Automatic morphology phenotyping of tetra- and hexaploid wheat spike using computer vision methods
Intraspecific classification of cultivated plants is necessary for the conservation of biological diversity, study of their origin and their phylogeny. The modern cultivated wheat species originated from three wild diploid ancestors as a result of several rounds of genome doubling and are represente...
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2021-03-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/2918 |
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| author | A. Yu. Pronozin A. A. Paulish E. A. Zavarzin A. Yu. Prikhodko N. M. Prokhoshin Yu. V. Kruchinina N. P. Goncharov E. G. Komyshev M. A. Genaev |
| author_facet | A. Yu. Pronozin A. A. Paulish E. A. Zavarzin A. Yu. Prikhodko N. M. Prokhoshin Yu. V. Kruchinina N. P. Goncharov E. G. Komyshev M. A. Genaev |
| author_sort | A. Yu. Pronozin |
| collection | DOAJ |
| description | Intraspecific classification of cultivated plants is necessary for the conservation of biological diversity, study of their origin and their phylogeny. The modern cultivated wheat species originated from three wild diploid ancestors as a result of several rounds of genome doubling and are represented by di-, tetra- and hexaploid species. The identification of wheat ploidy level is one of the main stages of their taxonomy. Such classification is possible based on visual analysis of the wheat spike traits. The aim of this study is to investigate the morphological characteristics of spikes for hexa- and tetraploid wheat species based on the method of high-performance phenotyping. Phenotyping of the quantitative characteristics of the spike of 17 wheat species (595 plants, 3348 images), including eight tetraploids (Triticum aethiopicum, T. dicoccoides, T. dicoccum, T. durum, T. militinae, T. polonicum, T. timopheevii, and T. turgidum) and nine hexaploids (T. compactum, T. aestivum, i:ANK-23 (near-isogenic line of T. aestivum cv. Novosibirskaya 67), T. antiquorum, T. spelta (including cv. Rother Sommer Kolben), T. petropavlovskyi, T. yunnanense, T. macha, T. sphaerococcum, and T. vavilovii), was performed. Wheat spike morphology was described on the basis of nine quantitative traits including shape, size and awns area of the spike. The traits were obtained as a result of image analysis using the WERecognizer program. A cluster analysis of plants according to the characteristics of the spike shape and comparison of their distributions in tetraploid and hexaploid species showed a higher variability of traits in hexaploid species compared to tetraploid ones. At the same time, the species themselves form two clusters in the visual characteristics of the spike. One type is predominantly hexaploid species (with the exception of one tetraploid, T. dicoccoides). The other group includes tetraploid ones (with the exception of three hexaploid ones, T. compactum, T. antiquorum, T. sphaerococcum, and i:ANK-23). Thus, it has been shown that the morphological characteristics of spikes for hexaploid and tetraploid wheat species, obtained on the basis of computer analysis of images, include differences, which are further used to develop methods for plant classifications by ploidy level and their species in an automatic mode. |
| format | Article |
| id | doaj-art-d2f6f896a04c42a4a2256b4895636b95 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2021-03-01 |
| 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-d2f6f896a04c42a4a2256b4895636b952025-02-01T09:58:09ZengSiberian 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 селекции2500-32592021-03-01251718110.18699/VJ21.0091134Automatic morphology phenotyping of tetra- and hexaploid wheat spike using computer vision methodsA. Yu. Pronozin0A. A. Paulish1E. A. Zavarzin2A. Yu. Prikhodko3N. M. Prokhoshin4Yu. V. Kruchinina5N. P. Goncharov6E. G. Komyshev7M. A. Genaev8Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesNovosibirsk State UniversityNovosibirsk State UniversityNovosibirsk State UniversityNovosibirsk State UniversityInstitute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomics Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesInstitute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Novosibirsk State Agrarian UniversityInstitute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University; Kurchatov Genomics Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesInstitute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University; Kurchatov Genomics Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesIntraspecific classification of cultivated plants is necessary for the conservation of biological diversity, study of their origin and their phylogeny. The modern cultivated wheat species originated from three wild diploid ancestors as a result of several rounds of genome doubling and are represented by di-, tetra- and hexaploid species. The identification of wheat ploidy level is one of the main stages of their taxonomy. Such classification is possible based on visual analysis of the wheat spike traits. The aim of this study is to investigate the morphological characteristics of spikes for hexa- and tetraploid wheat species based on the method of high-performance phenotyping. Phenotyping of the quantitative characteristics of the spike of 17 wheat species (595 plants, 3348 images), including eight tetraploids (Triticum aethiopicum, T. dicoccoides, T. dicoccum, T. durum, T. militinae, T. polonicum, T. timopheevii, and T. turgidum) and nine hexaploids (T. compactum, T. aestivum, i:ANK-23 (near-isogenic line of T. aestivum cv. Novosibirskaya 67), T. antiquorum, T. spelta (including cv. Rother Sommer Kolben), T. petropavlovskyi, T. yunnanense, T. macha, T. sphaerococcum, and T. vavilovii), was performed. Wheat spike morphology was described on the basis of nine quantitative traits including shape, size and awns area of the spike. The traits were obtained as a result of image analysis using the WERecognizer program. A cluster analysis of plants according to the characteristics of the spike shape and comparison of their distributions in tetraploid and hexaploid species showed a higher variability of traits in hexaploid species compared to tetraploid ones. At the same time, the species themselves form two clusters in the visual characteristics of the spike. One type is predominantly hexaploid species (with the exception of one tetraploid, T. dicoccoides). The other group includes tetraploid ones (with the exception of three hexaploid ones, T. compactum, T. antiquorum, T. sphaerococcum, and i:ANK-23). Thus, it has been shown that the morphological characteristics of spikes for hexaploid and tetraploid wheat species, obtained on the basis of computer analysis of images, include differences, which are further used to develop methods for plant classifications by ploidy level and their species in an automatic mode.https://vavilov.elpub.ru/jour/article/view/2918wheat spike morphologywheatphenomicsimage processingcomputer visionmachine learningbiotechnology |
| spellingShingle | A. Yu. Pronozin A. A. Paulish E. A. Zavarzin A. Yu. Prikhodko N. M. Prokhoshin Yu. V. Kruchinina N. P. Goncharov E. G. Komyshev M. A. Genaev Automatic morphology phenotyping of tetra- and hexaploid wheat spike using computer vision methods Вавиловский журнал генетики и селекции wheat spike morphology wheat phenomics image processing computer vision machine learning biotechnology |
| title | Automatic morphology phenotyping of tetra- and hexaploid wheat spike using computer vision methods |
| title_full | Automatic morphology phenotyping of tetra- and hexaploid wheat spike using computer vision methods |
| title_fullStr | Automatic morphology phenotyping of tetra- and hexaploid wheat spike using computer vision methods |
| title_full_unstemmed | Automatic morphology phenotyping of tetra- and hexaploid wheat spike using computer vision methods |
| title_short | Automatic morphology phenotyping of tetra- and hexaploid wheat spike using computer vision methods |
| title_sort | automatic morphology phenotyping of tetra and hexaploid wheat spike using computer vision methods |
| topic | wheat spike morphology wheat phenomics image processing computer vision machine learning biotechnology |
| url | https://vavilov.elpub.ru/jour/article/view/2918 |
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