Hyperspectral phenotyping on the microscopic scale: towards automated characterization of plant-pathogen interactions
Background The detection and characterization of resistance reactions of crop plants against fungal pathogens are essential to select resistant genotypes. In breeding practice phenotyping of plant genotypes is realized by time consuming and expensive visual rating. In this context hyperspectral imag...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Kuska, Matheus [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
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2015 |
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| Anmerkung: |
© Kuska et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( |
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| Übergeordnetes Werk: |
Enthalten in: Plant methods - London : BioMed Central, 2005, 11(2015), 1 vom: 15. Apr. |
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| Übergeordnetes Werk: |
volume:11 ; year:2015 ; number:1 ; day:15 ; month:04 |
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| DOI / URN: |
10.1186/s13007-015-0073-7 |
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| Katalog-ID: |
SPR029407273 |
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| 520 | |a Background The detection and characterization of resistance reactions of crop plants against fungal pathogens are essential to select resistant genotypes. In breeding practice phenotyping of plant genotypes is realized by time consuming and expensive visual rating. In this context hyperspectral imaging (HSI) is a promising non-invasive sensor technique in order to accelerate and to automate classical phenotyping methods. A hyperspectral microscope was established to determine spectral changes on the leaf and cellular level of barley (Hordeum vulgare) during resistance reactions against powdery mildew (Blumeria graminis f.sp. hordei, isolate K1). Experiments were conducted with near isogenic barley lines of cv. Ingrid, including the susceptible wild type (WT), mildew locus a 12 (Mla12 based resistance) and the resistant mildew locus o 3 (mlo3 based resistance), respectively. The reflection of inoculated and non-inoculated leaves was recorded daily with a hyperspectral linescanner in the visual (400 – 700 nm) and near infrared (700 – 1000 nm) range 3 to 14 days after inoculation. Results Data analysis showed no significant differences in spectral signatures between non-inoculated genotypes. Barley leaves of the near-isogenic genotypes, inoculated with B. graminis f.sp. hordei differed in the spectral reflectance over time, respectively. The susceptible genotypes (WT, Mla12) showed an increase in reflectance in the visible range according to symptom development. However, the spectral signature of the resistant mlo-genotype did not show significant changes over the experimental period. In addition, a recent data driven approach for automated discovery of disease specific signatures, which is based on a new representation of the data using Simplex Volume Maximization (SiVM) was applied. The automated approach - evaluated in only a fraction of time revealed results similar to the time and labor intensive manually assessed hyperspectral signatures. The new representation determined by SiVM was also used to generate intuitive and easy to interpretable summaries, e.g. fingerprints or traces of hyperspectral dynamics of the different genotypes. Conclusion With this HSI based and data driven phenotyping approach an evaluation of host-pathogen interactions over time and a discrimination of barley genotypes differing in susceptibility to powdery mildew is possible. | ||
| 650 | 4 | |a Hyperspectral imaging |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Hyperspectral microscope |7 (dpeaa)DE-He213 | |
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| 700 | 1 | |a Kersting, Kristian |4 aut | |
| 700 | 1 | |a Oerke, Erich-Christian |4 aut | |
| 700 | 1 | |a Steiner, Ulrike |4 aut | |
| 700 | 1 | |a Mahlein, Anne-Katrin |4 aut | |
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10.1186/s13007-015-0073-7 doi (DE-627)SPR029407273 (SPR)s13007-015-0073-7-e DE-627 ger DE-627 rakwb eng Kuska, Matheus verfasserin aut Hyperspectral phenotyping on the microscopic scale: towards automated characterization of plant-pathogen interactions 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Kuska et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background The detection and characterization of resistance reactions of crop plants against fungal pathogens are essential to select resistant genotypes. In breeding practice phenotyping of plant genotypes is realized by time consuming and expensive visual rating. In this context hyperspectral imaging (HSI) is a promising non-invasive sensor technique in order to accelerate and to automate classical phenotyping methods. A hyperspectral microscope was established to determine spectral changes on the leaf and cellular level of