Quantification of roots and seeds in soil with real-time PCR
Study of roots and associated organisms in soil particularly in mixed plant populations, such as pastures, is limited by difficulties in quantification of root growth and function. The research evaluated the potential of DNA quantification by real-time PCR to improve our capacity to study and unders...
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| Veröffentlicht in: | Plant and soil 2010-06, Vol.331 (1-2), p.151-163 |
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| creator | Riley, Ian T Wiebkin, Sue Hartley, Diana McKay, Alan C |
| description | Study of roots and associated organisms in soil particularly in mixed plant populations, such as pastures, is limited by difficulties in quantification of root growth and function. The research evaluated the potential of DNA quantification by real-time PCR to improve our capacity to study and understand roots in such contexts. Probes and primers were developed for two common pasture species, Trifolium subterraneum and Lolium perenne (and closely related Lolium spp.), and evaluated for specificity and sensitivity in TaqMan assays on DNA extracted from soil. Further experiments examined the ability to detect DNA in dead roots, the changes in root DNA levels of plants defoliated or treated with herbicide and the relationship between DNA and root dry weight for single and mixed plant species grown in pots. T. subterraneum DNA/PCR 200 fg/µl was detected at 17.5 cycles and L. perenne at 19.5 cycles. The assay for T. subterraneum was species specific but the L. perenne assay, as anticipated from the choice of probe, also detected some closely related species. The assays were sensitive and capable of detecting equivalent to |
| doi_str_mv | 10.1007/s11104-009-0241-5 |
| format | Article |
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The research evaluated the potential of DNA quantification by real-time PCR to improve our capacity to study and understand roots in such contexts. Probes and primers were developed for two common pasture species, Trifolium subterraneum and Lolium perenne (and closely related Lolium spp.), and evaluated for specificity and sensitivity in TaqMan assays on DNA extracted from soil. Further experiments examined the ability to detect DNA in dead roots, the changes in root DNA levels of plants defoliated or treated with herbicide and the relationship between DNA and root dry weight for single and mixed plant species grown in pots. T. subterraneum DNA/PCR 200 fg/µl was detected at 17.5 cycles and L. perenne at 19.5 cycles. The assay for T. subterraneum was species specific but the L. perenne assay, as anticipated from the choice of probe, also detected some closely related species. The assays were sensitive and capable of detecting equivalent to <2 mg roots/kg of dry soil and able to quantify targets in mixed populations. DNA concentration varied with plant age and genotype and DNA in dead roots found to decay rapidly over a few days. DNA concentrations in roots were found to respond more rapidly to defoliation and herbicide treatments than root mass. This approach appears to offer a new way to study roots in soil and indicates that quantifying root DNA could provide insights into root function and responses not readily provided by other methods.</description><identifier>ISSN: 0032-079X</identifier><identifier>EISSN: 1573-5036</identifier><identifier>DOI: 10.1007/s11104-009-0241-5</identifier><identifier>CODEN: PLSOA2</identifier><language>eng</language><publisher>Dordrecht: Dordrecht : Springer Netherlands</publisher><subject>Agricultural soils ; Agronomy. Soil science and plant productions ; Animal, plant and microbial ecology ; Biological and medical sciences ; Biomedical and Life Sciences ; Defoliation ; Deoxyribonucleic acid ; DNA ; Ecology ; Fundamental and applied biological sciences. Psychology ; General agronomy. Plant production ; Herbicides ; L. multiflorum ; L. rigidum ; Life Sciences ; Lolium perenne ; Pasture ; Plant biology ; Plant growth ; Plant Physiology ; Plant populations ; Plant roots ; Plant Sciences ; Plant species ; Plants ; Polymerase chain reaction ; Quantification ; quantitative analysis ; Real-time PCR ; Regular Article ; Ribosomal DNA ; Roots ; Seeds ; soil ; Soil microorganisms ; Soil samples ; Soil science ; Soil Science & Conservation ; Soil water ; Soil-plant relationships. Soil fertility ; Soil-plant relationships. Soil fertility. Fertilization. Amendments ; Soils ; Trifolium subterraneum</subject><ispartof>Plant and soil, 2010-06, Vol.331 (1-2), p.151-163</ispartof><rights>Springer Science+Business Media B.V. 2009</rights><rights>2015 INIST-CNRS</rights><rights>COPYRIGHT 2010 Springer</rights><rights>Springer Science+Business Media B.V. 2010</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c430t-2e49a90583950c27d753419fee0749bd37c63b76f008d1d33ccce6ec46cff4da3</citedby><cites>FETCH-LOGICAL-c430t-2e49a90583950c27d753419fee0749bd37c63b76f008d1d33ccce6ec46cff4da3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/24130554$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/24130554$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,780,784,803,27923,27924,41487,42556,51318,58016,58249</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=22835514$$DView