A simple method for measuring pollen germination rate using machine learning.

Abiotic stress Chili pepper Microscope Object detection Yolov5

Journal

Plant reproduction
ISSN: 2194-7961
Titre abrégé: Plant Reprod
Pays: Germany
ID NLM: 101602701

Informations de publication

Date de publication:
Dec 2023
Historique:
received: 25 08 2022
accepted: 30 05 2023
medline: 23 10 2023
pubmed: 6 6 2023
entrez: 6 6 2023
Statut: ppublish

Résumé

The pollen germination rate decreases under various abiotic stresses, such as high-temperature stress, and it is one of the causes of inhibition of plant reproduction. Thus, measuring pollen germination rate is vital for understanding the reproductive ability of plants. However, measuring the pollen germination rate requires much labor when counting pollen. Therefore, we used the Yolov5 machine learning package in order to perform transfer learning and constructed a model that can detect germinated and non-germinated pollen separately. Pollen images of the chili pepper, Capsicum annuum, were used to create this model. Using images with a width of 640 pixels for training constructed a more accurate model than using images with a width of 320 pixels. This model could estimate the pollen germination rate of the F

Identifiants

pubmed: 37278944
doi: 10.1007/s00497-023-00472-9
pii: 10.1007/s00497-023-00472-9
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

355-364

Subventions

Organisme : Kaken Pharmaceutical
ID : 21K05575

Informations de copyright

© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.

