Early Detection of Both Pyrenophora teres f. teres and f. maculata in Asymptomatic Barley Leaves Using Digital Droplet PCR (ddPCR)
Efficient early pathogen detection, before symptom apparition, is crucial for optimizing disease management. In barley, the fungal pathogen is the causative agent of net blotch disease, which exists in two forms: f. sp. ( ), causing net-form of net blotch (NTNB), and f. sp. ( ), responsible for spot...
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| Veröffentlicht in: | International journal of molecular sciences 2024-11, Vol.25 (22), p.11980 |
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| creator | Bouhouch, Yassine Aggad, Dina Richet, Nicolas Rehman, Sajid Al-Jaboobi, Muamar Kehel, Zakaria Esmaeel, Qassim Hafidi, Majida Jacquard, Cédric Sanchez, Lisa |
| description | Efficient early pathogen detection, before symptom apparition, is crucial for optimizing disease management. In barley, the fungal pathogen
is the causative agent of net blotch disease, which exists in two forms:
f. sp.
(
), causing net-form of net blotch (NTNB), and
f. sp.
(
), responsible for spot-form of net blotch (STNB). In this study, we developed primers and a TaqMan probe to detect both
and
. A comprehensive k-mer based analysis was performed across a collection of
genomes to identify the conserved regions that had potential as universal genetic markers. These regions were then analyzed for their prevalence and copy number across diverse Moroccan
strains, using both a k-mer analysis for sequence identification and a phylogenetic assessment to establish genetic relatedness. The designed primer-probe set was successfully validated through qPCR, and early disease detection, prior to symptom development, was achieved using ddPCR. The k-mer analysis performed across the available
genomes suggests the potential for these sequences to serve as universal markers for
, transcending environmental variations. |
| doi_str_mv | 10.3390/ijms252211980 |
| format | Article |
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is the causative agent of net blotch disease, which exists in two forms:
f. sp.
(
), causing net-form of net blotch (NTNB), and
f. sp.
(
), responsible for spot-form of net blotch (STNB). In this study, we developed primers and a TaqMan probe to detect both
and
. A comprehensive k-mer based analysis was performed across a collection of
genomes to identify the conserved regions that had potential as universal genetic markers. These regions were then analyzed for their prevalence and copy number across diverse Moroccan
strains, using both a k-mer analysis for sequence identification and a phylogenetic assessment to establish genetic relatedness. The designed primer-probe set was successfully validated through qPCR, and early disease detection, prior to symptom development, was achieved using ddPCR. The k-mer analysis performed across the available
genomes suggests the potential for these sequences to serve as universal markers for
, transcending environmental variations.</description><identifier>ISSN: 1422-0067</identifier><identifier>ISSN: 1661-6596</identifier><identifier>EISSN: 1422-0067</identifier><identifier>DOI: 10.3390/ijms252211980</identifier><identifier>PMID: 39596050</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Ascomycota ; Ascomycota - genetics ; Ascomycota - isolation & purification ; Barley ; Causes of ; Chromosomes ; Diseases and pests ; DNA Primers - genetics ; Fungal diseases of plants ; Fungi ; Fungi, Phytopathogenic ; Genetic aspects ; Genetic diversity ; Genomes ; Genomics ; Health aspects ; Hordeum - genetics ; Hordeum - microbiology ; Identification and classification ; Pathogens ; Phylogeny ; Plant Diseases - microbiology ; Plant Leaves - genetics ; Plant Leaves - microbiology ; Polymerase chain reaction ; Polymerase Chain Reaction - methods ; Polymorphism ; Virulence</subject><ispartof>International journal of molecular sciences, 2024-11, Vol.25 (22), p.11980</ispartof><rights>COPYRIGHT 2024 MDPI AG</rights><rights>2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2024 by the authors. 2024</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c330t-1ea585f3c9e7ec47aa1cd22c9dbb9418d21b9b4d8785ad7614c1d22ff52833ef3</cites><orcidid>0000-0002-8085-0800 ; 0000-0002-1625-043X ; 0000-0002-4212-4197 ; 0000-0002-8531-9082 ; 0000-0003-4284-6082 ; 0000-0001-7382-3241 ; 0000-0002-6207-2822 ; 0000-0002-4196-8697</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11593351/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11593351/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27903,27904,53769,53771</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39596050$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bouhouch, Yassine</creatorcontrib><creatorcontrib>Aggad, Dina</creatorcontrib><creatorcontrib>Richet, Nicolas</creatorcontrib><creatorcontrib>Rehman, Sajid</creatorcontrib><creatorcontrib>Al-Jaboobi, Muamar</creatorcontrib><creatorcontrib>Kehel, Zakaria</creatorcontrib><creatorcontrib>Esmaeel, Qassim</creatorcontrib><creatorcontrib>Hafidi, Majida</creatorcontrib><creatorcontrib>Jacquard, Cédric</creatorcontrib><creatorcontrib>Sanchez, Lisa</creatorcontrib><title>Early Detection of Both Pyrenophora teres f. teres and f. maculata in Asymptomatic Barley Leaves Using Digital Droplet PCR (ddPCR)</title><title>International journal of molecular sciences</title><addtitle>Int J Mol Sci</addtitle><description>Efficient early pathogen detection, before symptom apparition, is crucial for optimizing disease management. In barley, the fungal pathogen
is the causative agent of net blotch disease, which exists in two forms:
f. sp.