barley (Hordeum vulgare) during resistance reactions against powdery mildew (Blumeria graminis f.sp. hordei, isolate K1). Experiments were conducted with near isogenic barley lines of cv. Ingrid, including the susceptible wild type (WT), mildew locus a 12 (Mla12 based resistance) and the resistant mildew locus o 3 (mlo3 based resistance), respectively. The reflection of inoculated and non-inoculated leaves was recorded daily with a hyperspectral linescanner in the visual (400 – 700 nm) and near infrared (700 – 1000 nm) range 3 to 14 days after inoculation. Results Data analysis showed no significant differences in spectral signatures between non-inoculated genotypes. Barley leaves of the near-isogenic genotypes, inoculated with B. graminis f.sp. hordei differed in the spectral reflectance over time, respectively. The susceptible genotypes (WT, Mla12) showed an increase in reflectance in the visible range according to symptom development. However, the spectral signature of the resistant mlo-genotype did not show significant changes over the experimental period. In addition, a recent data driven approach for automated discovery of disease specific signatures, which is based on a new representation of the data using Simplex Volume Maximization (SiVM) was applied. The automated approach - evaluated in only a fraction of time revealed results similar to the time and labor intensive manually assessed hyperspectral signatures. The new representation determined by SiVM was also used to generate intuitive and easy to interpretable summaries, e.g. fingerprints or traces of hyperspectral dynamics of the different genotypes. Conclusion With this HSI based and data driven phenotyping approach an evaluation of host-pathogen interactions over time and a discrimination of barley genotypes differing in susceptibility to powdery mildew is possible. Hyperspectral imaging (dpeaa)DE-He213 Hyperspectral microscope (dpeaa)DE-He213 Spectral reflectance (dpeaa)DE-He213 Plant disease (dpeaa)DE-He213 Disease resistance (dpeaa)DE-He213 Mildew locus o ( (dpeaa)DE-He213 ) (dpeaa)DE-He213 Near-isogenic lines (dpeaa)DE-He213 f.sp. (dpeaa)DE-He213 Wahabzada, Mirwaes aut Leucker, Marlene aut Dehne, Heinz-Wilhelm aut Kersting, Kristian aut Oerke, Erich-Christian aut Steiner, Ulrike aut Mahlein, Anne-Katrin aut Enthalten in Plant methods London : BioMed Central, 2005 11(2015), 1 vom: 15. Apr. (DE-627)500321191 (DE-600)2203723-8 1746-4811 nnns volume:11 year:2015 number:1 day:15 month:04 https://dx.doi.org/10.1186/s13007-015-0073-7 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2015 1 15 04 |
| spelling |
10.1186/s13007-015-0073-7 doi (DE-627)SPR029407273 (SPR)s13007-015-0073-7-e DE-627 ger DE-627 rakwb eng Kuska, Matheus verfasserin aut Hyperspectral phenotyping on the microscopic scale: towards automated characterization of plant-pathogen interactions 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Kuska et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background The detection and characterization of resistance reactions of crop plants against fungal pathogens are essential to select resistant genotypes. In breeding practice phenotyping of plant genotypes is realized by time consuming and expensive visual rating. In this context hyperspectral imaging (HSI) is a promising non-invasive sensor technique in order to accelerate and to automate classical phenotyping methods. A hyperspectral microscope was established to determine spectral changes on the leaf and cellular level of barley (Hordeum vulgare) during resistance reactions against powdery mildew (Blumeria graminis f.sp. hordei, isolate K1). Experiments were conducted with near isogenic barley lines of cv. Ingrid, including the susceptible wild type (WT), mildew locus a 12 (Mla12 based resistance) and the resistant mildew locus o 3 (mlo3 based resistance), respectively. The reflection of inoculated and non-inoculated leaves was recorded daily with a hyperspectral linescanner in the visual (400 – 700 nm) and near infrared (700 – 1000 nm) range 3 to 14 days after inoculation. Results Data analysis showed no significant differences in spectral signatures between non-inoculated genotypes. Barley leaves of the near-isogenic genotypes, inoculated with B. graminis f.sp. hordei differed in the spectral reflectance over time, respectively. The susceptible genotypes (WT, Mla12) showed an increase in reflectance in the visible range according to symptom development. However, the spectral signature of the resistant mlo-genotype did not show significant changes over the experimental period. In addition, a recent data driven approach for automated discovery of disease specific signatures, which is based on a new representation of the data using Simplex Volume Maximization (SiVM) was applied. The automated approach - evaluated in only a fraction of time revealed results similar to the time and labor intensive manually assessed hyperspectral signatures. The new representation determined by SiVM was