record in Pascal Francis$$Hfree_for_read</backlink></links><search><creatorcontrib>Riley, Ian T</creatorcontrib><creatorcontrib>Wiebkin, Sue</creatorcontrib><creatorcontrib>Hartley, Diana</creatorcontrib><creatorcontrib>McKay, Alan C</creatorcontrib><title>Quantification of roots and seeds in soil with real-time PCR</title><title>Plant and soil</title><addtitle>Plant Soil</addtitle><description>Study of roots and associated organisms in soil particularly in mixed plant populations, such as pastures, is limited by difficulties in quantification of root growth and function. The research evaluated the potential of DNA quantification by real-time PCR to improve our capacity to study and understand roots in such contexts. Probes and primers were developed for two common pasture species, Trifolium subterraneum and Lolium perenne (and closely related Lolium spp.), and evaluated for specificity and sensitivity in TaqMan assays on DNA extracted from soil. Further experiments examined the ability to detect DNA in dead roots, the changes in root DNA levels of plants defoliated or treated with herbicide and the relationship between DNA and root dry weight for single and mixed plant species grown in pots. T. subterraneum DNA/PCR 200 fg/µl was detected at 17.5 cycles and L. perenne at 19.5 cycles. The assay for T. subterraneum was species specific but the L. perenne assay, as anticipated from the choice of probe, also detected some closely related species. The assays were sensitive and capable of detecting equivalent to <2 mg roots/kg of dry soil and able to quantify targets in mixed populations. DNA concentration varied with plant age and genotype and DNA in dead roots found to decay rapidly over a few days. DNA concentrations in roots were found to respond more rapidly to defoliation and herbicide treatments than root mass. This approach appears to offer a new way to study roots in soil and indicates that quantifying root DNA could provide insights into root function and responses not readily provided by other methods.</description><subject>Agricultural soils</subject><subject>Agronomy. Soil science and plant productions</subject><subject>Animal, plant and microbial ecology</subject><subject>Biological and medical sciences</subject><subject>Biomedical and Life Sciences</subject><subject>Defoliation</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Ecology</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>General agronomy. Plant production</subject><subject>Herbicides</subject><subject>L. multiflorum</subject><subject>L. rigidum</subject><subject>Life Sciences</subject><subject>Lolium perenne</subject><subject>Pasture</subject><subject>Plant biology</subject><subject>Plant growth</subject><subject>Plant Physiology</subject><subject>Plant populations</subject><subject>Plant roots</subject><subject>Plant Sciences</subject><subject>Plant species</subject><subject>Plants</subject><subject>Polymerase chain reaction</subject><subject>Quantification</subject><subject>quantitative analysis</subject><subject>Real-time PCR</subject><subject>Regular Article</subject><subject>Ribosomal DNA</subject><subject>Roots</subject><subject>Seeds</subject><subject>soil</subject><subject>Soil microorganisms</subject><subject>Soil samples</subject><subject>Soil science</subject><subject>Soil Science & Conservation</subject><subject>Soil water</subject><subject>Soil-plant relationships. Soil fertility</subject><subject>Soil-plant relationships. Soil fertility. Fertilization. Amendments</subject><subject>Soils</subject><subject>Trifolium subterraneum</subject><issn>0032-079X</issn><issn>1573-5036</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kEuLFDEUhYMo2I7-ABdiEFxmvMlNKlXgZmjGBwz4HHAXMqmkTVOdjEka8d-bpgZnJ1mE5Jzv3Msh5DmHcw6g31TOOUgGMDEQkjP1gGy40sgU4PCQbABQMNDTj8fkSa17OL35sCFvvxxtajFEZ1vMieZAS86tUptmWr2fK42J1hwX-ju2n7R4u7AWD55-3n59Sh4Fu1T_7O4-I9fvLr9vP7CrT-8_bi-umJMIjQkvJzuBGnFS4ISetULJp-A9aDndzKjdgDd6CADjzGdE55wfvJODC0HOFs_IqzX3tuRfR1-b2edjSX2kEQCDEkLxbjpfTTu7eBNTyK1Y18_sD9Hl5EPs_xc4CKFxQuwAXwFXcq3FB3Nb4sGWP4aDOZVq1lJNL9WcSjWqM6_vNrHV2SUUm1ys_0AhRlSKy-4Tq692Ke18ud_4f-EvVmhfWy73oZIjKHUKfbnqwWZjd6UPvv4moKt8lFzhiH8BPbuXCw</recordid><startdate>20100601</startdate><enddate>20100601</enddate><creator>Riley, Ian T</creator><creator>Wiebkin, Sue</creator><creator>Hartley, Diana</creator><creator>McKay, Alan C</creator><general>Dordrecht : Springer Netherlands</general><general>Springer</general><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>FBQ</scope><scope>IQODW</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7SN</scope><scope>7ST</scope><scope>7T7</scope><scope>7X2</scope><scope>88A</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M0K</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>SOI</scope></search><sort><creationdate>20100601</creationdate><title>Quantification of roots and seeds in soil with real-time PCR</title><author>Riley, Ian T ; Wiebkin, Sue ; Hartley, Diana ; McKay, Alan C</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c430t-2e49a90583950c27d753419fee0749bd37c63b76f008d1d33ccce6ec46cff4da3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Agricultural soils</topic><topic>Agronomy. Soil science and plant productions</topic><topic>Animal, plant