Image-based analysis of quantitative morphological characteristics of wild potato tubers using the desktop application SeedСounter
The development of quantitative digital phenotyping methods for evaluation of wild potato (section Petota Dumort., genus Solanum L.) tuberization is required for annotation of genebank collections and selection of the suitable donor material for potato breeding. There are no available methods specif...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2019-08-01
|
| Series: | Вавиловский журнал генетики и селекции |
| Subjects: | |
| Online Access: | https://vavilov.elpub.ru/jour/article/view/1999 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832575184283893760 |
|---|---|
| author | K. A. Ivanova E. G. Komyshev M. A. Genaev A. A. Egorova K. A. Koloshina N. A. Chalaya D. A. Afonnikov A. V. Kochetov E. V. Rogozina S. V. Gerasimova |
| author_facet | K. A. Ivanova E. G. Komyshev M. A. Genaev A. A. Egorova K. A. Koloshina N. A. Chalaya D. A. Afonnikov A. V. Kochetov E. V. Rogozina S. V. Gerasimova |
| author_sort | K. A. Ivanova |
| collection | DOAJ |
| description | The development of quantitative digital phenotyping methods for evaluation of wild potato (section Petota Dumort., genus Solanum L.) tuberization is required for annotation of genebank collections and selection of the suitable donor material for potato breeding. There are no available methods specifically designed for the quantitative analysis of wild potato tuber morphology. The current study is devoted to evaluation of wild potato tubers’ morphological characteristics using a digital image processing technique. For this purpose, the mobile application SeedSounter developed previously for grain analysis was specifically adapted for tuber phenotyping. The application estimates the number and shape of objects scattered on a standard sheet of white paper (i. e. A3 or A4). Twelve accessions from the VIR genebank collection belonging to nine Petota species were grown in pots protected with garden fabric during the growing season of cultivated potato (Novosibirsk region). Tubers were collected form plants of nine genotypes. Three genotypes did not produce tubers. The weight of tubers collected from each plant was measured. The tuber yield from each plant was analyzed using SeedCounter (http://wheatdb.org/seedcounter). The number of tubers per plant was counted; the following characteristics were extracted from the images of individual tubers: length, width, projected area, length to width ratio, сircularity, roundness, rugosity and solidity. One-way ANOVA showed a significant effect of genotype on all measured characteristics. A pairwise comparison of nine Petota accessions using all measured parameters revealed statistically significant differences between 86 % of pairs. The overall tuber yield volume for each plant was calculated as a sum of volumes of individual tubers; tuber volume was calculated from its length to width ratio and projected area. A strong correlation between the evaluated tuber yield volume and yield weight was shown. We propose tuber yield volume as a characteristic for a general evaluation of tuberization for wild potato, implementing the four-step scale from 0 to 3. According to this characteristic, the twelve wild potato accessions studied could be divided into four groups with different tuberization abilities. The evaluated tuberization ability is partially in accordance with previously obtained VIR data. The results presented demonstrate the possibility to use SeedCounter for wild potato collections phenotyping. |
| format | Article |
| id | doaj-art-bffb9997114a4cb58c8682ca9d6337fe |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2019-08-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-bffb9997114a4cb58c8682ca9d6337fe2025-02-01T09:58:07ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592019-08-0123551952610.18699/VJ19.35-o900Image-based analysis of quantitative morphological characteristics of wild potato tubers using the desktop application SeedСounterK. A. Ivanova0E. G. Komyshev1M. A. Genaev2A. A. Egorova3K. A. Koloshina4N. A. Chalaya5D. A. Afonnikov6A. V. Kochetov7E. V. Rogozina8S. V. Gerasimova9Institute of Cytology and Genetics, SB RASInstitute of Cytology and Genetics, SB RASInstitute of Cytology and Genetics, SB RAS; Novosibirsk State UniversityInstitute of Cytology and Genetics, SB RAS; Novosibirsk State UniversityInstitute of Cytology and Genetics, SB RASFederal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)Institute of Cytology and Genetics, SB RAS; Novosibirsk State UniversityInstitute of Cytology and Genetics, SB RAS; Novosibirsk State UniversityFederal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)Institute of Cytology and Genetics, SB RAS; Novosibirsk State UniversityThe development of quantitative digital phenotyping methods for evaluation of wild potato (section Petota Dumort., genus Solanum L.) tuberization is required for annotation of genebank collections and selection of the suitable donor material for potato breeding. There are no available methods