(
), causing net-form of net blotch (NTNB), and
f. sp.
(
), responsible for spot-form of net blotch (STNB). In this study, we developed primers and a TaqMan probe to detect both
and
. A comprehensive k-mer based analysis was performed across a collection of
genomes to identify the conserved regions that had potential as universal genetic markers. These regions were then analyzed for their prevalence and copy number across diverse Moroccan
strains, using both a k-mer analysis for sequence identification and a phylogenetic assessment to establish genetic relatedness. The designed primer-probe set was successfully validated through qPCR, and early disease detection, prior to symptom development, was achieved using ddPCR. The k-mer analysis performed across the available
genomes suggests the potential for these sequences to serve as universal markers for
, transcending environmental variations.</description><subject>Ascomycota</subject><subject>Ascomycota - genetics</subject><subject>Ascomycota - isolation & purification</subject><subject>Barley</subject><subject>Causes of</subject><subject>Chromosomes</subject><subject>Diseases and pests</subject><subject>DNA Primers - genetics</subject><subject>Fungal diseases of plants</subject><subject>Fungi</subject><subject>Fungi, Phytopathogenic</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Health aspects</subject><subject>Hordeum - genetics</subject><subject>Hordeum - microbiology</subject><subject>Identification and classification</subject><subject>Pathogens</subject><subject>Phylogeny</subject><subject>Plant Diseases - microbiology</subject><subject>Plant Leaves - genetics</subject><subject>Plant Leaves - microbiology</subject><subject>Polymerase chain reaction</subject><subject>Polymerase Chain Reaction - methods</subject><subject>Polymorphism</subject><subject>Virulence</subject><issn>1422-0067</issn><issn>1661-6596</issn><issn>1422-0067</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNptkk1vEzEQhlcIREvhyBVZ4lIOG_yxzq5PKE3KhxSJCtGz5bVnE0e79mJ7K-XKL8ehoTQI-TC255l3ZuwpitcEzxgT-L3dDZFySgkRDX5SnJOK0hLjef300f6seBHjDmPKKBfPizMmuJhjjs-Ln9cq9Hu0ggQ6We-Q79CVT1t0sw_g_Lj1QaEEASLqZseNcuZwGJSeepUUsg4t4n4Ykx9UshpdZUnYozWou0zfRus2aGU3NqkerYIfe0joZvkNXRqTzbuXxbNO9RFeHe1Fcfvx-vvyc7n--unLcrEuNWM4lQQUb3jHtIAadFUrRbShVAvTtqIijaGkFW1lmrrhytRzUmmS_V3HacMYdOyi-HCvO07tAEaDS0H1cgx2UGEvvbLy1OPsVm78nSSEC8Y4yQqXR4Xgf0wQkxxs1ND3yoGfomSEsYrXucyMvv0H3fkpuNzfbwoLkv_sL7VRPUjrOp8T64OoXDQkl10Ldkg7-w-Vl4HBau-gs_n-JKC8D9DBxxige2iSYHmYGnkyNZl_8_hlHug_Y8J-ATeyvIw</recordid><startdate>20241107</startdate><enddate>20241107</enddate><creator>Bouhouch, Yassine</creator><creator>Aggad, Dina</creator><creator>Richet, Nicolas</creator><creator>Rehman, Sajid</creator><creator>Al-Jaboobi, Muamar</creator><creator>Kehel, Zakaria</creator><creator>Esmaeel, Qassim</creator><creator>Hafidi, Majida</creator><creator>Jacquard, Cédric</creator><creator>Sanchez, Lisa</creator><general>MDPI AG</general><general>MDPI</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>K9.</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>MBDVC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-8085-0800</orcidid><orcidid>https://orcid.org/0000-0002-1625-043X</orcidid><orcidid>https://orcid.org/0000-0002-4212-4197</orcidid><orcidid>https://orcid.org/0000-0002-8531-9082</orcidid><orcidid>https://orcid.org/0000-0003-4284-6082</orcidid><orcidid>https://orcid.org/0000-0001-7382-3241</orcidid><orcidid>https://orcid.org/0000-0002-6207-2822</orcidid><orcidid>https://orcid.org/0000-0002-4196-8697</orcidid></search><sort><creationdate>20241107</creationdate><title>Early Detection of Both Pyrenophora teres f. teres and f. maculata in Asymptomatic Barley Leaves Using Digital Droplet PCR (ddPCR)</title><author>Bouhouch, Yassine ; Aggad, Dina ; Richet, Nicolas ; Rehman, Sajid ; Al-Jaboobi, Muamar ; Kehel, Zakaria ; Esmaeel, Qassim ; Hafidi, Majida ; Jacquard, Cédric ; Sanchez, Lisa</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c330t-1ea585f3c9e7ec47aa1cd22c9dbb9418d21b9b4d8785ad7614c1d22ff52833ef3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Ascomycota</topic><topic>Ascomycota - genetics</topic><topic>Ascomycota - isolation & purification</topic><topic>Barley</topic><topic>Causes of</topic><topic>Chromosomes</topic><topic>Diseases and pests</topic><topic>DNA Primers - genetics</topic><topic>Fungal diseases of plants</topic><topic>Fungi</topic><topic>Fungi, Phytopathogenic</topic><topic>Genetic aspects</topic><topic>Genetic diversity</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Health