Références

Ahmed Z, Khalid M, Ghafoor A, Kausar M, Shah N, Raja GK, Rana RM, Mahmood T, Thompson AM (2022) SNP-Based Genome-wide association mapping of pollen viability under heat stress in tropical Zea mays L. inbred lines. Front Genet 13:819849
doi: 10.3389/fgene.2022.819849 pubmed: 35368702 pmcid: 8966704
Ascari L, Novara C, Dusio V, Oddi L, Siniscalco C (2020) Quantitative methods in microscopy to assess pollen viability in different plant taxa. Plant Reprod 33:205–219
doi: 10.1007/s00497-020-00398-6 pubmed: 33123804 pmcid: 7648740
Bolat I, Pirlak L (1999) An investigation on pollen viability, germination and tube growth in some stone fruits. Turk J Agric for 23:383–388
Coast O, Murdoch AJ, Ellis RH, Hay FR, Jagadish KSV (2016) Resilience of rice (Oryza spp.) pollen germination and tube growth to temperature stress. Plant Cell Environ 39:26–37
doi: 10.1111/pce.12475 pubmed: 25346255
Driedonks N, Rieu I, Vriezen WH (2016) Breeding for plant heat tolerance at vegetative and reproductive stages. Plant Reprod 29:67–79
doi: 10.1007/s00497-016-0275-9 pubmed: 26874710 pmcid: 4909801
Gajanayake B, Trader BW, Reddy KR, Harkess RL (2011) Screening ornamental pepper cultivars for temperature tolerance using pollen and physiological parameters. HortScience 46:878–884
doi: 10.21273/HORTSCI.46.6.878
Güçlü SF, Öncü Z, Koyuncu F (2020) Pollen performance modelling with an artificial neural network on commercial stone fruit cultivars. Hortic Environ Biotechnol 61:61–67
doi: 10.1007/s13580-019-00208-7
Gudin S, Arene L, Bulard C (1991) Influence of season on rose pollen quality. Sex Plant Reprod 4:113–117
doi: 10.1007/BF00196497
Hebbar KB, Rose HM, Nair AR, Kannan S, Niral V, Arivalagan M, Gupta A, Samsudeen K, Chandran KP, Chowdappa P, Prasad PVV (2018) Differences in in vitro pollen germination and pollen tube growth of coconut (Cocos nucifera L.) cultivars in response to high temperature stress. Environ Exp Bot 153:35–44
doi: 10.1016/j.envexpbot.2018.04.014
Hedhly A, Hormaza JI, Herrero M (2009) Global warming and sexual plant reproduction. Trends Plant Sci 14:30–36
doi: 10.1016/j.tplants.2008.11.001 pubmed: 19062328
Intergovernmental Panel on Climate Change (IPCC) (2022). Climate Change 2022: Impacts, adaptation, and vulnerability. contribution of working group II to the sixth assessment report of the intergovernmental panel on climate change. (Pörtner HO, Roberts DC, Tignor M, Poloczanska ES, Mintenbeck K, Alegría A, Craig M, Langsdorf S, Löschke S, Möller V, Okem A, Rama B (eds.), Cambridge University Press, Cambridge, New York. pp 1–3056. doi: https://doi.org/10.1017/9781009325844 . Accessed 13 March 2023.
Jiang Y, Li C (2020) Convolutional neural networks for image-based high-throughput plant phenotyping: a review. Plant Phenomics 2020:4152816
doi: 10.34133/2020/4152816 pubmed: 33313554 pmcid: 7706326
Jocher G, Chaurasia A, Stoken A, Borovec J, NanoCode012, Kwon Y, TaoXie, Fang J, imyhxy, Michael K, Lorna, Abhiram V, Montes D, Nadar J, Laughing, tkianai, yxNONG, Skalski P, Wang Z, Hogan A, Fati C, Mammana L, AlexWang1900, Deep Patel, Yiwei D, You F, Hajek J, Diaconu L, Minh MT (2022) ultralytics/yolov5: v6.1—TensorRT, TensorFlow Edge TPU and OpenVINO Export and Inference (v6.1). Zenodo. https://doi.org/10.5281/zenodo.6222936 . Accessed 15 Jun 2022
Kakani VG, Prasad PVV, Craufurd PQ, Wheeler TR (2002) Response of in vitro pollen germination and pollen tube growth of groundnut (Arachis hypogaea L.) genotypes to temperature. Plant Cell Environ 25:1651–1661
doi: 10.1046/j.1365-3040.2002.00943.x
Kakani VG, Reddy KR, Koti S, Wallace TP, Prasad PVV, Reddy VR, Zhao D (2005) Differences in in vitro pollen germination and pollen tube growth of cotton cultivars in response to high temperature. Ann Bot 96:59–67
doi: 10.1093/aob/mci149 pubmed: 15851397 pmcid: 4246808
Komiya R, Goto S (2022) Evaluation of citrus male sterility by machine learning and the practicality. Hort Res (japan) 21(Suppl. 1):159 ((In Japanese))
Koti S, Reddy KR, Reddy VR, Kakani VG, Zhao D (2005) Interactive effects of carbon dioxide, temperature, and ultraviolet-B radiation on soybean (Glycine max L.) flower and pollen morphology, pollen production, germination, and tube lengths. J Exp Bot 56:725–736
doi: 10.1093/jxb/eri044 pubmed: 15611147
Kovaleva LV, Zakharova EV, Minkina YV, Timofeeva GV, Andreev IM (2005) Germination and in vitro growth of petunia male gametophyte are affected by exogenous hormones and involve the changes in the endogenous hormone level. Russ J Plant Physiol 52:521–526
doi: 10.1007/s11183-005-0077-7
Masuda M, Ojiewo CO, Nagai M, Murakami K, Masinde PW, Yu W (2010) Simulating hybrid-seed contamination risk with selfed seeds from residual fertility in a male-sterile t-4 mutant tomato, Solanum Lycopersicum L. J Jpn Soc Hortic Sci 79:34–39
doi: 10.2503/jjshs1.79.34
Mathew MP, Yamuna T (2022) Leaf-based disease detection in bell pepper plant using YOLO v5. Signal Image Video Process 16:841–847
doi: 10.1007/s11760-021-02024-y
Mesihovic A, Iannacone R, Firon N, Fragkostefanakis S (2016) Heat stress regimes for the investigation of pollen thermotolerance in crop plants. Plant Reprod 29:93–105
Miller G, Beery A, Singh PK, Wang F, Zelingher R, Motenko E, Lieberman-Lazarovich M (2021) Contrasting processing tomato cultivars unlink yield and pollen viability under heat stress. AoB PLANTS 13:plab046
doi: 10.1093/aobpla/plab046 pubmed: 34394907 pmcid: 8356174
Pipattanawong R, Yamane K, Fujishige N, Bang SW, Yamaki Y (2009) Effects of high temperature on pollen quality, ovule fertilization and development of embryo and achene in ‘Tochiotome’ strawberry. J Jpn Soc Hortic Sci 78:300–306
doi: 10.2503/jjshs1.78.300
Qi J, Liu X, Liu K, Xu F, Guo H, Tian X (2022) An improved YOLOv5 model based on visual attention mechanism: application to recognition of tomato virus disease. Comput Electron Agric 194:106780
doi: 10.1016/j.compag.2022.106780
Reddy KR, Kakani VG (2007) Screening Capsicum species of different origins for high temperature tolerance by in vitro pollen germination and pollen tube length. Sci Hortic 112:130–135
doi: 10.1016/j.scienta.2006.12.014
Redmon J, Farhadi A (2018) Yolov3: An incremental improvement. arXiv:1804.02767
Redmon J, Divvala S, Girshick R, Farhadi A (2016) You only look once: Unified, real-time object detection. In: Proceedings of the IEEE conference on computer vision and pattern recognition. pp. 779–788
Redmon J, Farhadi A (2017) YOLO9000: better, faster, stronger. In: IEEE conference on computer vision and pattern recognition. pp. 6517–6525.
Richter J, Powles SB (1993) Pollen expression of herbicide target site resistance genes in annual ryegrass (Lolium rigidum). Plant Physiol 102:1037–1041
doi: 10.1104/pp.102.3.1037 pubmed: 12231886 pmcid: 158879
Roberts IN, Gaude TC, Harrod G, Dickinson HG (1983) Pollen-stigma interactions in Brassica oleracea; a new pollen germination medium and its use in elucidating the mechanism of self incompatibility. Theor Appl Genet 65:231–238
doi: 10.1007/BF00308074 pubmed: 24263420
Roitsch T, Cabrera-Bosquet L, Fournier A, Ghamkhar K, Jiménez-Berni J, Pinto F, Ober ES (2019) Review: new sensors and data-driven approaches–a path to next generation phenomics. Plant Sci 282:2–10
doi: 10.1016/j.plantsci.2019.01.011 pubmed: 31003608 pmcid: 6483971
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez J-Y, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9:676–682
doi: 10.1038/nmeth.2019 pubmed: 22743772
Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9:671–675
doi: 10.1038/nmeth.2089 pubmed: 22930834 pmcid: 5554542
Yamazaki A, Hosokawa M (2019) Increased percentage of fruit set of F
doi: 10.1016/j.scienta.2018.08.049
Yamazaki A, Shirasawa K, Hosokawa M (2020) Transgressive segregation and gene regions controlling thermotolerance of fruit set and pollen germination in Capsicum chinense. Euphytica 216:179
doi: 10.1007/s10681-020-02712-9
Yamazaki A, Takezawa A, Nakano R, Nishimura K, Motoki K, Hosokawa M, Nakazaki T (2022) Indicator candidate traits for autonomous fruit set ability under high temperatures in Capsicum. J Hortic Res 30:105–116
doi: 10.2478/johr-2022-0017
Yang U, Oh S, Wi SG, Lee B-R, Lee S-H, Kim M-S (2021) Classification of germination images of pear pollen using random forest and convolution neural network models. IEEE Access 9:45993–45999
doi: 10.1109/ACCESS.2021.3067677