also used to generate intuitive and easy to interpretable summaries, e.g. fingerprints or traces of hyperspectral dynamics of the different genotypes. Conclusion With this HSI based and data driven phenotyping approach an evaluation of host-pathogen interactions over time and a discrimination of barley genotypes differing in susceptibility to powdery mildew is possible. Hyperspectral imaging (dpeaa)DE-He213 Hyperspectral microscope (dpeaa)DE-He213 Spectral reflectance (dpeaa)DE-He213 Plant disease (dpeaa)DE-He213 Disease resistance (dpeaa)DE-He213 Mildew locus o ( (dpeaa)DE-He213 ) (dpeaa)DE-He213 Near-isogenic lines (dpeaa)DE-He213 f.sp. (dpeaa)DE-He213 Wahabzada, Mirwaes aut Leucker, Marlene aut Dehne, Heinz-Wilhelm aut Kersting, Kristian aut Oerke, Erich-Christian aut Steiner, Ulrike aut Mahlein, Anne-Katrin aut Enthalten in Plant methods London : BioMed Central, 2005 11(2015), 1 vom: 15. Apr. (DE-627)500321191 (DE-600)2203723-8 1746-4811 nnns volume:11 year:2015 number:1 day:15 month:04 https://dx.doi.org/10.1186/s13007-015-0073-7 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2015 1 15 04 |
| allfields_unstemmed |
10.1186/s13007-015-0073-7 doi (DE-627)SPR029407273 (SPR)s13007-015-0073-7-e DE-627 ger DE-627 rakwb eng Kuska, Matheus verfasserin aut Hyperspectral phenotyping on the microscopic scale: towards automated characterization of plant-pathogen interactions 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Kuska et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background The detection and characterization of resistance reactions of crop plants against fungal pathogens are essential to select resistant genotypes. In breeding practice phenotyping of plant genotypes is realized by time consuming and expensive visual rating. In this context hyperspectral imaging (HSI) is a promising non-invasive sensor technique in order to accelerate and to automate classical phenotyping methods. A hyperspectral microscope was established to determine spectral changes on the leaf and cellular level of barley (Hordeum vulgare) during resistance reactions against powdery mildew (Blumeria graminis f.sp. hordei, isolate K1). Experiments were conducted with near isogenic barley lines of cv. Ingrid, including the susceptible wild type (WT), mildew locus a 12 (Mla12 based resistance) and the resistant mildew locus o 3 (mlo3 based resistance), respectively. The reflection of inoculated and non-inoculated leaves was recorded daily with a hyperspectral linescanner in the visual (400 – 700 nm) and near infrared (700 – 1000 nm) range 3 to 14 days after inoculation. Results Data analysis showed no significant differences in spectral signatures between non-inoculated genotypes. Barley leaves of the near-isogenic genotypes, inoculated with B. graminis f.sp. hordei differed in the spectral reflectance over time, respectively. The susceptible genotypes (WT, Mla12) showed an increase in reflectance in the visible range according to symptom development. However, the spectral signature of the resistant mlo-genotype did not show significant changes over the experimental period. In addition, a recent data driven approach for automated discovery of disease specific signatures, which is based on a new representation of the data using Simplex Volume Maximization (SiVM) was applied. The automated approach - evaluated in only a fraction of time revealed results similar to the time and labor intensive manually assessed hyperspectral signatures. The new representation determined by SiVM was also used to generate intuitive and easy to interpretable summaries, e.g. fingerprints or traces of hyperspectral dynamics of the different genotypes. Conclusion With this HSI based and data driven phenotyping approach an evaluation of host-pathogen interactions over time and a discrimination of barley genotypes differing in susceptibility to powdery mildew is possible. Hyperspectral imaging (dpeaa)DE-He213 Hyperspectral microscope (dpeaa)DE-He213 Spectral reflectance (dpeaa)DE-He213 Plant disease (dpeaa)DE-He213 Disease resistance (dpeaa)DE-He213 Mildew locus o ( (dpeaa)DE-He213 ) (dpeaa)DE-He213 Near-isogenic lines (dpeaa)DE-He213 f.sp. (dpeaa)DE-He213 Wahabzada, Mirwaes aut Leucker, Marlene aut Dehne, Heinz-Wilhelm aut Kersting, Kristian aut Oerke, Erich-Christian aut Steiner, Ulrike aut Mahlein, Anne-Katrin aut Enthalten in Plant methods London : BioMed Central, 2005 11(2015), 1 vom: 15. Apr. (DE-627)500321191 (DE-600)2203723-8 1746-4811 nnns volume:11 year:2015 number:1 day:15 month:04 https://dx.doi.org/10.1186/s13007-015-0073-7 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2015 1 15 04 |
| allfieldsGer |
