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Jafari M, Daneshvar MH. Machine learning-mediated Passiflora caerulea callogenesis optimization. PLoS One 2024; 19:e0292359. [PMID: 38266002 PMCID: PMC10807783 DOI: 10.1371/journal.pone.0292359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/19/2023] [Indexed: 01/26/2024] Open
Abstract
Callogenesis is one of the most powerful biotechnological approaches for in vitro secondary metabolite production and indirect organogenesis in Passiflora caerulea. Comprehensive knowledge of callogenesis and optimized protocol can be obtained by the application of a combination of machine learning (ML) and optimization algorithms. In the present investigation, the callogenesis responses (i.e., callogenesis rate and callus fresh weight) of P. caerulea were predicted based on different types and concentrations of plant growth regulators (PGRs) (i.e., 2,4-dichlorophenoxyacetic acid (2,4-D), 6-benzylaminopurine (BAP), 1-naphthaleneacetic acid (NAA), and indole-3-Butyric Acid (IBA)) as well as explant types (i.e., leaf, node, and internode) using multilayer perceptron (MLP). Moreover, the developed models were integrated into the genetic algorithm (GA) to optimize the concentration of PGRs and explant types for maximizing callogenesis responses. Furthermore, sensitivity analysis was conducted to assess the importance of each input variable on the callogenesis responses. The results showed that MLP had high predictive accuracy (R2 > 0.81) in both training and testing sets for modeling all studied parameters. Based on the results of the optimization process, the highest callogenesis rate (100%) would be obtained from the leaf explant cultured in the medium supplemented with 0.52 mg/L IBA plus 0.43 mg/L NAA plus 1.4 mg/L 2,4-D plus 0.2 mg/L BAP. The results of the sensitivity analysis showed the explant-dependent impact of the exogenous application of PGRs on callogenesis. Generally, the results showed that a combination of MLP and GA can display a forward-thinking aid to optimize and predict in vitro culture systems and consequentially cope with several challenges faced currently in Passiflora tissue culture.
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Affiliation(s)
- Marziyeh Jafari
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz, Iran
- Department of Horticultural Sciences, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Iran
| | - Mohammad Hosein Daneshvar
- Department of Horticultural Sciences, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Iran
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Plant Regeneration Protocol for Recalcitrant Passionflower (Passiflora quadrangularis L.). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8040337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This research was designed to provide the first protocol to establish an efficient solution for direct organogenesis regeneration in Passiflora quadrangularis using nodal explants from young shoots. Passifloraceae tissue culture has been associated with problems such as recalcitrance, sensitivity to ethylene accumulation and browning of explants due to the presence of phenols in the tissues. Due to the high rate of endogenous contamination of the explants, a preliminary experiment was performed. The best results of surface sterilization were obtained using the pretreatment with 70% EtOH, 1 min and 50% NaOCl, 10 min along with the treatment of Rifampicin 15 µg/mL and Benomyl 2 g/L. The effects of plant growth regulators on the induction of direct organogenesis, multiplication of shoots in subcultures and in vitro rooting were evaluated. Additional compounds such as AgNO3 and Pluronic F-68 were added to the culture media in order to reduce the effects of phenols and the sudden browning of the explants. Shoot proliferation increased to the sixth subculture after which it decreased. A maximum of 7.17 shoots were obtained from one shoot on Murashige and Skoog (MS) medium supplemented with 2 mg/L 6-benzylaminopurine and 1 mg/L thidiazuron. Supplementation of ½ MS medium with 1 mg/L 1-naphthaleneacetic acid was conducing to root formation in 61.11% of shoots. After acclimatization, the plants showed vigorous growth, green leaves, and well-developed roots. Although this species has previously shown difficulty in in vitro propagation, this protocol established based on the results proved to be efficient and reproducible.