Auteurs

Akira Yamazaki (A)

Faculty of Agriculture, Kindai University, Nara, 631-8505, Japan. yamazaki@nara.kindai.ac.jp.

Ao Takezawa (A)

Graduate School of Agriculture, Kyoto University, Kizugawa, 619-0218, Japan.

Kyoka Nagasaka (K)

Graduate School of Agriculture, Kyoto University, Kizugawa, 619-0218, Japan.

Ko Motoki (K)

Graduate School of Agriculture, Kyoto University, Kizugawa, 619-0218, Japan.

Kazusa Nishimura (K)

Graduate School of Agriculture, Kyoto University, Kizugawa, 619-0218, Japan.

Ryohei Nakano (R)

Graduate School of Agriculture, Kyoto University, Kizugawa, 619-0218, Japan.

Tetsuya Nakazaki (T)

Graduate School of Agriculture, Kyoto University, Kizugawa, 619-0218, Japan.

Articles similaires

Humans Macular Degeneration Mendelian Randomization Analysis Life Style Genome-Wide Association Study
Capsicum Disease Resistance Plant Diseases Polymorphism, Single Nucleotide Ralstonia solanacearum
Humans Metabolic Syndrome Sleep Apnea, Obstructive Mendelian Randomization Analysis Gastrointestinal Diseases
Humans Mendelian Randomization Analysis Graves Disease Aging Genome-Wide Association Study

Classifications MeSH