specifically designed for the quantitative analysis of wild potato tuber morphology. The current study is devoted to evaluation of wild potato tubers’ morphological characteristics using a digital image processing technique. For this purpose, the mobile application SeedSounter developed previously for grain analysis was specifically adapted for tuber phenotyping. The application estimates the number and shape of objects scattered on a standard sheet of white paper (i. e. A3 or A4). Twelve accessions from the VIR genebank collection belonging to nine Petota species were grown in pots protected with garden fabric during the growing season of cultivated potato (Novosibirsk region). Tubers were collected form plants of nine genotypes. Three genotypes did not produce tubers. The weight of tubers collected from each plant was measured. The tuber yield from each plant was analyzed using SeedCounter (http://wheatdb.org/seedcounter). The number of tubers per plant was counted; the following characteristics were extracted from the images of individual tubers: length, width, projected area, length to width ratio, сircularity, roundness, rugosity and solidity. One-way ANOVA showed a significant effect of genotype on all measured characteristics. A pairwise comparison of nine Petota accessions using all measured parameters revealed statistically significant differences between 86 % of pairs. The overall tuber yield volume for each plant was calculated as a sum of volumes of individual tubers; tuber volume was calculated from its length to width ratio and projected area. A strong correlation between the evaluated tuber yield volume and yield weight was shown. We propose tuber yield volume as a characteristic for a general evaluation of tuberization for wild potato, implementing the four-step scale from 0 to 3. According to this characteristic, the twelve wild potato accessions studied could be divided into four groups with different tuberization abilities. The evaluated tuberization ability is partially in accordance with previously obtained VIR data. The results presented demonstrate the possibility to use SeedCounter for wild potato collections phenotyping.https://vavilov.elpub.ru/jour/article/view/1999solanumpetotadigital phenotyping of plantswild potato speciesseedcountertuberization |
| spellingShingle | K. A. Ivanova E. G. Komyshev M. A. Genaev A. A. Egorova K. A. Koloshina N. A. Chalaya D. A. Afonnikov A. V. Kochetov E. V. Rogozina S. V. Gerasimova Image-based analysis of quantitative morphological characteristics of wild potato tubers using the desktop application SeedСounter Вавиловский журнал генетики и селекции solanum petota digital phenotyping of plants wild potato species seedcounter tuberization |
| title | Image-based analysis of quantitative morphological characteristics of wild potato tubers using the desktop application SeedСounter |
| title_full | Image-based analysis of quantitative morphological characteristics of wild potato tubers using the desktop application SeedСounter |
| title_fullStr | Image-based analysis of quantitative morphological characteristics of wild potato tubers using the desktop application SeedСounter |
| title_full_unstemmed | Image-based analysis of quantitative morphological characteristics of wild potato tubers using the desktop application SeedСounter |
| title_short | Image-based analysis of quantitative morphological characteristics of wild potato tubers using the desktop application SeedСounter |
| title_sort | image based analysis of quantitative morphological characteristics of wild potato tubers using the desktop application seedсounter |
| topic | solanum petota digital phenotyping of plants wild potato species seedcounter tuberization |
| url | https://vavilov.elpub.ru/jour/article/view/1999 |
| work_keys_str_mv | AT kaivanova imagebasedanalysisofquantitativemorphologicalcharacteristicsofwildpotatotubersusingthedesktopapplicationseedsounter AT egkomyshev imagebasedanalysisofquantitativemorphologicalcharacteristicsofwildpotatotubersusingthedesktopapplicationseedsounter AT magenaev imagebasedanalysisofquantitativemorphologicalcharacteristicsofwildpotatotubersusingthedesktopapplicationseedsounter AT aaegorova imagebasedanalysisofquantitativemorphologicalcharacteristicsofwildpotatotubersusingthedesktopapplicationseedsounter AT kakoloshina imagebasedanalysisofquantitativemorphologicalcharacteristicsofwildpotatotubersusingthedesktopapplicationseedsounter AT nachalaya imagebasedanalysisofquantitativemorphologicalcharacteristicsofwildpotatotubersusingthedesktopapplicationseedsounter AT daafonnikov imagebasedanalysisofquantitativemorphologicalcharacteristicsofwildpotatotubersusingthedesktopapplicationseedsounter AT avkochetov imagebasedanalysisofquantitativemorphologicalcharacteristicsofwildpotatotubersusingthedesktopapplicationseedsounter AT evrogozina imagebasedanalysisofquantitativemorphologicalcharacteristicsofwildpotatotubersusingthedesktopapplicationseedsounter AT svgerasimova imagebasedanalysisofquantitativemorphologicalcharacteristicsofwildpotatotubersusingthedesktopapplicationseedsounter |