • 出版时间：2026-02-22
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  • 收稿日期：2025-06-10
  • 录用日期：2025-07-31
基金
Scientific Research Projects of the General Administration of Customs(2023HK001)
海关总署科研项目(2023HK001)
Key Research and Development Projects of the Xizang Autonomous Region Science and Technology Plan(XZ202201ZY0011N)
西藏自治区科技计划项目重点研发计划项目(XZ202201ZY0011N)
作者信息
    1 深圳海关动植物检验检疫技术中心，广东 深圳 518045
    2 中国科学院微生物研究所，北京 100101

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2种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
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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