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Rizwan HM, Yang Q, Yousef AF, Zhang X, Sharif Y, Kaijie J, Shi M, Li H, Munir N, Yang X, Wei X, Oelmüller R, Cheng C, Chen F. Establishment of a Novel and Efficient Agrobacterium-Mediated in Planta Transformation System for Passion Fruit ( Passiflora edulis). PLANTS (BASEL, SWITZERLAND) 2021; 10:2459. [PMID: 34834821 PMCID: PMC8621743 DOI: 10.3390/plants10112459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 05/31/2023]
Abstract
Passion fruit (Passiflora edulis) is an important fruit crop with high economic value. Genetic engineering plays an important role in crop improvement with desired traits and gene functional studies. The lack of a simple, efficient, and stable transformation system for passion fruit has greatly limited gene functional studies. In this study, a simple and efficient Agrobacterium-mediated in planta transformation system for passion fruit was established, using Agrobacterium virulent strain EHA105 harboring the binary vectors pCAMBIA1301 and pCAMBIA1302 with GUS and GFP reporter genes. The system requires less time and labor costs than conventional transformation systems, and no additional phytohormones and sterile conditions are required. Regeneration efficiency of 86% and transformation efficiency of 29% were achieved, when the wounds were wrapped with Parafilm and the plants were kept in darkness for 15 days. Approximately 75% of the regenerated plants had a single shoot and 26% multiple shoots. The transformation was confirmed at the DNA and RNA levels as well as by GUS staining and GFP fluorescent measurements. The developed protocol will contribute to the genetic improvement of passion fruit breeding.
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Affiliation(s)
- Hafiz Muhammad Rizwan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.M.R.); (Q.Y.); (A.F.Y.); (X.Z.); (J.K.); (M.S.); (H.L.); (N.M.); (X.Y.); (R.O.)
| | - Qiang Yang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.M.R.); (Q.Y.); (A.F.Y.); (X.Z.); (J.K.); (M.S.); (H.L.); (N.M.); (X.Y.); (R.O.)
| | - Ahmed Fathy Yousef
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.M.R.); (Q.Y.); (A.F.Y.); (X.Z.); (J.K.); (M.S.); (H.L.); (N.M.); (X.Y.); (R.O.)
- Department of Horticulture, College of Agriculture, University of Al-Azhar (Branch Assiut), Assiut 71524, Egypt
| | - Xiaoxue Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.M.R.); (Q.Y.); (A.F.Y.); (X.Z.); (J.K.); (M.S.); (H.L.); (N.M.); (X.Y.); (R.O.)
| | - Yasir Sharif
- Institute of Oil Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Jia Kaijie
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.M.R.); (Q.Y.); (A.F.Y.); (X.Z.); (J.K.); (M.S.); (H.L.); (N.M.); (X.Y.); (R.O.)
| | - Meng Shi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.M.R.); (Q.Y.); (A.F.Y.); (X.Z.); (J.K.); (M.S.); (H.L.); (N.M.); (X.Y.); (R.O.)
| | - Han Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.M.R.); (Q.Y.); (A.F.Y.); (X.Z.); (J.K.); (M.S.); (H.L.); (N.M.); (X.Y.); (R.O.)
| | - Nigarish Munir
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.M.R.); (Q.Y.); (A.F.Y.); (X.Z.); (J.K.); (M.S.); (H.L.); (N.M.); (X.Y.); (R.O.)
| | - Xuelian Yang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.M.R.); (Q.Y.); (A.F.Y.); (X.Z.); (J.K.); (M.S.); (H.L.); (N.M.); (X.Y.); (R.O.)
| | - Xiaoxia Wei
- Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China;
| | - Ralf Oelmüller
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.M.R.); (Q.Y.); (A.F.Y.); (X.Z.); (J.K.); (M.S.); (H.L.); (N.M.); (X.Y.); (R.O.)
- Matthias Schleiden Institute, Plant Physiology, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Chunzhen Cheng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.M.R.); (Q.Y.); (A.F.Y.); (X.Z.); (J.K.); (M.S.); (H.L.); (N.M.); (X.Y.); (R.O.)
| | - Faxing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.M.R.); (Q.Y.); (A.F.Y.); (X.Z.); (J.K.); (M.S.); (H.L.); (N.M.); (X.Y.); (R.O.)
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