10.1186/s13007-015-0073-7 doi (DE-627)SPR029407273 (SPR)s13007-015-0073-7-e DE-627 ger DE-627 rakwb eng Kuska, Matheus verfasserin aut Hyperspectral phenotyping on the microscopic scale: towards automated characterization of plant-pathogen interactions 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Kuska et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background The detection and characterization of resistance reactions of crop plants against fungal pathogens are essential to select resistant genotypes. In breeding practice phenotyping of plant genotypes is realized by time consuming and expensive visual rating. In this context hyperspectral imaging (HSI) is a promising non-invasive sensor technique in order to accelerate and to automate classical phenotyping methods. A hyperspectral microscope was established to determine spectral changes on the leaf and cellular level of barley (Hordeum vulgare) during resistance reactions against powdery mildew (Blumeria graminis f.sp. hordei, isolate K1). Experiments were conducted with near isogenic barley lines of cv. Ingrid, including the susceptible wild type (WT), mildew locus a 12 (Mla12 based resistance) and the resistant mildew locus o 3 (mlo3 based resistance), respectively. The reflection of inoculated and non-inoculated leaves was recorded daily with a hyperspectral linescanner in the visual (400 – 700 nm) and near infrared (700 – 1000 nm) range 3 to 14 days after inoculation. Results Data analysis showed no significant differences in spectral signatures between non-inoculated genotypes. Barley leaves of the near-isogenic genotypes, inoculated with B. graminis f.sp. hordei differed in the spectral reflectance over time, respectively. The susceptible genotypes (WT, Mla12) showed an increase in reflectance in the visible range according to symptom development. However, the spectral signature of the resistant mlo-genotype did not show significant changes over the experimental period. In addition, a recent data driven approach for automated discovery of disease specific signatures, which is based on a new representation of the data using Simplex Volume Maximization (SiVM) was applied. The automated approach - evaluated in only a fraction of time revealed results similar to the time and labor intensive manually assessed hyperspectral signatures. The new representation determined by SiVM was also used to generate intuitive and easy to interpretable summaries, e.g. fingerprints or traces of hyperspectral dynamics of the different genotypes. Conclusion With this HSI based and data driven phenotyping approach an evaluation of host-pathogen interactions over time and a discrimination of barley genotypes differing in susceptibility to powdery mildew is possible. Hyperspectral imaging (dpeaa)DE-He213 Hyperspectral microscope (dpeaa)DE-He213 Spectral reflectance (dpeaa)DE-He213 Plant disease (dpeaa)DE-He213 Disease resistance (dpeaa)DE-He213 Mildew locus o ( (dpeaa)DE-He213 ) (dpeaa)DE-He213 Near-isogenic lines (dpeaa)DE-He213 f.sp. (dpeaa)DE-He213 Wahabzada, Mirwaes aut Leucker, Marlene aut Dehne, Heinz-Wilhelm aut Kersting, Kristian aut Oerke, Erich-Christian aut Steiner, Ulrike aut Mahlein, Anne-Katrin aut Enthalten in Plant methods London : BioMed Central, 2005 11(2015), 1 vom: 15. Apr. (DE-627)500321191 (DE-600)2203723-8 1746-4811 nnns volume:11 year:2015 number:1 day:15 month:04 https://dx.doi.org/10.1186/s13007-015-0073-7 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2015 1 15 04 |
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10.1186/s13007-015-0073-7 doi (DE-627)SPR029407273 (SPR)s13007-015-0073-7-e DE-627 ger DE-627 rakwb eng Kuska, Matheus verfasserin aut Hyperspectral phenotyping on the microscopic scale: towards automated characterization of plant-pathogen interactions 2015 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Kuska et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background The detection and characterization of resistance reactions of crop plants against fungal pathogens are essential to select resistant genotypes. In breeding practice phenotyping of plant genotypes is realized by time consuming and expensive visual rating. In this context hyperspectral imaging (HSI) is a promising non-invasive sensor technique in order to accelerate and to automate classical phenotyping methods. A hyperspectral microscope was established to determine spectral changes on the leaf and cellular level of barley (Hordeum vulgare) during resistance reactions against powdery mildew (Blumeria graminis f.sp. hordei, isolate K1). Experiments were conducted with near isogenic barley lines of cv. Ingrid, including the susceptible wild type (WT), mildew locus a 12 (Mla12 based resistance) and the resistant mildew locus o 3 (mlo3 based resistance), respectively. The reflection of inoculated and non-inoculated leaves was recorded daily with a hyperspectral linescanner in the visual (400 – 700 nm) and near infrared (700 – 1000 nm) range 3 to 14 days after inoculation. Results Data analysis showed no significant differences in spectral signatures between non-inoculated genotypes. Barley leaves of the near-isogenic genotypes, inoculated with B. graminis f.sp. hordei differed in the spectral reflectance over time, respectively. The susceptible genotypes (WT, Mla12) showed an increase in