aspects</topic><topic>Hordeum - genetics</topic><topic>Hordeum - microbiology</topic><topic>Identification and classification</topic><topic>Pathogens</topic><topic>Phylogeny</topic><topic>Plant Diseases - microbiology</topic><topic>Plant Leaves - genetics</topic><topic>Plant Leaves - microbiology</topic><topic>Polymerase chain reaction</topic><topic>Polymerase Chain Reaction - methods</topic><topic>Polymorphism</topic><topic>Virulence</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bouhouch, Yassine</creatorcontrib><creatorcontrib>Aggad, Dina</creatorcontrib><creatorcontrib>Richet, Nicolas</creatorcontrib><creatorcontrib>Rehman, Sajid</creatorcontrib><creatorcontrib>Al-Jaboobi, Muamar</creatorcontrib><creatorcontrib>Kehel, Zakaria</creatorcontrib><creatorcontrib>Esmaeel, Qassim</creatorcontrib><creatorcontrib>Hafidi, Majida</creatorcontrib><creatorcontrib>Jacquard, Cédric</creatorcontrib><creatorcontrib>Sanchez, Lisa</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Research Library (Corporate)</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>International journal of molecular sciences</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bouhouch, Yassine</au><au>Aggad, Dina</au><au>Richet, Nicolas</au><au>Rehman, Sajid</au><au>Al-Jaboobi, Muamar</au><au>Kehel, Zakaria</au><au>Esmaeel, Qassim</au><au>Hafidi, Majida</au><au>Jacquard, Cédric</au><au>Sanchez, Lisa</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Early Detection of Both Pyrenophora teres f. teres and f. maculata in Asymptomatic Barley Leaves Using Digital Droplet PCR (ddPCR)</atitle><jtitle>International journal of molecular sciences</jtitle><addtitle>Int J Mol Sci</addtitle><date>2024-11-07</date><risdate>2024</risdate><volume>25</volume><issue>22</issue><spage>11980</spage><pages>11980-</pages><issn>1422-0067</issn><issn>1661-6596</issn><eissn>1422-0067</eissn><abstract>Efficient early pathogen detection, before symptom apparition, is crucial for optimizing disease management. In barley, the fungal pathogen
is the causative agent of net blotch disease, which exists in two forms:
f. sp.
(
), causing net-form of net blotch (NTNB), and
f. sp.
(
), responsible for spot-form of net blotch (STNB). In this study, we developed primers and a TaqMan probe to detect both
and
. A comprehensive k-mer based analysis was performed across a collection of
genomes to identify the conserved regions that had potential as universal genetic markers. These regions were then analyzed for their prevalence and copy number across diverse Moroccan
strains, using both a k-mer analysis for sequence identification and a phylogenetic assessment to establish genetic relatedness. The designed primer-probe set was successfully validated through qPCR, and early disease detection, prior to symptom development, was achieved using ddPCR. The k-mer analysis performed across the available
genomes suggests the potential for these sequences to serve as universal markers for
, transcending environmental variations.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>39596050</pmid><doi>10.3390/ijms252211980</doi><orcidid>https://orcid.org/0000-0002-8085-0800</orcidid><orcidid>https://orcid.org/0000-0002-1625-043X</orcidid><orcidid>https://orcid.org/0000-0002-4212-4197</orcidid><orcidid>https://orcid.org/0000-0002-8531-9082</orcidid><orcidid>https://orcid.org/0000-0003-4284-6082</orcidid><orcidid>https://orcid.org/0000-0001-7382-3241</orcidid><orcidid>https://orcid.org/0000-0002-6207-2822</orcidid><orcidid>https://orcid.org/0000-0002-4196-8697</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | International journal of molecular sciences, 2024-11, Vol.25 (22), p.11980 |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; MDPI - Multidisciplinary Digital Publishing Institute; PubMed Central |
| subjects | Ascomycota Ascomycota - genetics Ascomycota - isolation & purification Barley Causes of Chromosomes Diseases and pests DNA Primers - genetics Fungal diseases of plants Fungi Fungi, Phytopathogenic Genetic aspects Genetic diversity Genomes Genomics Health aspects Hordeum - genetics Hordeum - microbiology Identification and classification Pathogens Phylogeny Plant Diseases - microbiology Plant Leaves - genetics Plant Leaves - microbiology Polymerase chain reaction Polymerase Chain Reaction - methods Polymorphism Virulence |
| title | Early Detection of Both Pyrenophora teres f. teres and f. maculata in Asymptomatic Barley Leaves Using Digital Droplet PCR (ddPCR) |
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