Determination of the melanin and anthocyanin content in barley grains by digital image analysis using machine learning methods
The pigment composition of plant seed coat affects important properties such as resistance to pathogens, pre-harvest sprouting, and mechanical hardness. The dark color of barley (Hordeum vulgare L.) grain can be attributed to the synthesis and accumulation of two groups of pigments. Blue and purple...
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| Format: | Article |
| Language: | English |
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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
2023-12-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/3986 |
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| author | E. G. Komyshev M. A. Genaev I. D. Busov M. V. Kozhekin N. V. Artemenko A. Y. Glagoleva V. S. Koval D. A. Afonnikov |
| author_facet | E. G. Komyshev M. A. Genaev I. D. Busov M. V. Kozhekin N. V. Artemenko A. Y. Glagoleva V. S. Koval D. A. Afonnikov |
| author_sort | E. G. Komyshev |
| collection | DOAJ |
| description | The pigment composition of plant seed coat affects important properties such as resistance to pathogens, pre-harvest sprouting, and mechanical hardness. The dark color of barley (Hordeum vulgare L.) grain can be attributed to the synthesis and accumulation of two groups of pigments. Blue and purple grain color is associated with the biosynthesis of anthocyanins. Gray and black grain color is caused by melanin. These pigments may accumulate in the grain shells both individually and together. Therefore, it is difficult to visually distinguish which pigments are responsible for the dark color of the grain. Chemical methods are used to accurately determine the presence/absence of pigments; however, they are expensive and labor-intensive. Therefore, the development of a new method for quickly assessing the presence of pigments in the grain would help in investigating the mechanisms of genetic control of the pigment composition of barley grains. In this work, we developed a method for assessing the presence or absence of anthocyanins and melanin in the barley grain shell based on digital image analysis using computer vision and machine learning algo rithms. A protocol was developed to obtain digital RGB images of barley grains. Using this protocol, a total of 972 images were acquired for 108 barley accessions. Seed coat from these accessions may contain anthocyanins, melanins, or pigments of both types. Chemical methods were used to accurately determine the pigment content of the grains. Four models based on computer vision techniques and convolutional neural networks of different architectures were developed to predict grain pigment composition from images. The U-Net network model based on the EfficientNetB0 topology showed the best performance in the holdout set (the value of the “accuracy” parameter was 0.821). |
| format | Article |
| id | doaj-art-73359226eb7a42769048db01ea8d35e6 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2023-12-01 |
| 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-73359226eb7a42769048db01ea8d35e62025-02-01T09:58:12ZengSiberian 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 селекции2500-32592023-12-0127785986810.18699/VJGB-23-991414Determination of the melanin and anthocyanin content in barley grains by digital image analysis using machine learning methodsE. G. Komyshev0M. A. Genaev1I. D. Busov2M. V. Kozhekin3N. V. Artemenko4A. Y. Glagoleva5V. S. Koval6D. A. Afonnikov7Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of ICG SB RAS; Novosibirsk State UniversityInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State UniversityKurchatov Genomic Center of ICG SB RASKurchatov Genomic Center of ICG SB RAS; Novosibirsk State UniversityInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of ICG SB RAS; Novosibirsk State UniversityThe pigment composition of plant seed coat affects important properties such as resistance to pathogens, pre-harvest sprouting, and mechanical hardness. The dark color of barley (Hordeum vulgare L.) grain can be attributed to the synthesis and accumulation of two groups of pigments. Blue and purple grain color is associated with the biosynthesis of anthocyanins. Gray and black grain color is caused by melanin. These pigments may accumulate in the grain shells both individually and together. Therefore, it is difficult to visually distinguish which pigments are responsible for the dark color of the grain. Chemical methods are used to accurately determine the presence/absence of pigments; however, they are expensive and labor-intensive. Therefore, the development of a new method for quickly assessing the presence of pigments in the grain would help in investigating the mechanisms of genetic control of the pigment composition of barley grains. In this work, we developed a method for assessing the presence or absence of anthocyanins and melanin in the barley grain shell based on digital image analysis using computer vision and machine learning algo rithms. A protocol was developed to obtain digital RGB images of barley grains. Using this protocol, a total of 972 images were acquired for 108 barley accessions. Seed coat from these accessions may contain anthocyanins, melanins, or pigments of both types. Chemical methods were used to accurately determine the pigment content of the grains. Four models based on computer vision techniques and convolutional neural networks of different architectures were developed to predict grain pigment composition from images. The U-Net network model based on the EfficientNetB0 topology showed the best performance in the holdout set (the value of the “accuracy” parameter was 0.821).https://vavilov.elpub.ru/jour/article/view/3986digital image analysismachine learningbarley grainspigment composition |
| spellingShingle | E. G. Komyshev M. A. Genaev I. D. Busov M. V. Kozhekin N. V. Artemenko A. Y. Glagoleva V. S. Koval D. A. Afonnikov Determination of the melanin and anthocyanin content in barley grains by digital image analysis using machine learning methods Вавиловский журнал генетики и селекции digital image analysis machine learning barley grains pigment composition |
| title | Determination of the melanin and anthocyanin content in barley grains by digital image analysis using machine learning methods |
| title_full | Determination of the melanin and anthocyanin content in barley grains by digital image analysis using machine learning methods |
| title_fullStr | Determination of the melanin and anthocyanin content in barley grains by digital image analysis using machine learning methods |
| title_full_unstemmed | Determination of the melanin and anthocyanin content in barley grains by digital image analysis using machine learning methods |
| title_short | Determination of the melanin and anthocyanin content in barley grains by digital image analysis using machine learning methods |
| title_sort | determination of the melanin and anthocyanin content in barley grains by digital image analysis using machine learning methods |
| topic | digital image analysis machine learning barley grains pigment composition |
| url | https://vavilov.elpub.ru/jour/article/view/3986 |
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