reflectance in the visible range according to symptom development. However, the spectral signature of the resistant mlo-genotype did not show significant changes over the experimental period. In addition, a recent data driven approach for automated discovery of disease specific signatures, which is based on a new representation of the data using Simplex Volume Maximization (SiVM) was applied. The automated approach - evaluated in only a fraction of time revealed results similar to the time and labor intensive manually assessed hyperspectral signatures. The new representation determined by SiVM was also used to generate intuitive and easy to interpretable summaries, e.g. fingerprints or traces of hyperspectral dynamics of the different genotypes. Conclusion With this HSI based and data driven phenotyping approach an evaluation of host-pathogen interactions over time and a discrimination of barley genotypes differing in susceptibility to powdery mildew is possible. Hyperspectral imaging (dpeaa)DE-He213 Hyperspectral microscope (dpeaa)DE-He213 Spectral reflectance (dpeaa)DE-He213 Plant disease (dpeaa)DE-He213 Disease resistance (dpeaa)DE-He213 Mildew locus o ( (dpeaa)DE-He213 ) (dpeaa)DE-He213 Near-isogenic lines (dpeaa)DE-He213 f.sp. (dpeaa)DE-He213 Wahabzada, Mirwaes aut Leucker, Marlene aut Dehne, Heinz-Wilhelm aut Kersting, Kristian aut Oerke, Erich-Christian aut Steiner, Ulrike aut Mahlein, Anne-Katrin aut Enthalten in Plant methods London : BioMed Central, 2005 11(2015), 1 vom: 15. Apr. (DE-627)500321191 (DE-600)2203723-8 1746-4811 nnns volume:11 year:2015 number:1 day:15 month:04 https://dx.doi.org/10.1186/s13007-015-0073-7 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2015 1 15 04 |
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Kuska, Matheus Wahabzada, Mirwaes Leucker, Marlene Dehne, Heinz-Wilhelm Kersting, Kristian Oerke, Erich-Christian Steiner, Ulrike Mahlein, Anne-Katrin |
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Kuska, Matheus |
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hyperspectral phenotyping on the microscopic scale: towards automated characterization of plant-pathogen interactions |
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Hyperspectral phenotyping on the microscopic scale: towards automated characterization of plant-pathogen interactions |
| abstract |
Background The detection and characterization of resistance reactions of crop plants against fungal pathogens are essential to select resistant genotypes. In breeding practice phenotyping of plant genotypes is realized by time consuming and expensive visual rating. In this context hyperspectral imaging (HSI) is a promising non-invasive sensor technique in order to accelerate and to automate classical phenotyping methods. A hyperspectral microscope was established to determine spectral changes on the leaf and cellular level of barley (Hordeum vulgare) during resistance reactions against powdery mildew (Blumeria graminis f.sp. hordei, isolate K1). Experiments were conducted with near isogenic barley lines of cv. Ingrid, including the susceptible wild type (WT), mildew locus a 12 (Mla12 based resistance) and the resistant mildew locus o 3 (mlo3 based resistance), respectively. The reflection of inoculated and non-inoculated leaves was recorded daily with a hyperspectral linescanner in the visual (400 – 700 nm) and near infrared (700 – 1000 nm) range 3 to 14 days after inoculation. Results Data analysis showed no significant differences in spectral signatures between non-inoculated genotypes. Barley leaves of the near-isogenic genotypes, inoculated with B. graminis f.sp. hordei differed in the spectral reflectance over time, respectively. The susceptible genotypes (WT, Mla12) showed an increase in reflectance in the visible range according to symptom development. However, the spectral signature of the resistant mlo-genotype did not show significant changes over the experimental period. In addition, a recent data driven approach for automated discovery of disease specific signatures, which is based on a new representation of the data using Simplex Volume Maximization (SiVM) was applied. The automated approach - evaluated in only a fraction of time revealed results similar to the time and labor intensive manually assessed hyperspectral signatures. The new representation determined by SiVM was also used to generate intuitive and easy to interpretable summaries, e.g. fingerprints or traces of hyperspectral dynamics of the different genotypes. Conclusion With this HSI based and data driven phenotyping approach an evaluation of host-pathogen interactions over time and a discrimination of barley genotypes differing in susceptibility to powdery mildew is possible. © Kuska et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( |
| abstractGer |