and microbial ecology</topic><topic>Biological and medical sciences</topic><topic>Biomedical and Life Sciences</topic><topic>Defoliation</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Ecology</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>General agronomy. Plant production</topic><topic>Herbicides</topic><topic>L. multiflorum</topic><topic>L. rigidum</topic><topic>Life Sciences</topic><topic>Lolium perenne</topic><topic>Pasture</topic><topic>Plant biology</topic><topic>Plant growth</topic><topic>Plant Physiology</topic><topic>Plant populations</topic><topic>Plant roots</topic><topic>Plant Sciences</topic><topic>Plant species</topic><topic>Plants</topic><topic>Polymerase chain reaction</topic><topic>Quantification</topic><topic>quantitative analysis</topic><topic>Real-time PCR</topic><topic>Regular Article</topic><topic>Ribosomal DNA</topic><topic>Roots</topic><topic>Seeds</topic><topic>soil</topic><topic>Soil microorganisms</topic><topic>Soil samples</topic><topic>Soil science</topic><topic>Soil Science & Conservation</topic><topic>Soil water</topic><topic>Soil-plant relationships. Soil fertility</topic><topic>Soil-plant relationships. Soil fertility. Fertilization. Amendments</topic><topic>Soils</topic><topic>Trifolium subterraneum</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Riley, Ian T</creatorcontrib><creatorcontrib>Wiebkin, Sue</creatorcontrib><creatorcontrib>Hartley, Diana</creatorcontrib><creatorcontrib>McKay, Alan C</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Ecology Abstracts</collection><collection>Environment Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Agricultural Science Collection</collection><collection>Biology Database (Alumni Edition)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>Environment Abstracts</collection><jtitle>Plant and soil</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Riley, Ian T</au><au>Wiebkin, Sue</au><au>Hartley, Diana</au><au>McKay, Alan C</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Quantification of roots and seeds in soil with real-time PCR</atitle><jtitle>Plant and soil</jtitle><stitle>Plant Soil</stitle><date>2010-06-01</date><risdate>2010</risdate><volume>331</volume><issue>1-2</issue><spage>151</spage><epage>163</epage><pages>151-163</pages><issn>0032-079X</issn><eissn>1573-5036</eissn><coden>PLSOA2</coden><abstract>Study of roots and associated organisms in soil particularly in mixed plant populations, such as pastures, is limited by difficulties in quantification of root growth and function. The research evaluated the potential of DNA quantification by real-time PCR to improve our capacity to study and understand roots in such contexts. Probes and primers were developed for two common pasture species, Trifolium subterraneum and Lolium perenne (and closely related Lolium spp.), and evaluated for specificity and sensitivity in TaqMan assays on DNA extracted from soil. Further experiments examined the ability to detect DNA in dead roots, the changes in root DNA levels of plants defoliated or treated with herbicide and the relationship between DNA and root dry weight for single and mixed plant species grown in pots. T. subterraneum DNA/PCR 200 fg/µl was detected at 17.5 cycles and L. perenne at 19.5 cycles. The assay for T. subterraneum was species specific but the L. perenne assay, as anticipated from the choice of probe, also detected some closely related species. The assays were sensitive and capable of detecting equivalent to <2 mg roots/kg of dry soil and able to quantify targets in mixed populations. DNA concentration varied with plant age and genotype and DNA in dead roots found to decay rapidly over a few days. DNA concentrations in roots were found to respond more rapidly to defoliation and herbicide treatments than root mass. This approach appears to offer a new way to study roots in soil and indicates that quantifying root DNA could provide insights into root function and responses not readily provided by other methods.</abstract><cop>Dordrecht</cop><pub>Dordrecht : Springer Netherlands</pub><doi>10.1007/s11104-009-0241-5</doi><tpages>13</tpages></addata></record> |
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| ispartof | Plant and soil, 2010-06, Vol.331 (1-2), p.151-163 |
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| subjects | Agricultural soils Agronomy. Soil science and plant productions Animal, plant and microbial ecology Biological and medical sciences Biomedical and Life Sciences Defoliation Deoxyribonucleic acid DNA Ecology Fundamental and applied biological sciences. Psychology General agronomy. Plant production Herbicides L. multiflorum L. rigidum Life Sciences Lolium perenne Pasture Plant biology Plant growth Plant Physiology Plant populations Plant roots Plant Sciences Plant species Plants Polymerase chain reaction Quantification quantitative analysis Real-time PCR Regular Article Ribosomal DNA Roots Seeds soil Soil microorganisms Soil samples Soil science Soil Science & Conservation Soil water Soil-plant relationships. Soil fertility Soil-plant relationships. Soil fertility. Fertilization. Amendments Soils Trifolium subterraneum |
| title | Quantification of roots and seeds in soil with real-time PCR |
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