Background The detection and characterization of resistance reactions of crop plants against fungal pathogens are essential to select resistant genotypes. In breeding practice phenotyping of plant genotypes is realized by time consuming and expensive visual rating. In this context hyperspectral imaging (HSI) is a promising non-invasive sensor technique in order to accelerate and to automate classical phenotyping methods. A hyperspectral microscope was established to determine spectral changes on the leaf and cellular level of barley (Hordeum vulgare) during resistance reactions against powdery mildew (Blumeria graminis f.sp. hordei, isolate K1). Experiments were conducted with near isogenic barley lines of cv. Ingrid, including the susceptible wild type (WT), mildew locus a 12 (Mla12 based resistance) and the resistant mildew locus o 3 (mlo3 based resistance), respectively. The reflection of inoculated and non-inoculated leaves was recorded daily with a hyperspectral linescanner in the visual (400 – 700 nm) and near infrared (700 – 1000 nm) range 3 to 14 days after inoculation. Results Data analysis showed no significant differences in spectral signatures between non-inoculated genotypes. Barley leaves of the near-isogenic genotypes, inoculated with B. graminis f.sp. hordei differed in the spectral reflectance over time, respectively. The susceptible genotypes (WT, Mla12) showed an increase in reflectance in the visible range according to symptom development. However, the spectral signature of the resistant mlo-genotype did not show significant changes over the experimental period. In addition, a recent data driven approach for automated discovery of disease specific signatures, which is based on a new representation of the data using Simplex Volume Maximization (SiVM) was applied. The automated approach - evaluated in only a fraction of time revealed results similar to the time and labor intensive manually assessed hyperspectral signatures. The new representation determined by SiVM was also used to generate intuitive and easy to interpretable summaries, e.g. fingerprints or traces of hyperspectral dynamics of the different genotypes. Conclusion With this HSI based and data driven phenotyping approach an evaluation of host-pathogen interactions over time and a discrimination of barley genotypes differing in susceptibility to powdery mildew is possible. © Kuska et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( |
| abstract_unstemmed |
Background The detection and characterization of resistance reactions of crop plants against fungal pathogens are essential to select resistant genotypes. In breeding practice phenotyping of plant genotypes is realized by time consuming and expensive visual rating. In this context hyperspectral imaging (HSI) is a promising non-invasive sensor technique in order to accelerate and to automate classical phenotyping methods. A hyperspectral microscope was established to determine spectral changes on the leaf and cellular level of barley (Hordeum vulgare) during resistance reactions against powdery mildew (Blumeria graminis f.sp. hordei, isolate K1). Experiments were conducted with near isogenic barley lines of cv. Ingrid, including the susceptible wild type (WT), mildew locus a 12 (Mla12 based resistance) and the resistant mildew locus o 3 (mlo3 based resistance), respectively. The reflection of inoculated and non-inoculated leaves was recorded daily with a hyperspectral linescanner in the visual (400 – 700 nm) and near infrared (700 – 1000 nm) range 3 to 14 days after inoculation. Results Data analysis showed no significant differences in spectral signatures between non-inoculated genotypes. Barley leaves of the near-isogenic genotypes, inoculated with B. graminis f.sp. hordei differed in the spectral reflectance over time, respectively. The susceptible genotypes (WT, Mla12) showed an increase in reflectance in the visible range according to symptom development. However, the spectral signature of the resistant mlo-genotype did not show significant changes over the experimental period. In addition, a recent data driven approach for automated discovery of disease specific signatures, which is based on a new representation of the data using Simplex Volume Maximization (SiVM) was applied. The automated approach - evaluated in only a fraction of time revealed results similar to the time and labor intensive manually assessed hyperspectral signatures. The new representation determined by SiVM was also used to generate intuitive and easy to interpretable summaries, e.g. fingerprints or traces of hyperspectral dynamics of the different genotypes. Conclusion With this HSI based and data driven phenotyping approach an evaluation of host-pathogen interactions over time and a discrimination of barley genotypes differing in susceptibility to powdery mildew is possible. © Kuska et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( |
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Wahabzada, Mirwaes Leucker, Marlene Dehne, Heinz-Wilhelm Kersting, Kristian Oerke, Erich-Christian Steiner, Ulrike Mahlein, Anne-Katrin |
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