Innovation in the Breeding of Common Bean Through a Combined Approach of in vitro Regeneration and Machine Learning Algorithms

• Published in: Frontiers in genetics Vol. 13; p. 897696
• Main Authors: Aasim, Muhammad, Katirci, Ramazan, Baloch, Faheem Shehzad, Mustafa, Zemran, Bakhsh, Allah, Nadeem, Muhammad Azhar, Ali, Seyid Amjad, Hatipoğlu, Rüştü, Çiftçi, Vahdettin, Habyarimana, Ephrem, Karaköy, Tolga, Chung, Yong Suk
• Format: Journal Article
• Language: English
• Published: Frontiers Media S.A 24-08-2022
• Subjects: artificial neural network; coefficient of determination; Genetics; in vitro regeneration; machine learning algorithms; mean squared error; plumular apices
• ISSN: 1664-8021; 1664-8021
• DOI: 10.3389/fgene.2022.897696

Common bean is considered a recalcitrant crop for
in vitro
regeneration and needs a repeatable and efficient
in vitro
regeneration protocol for its improvement through biotechnological approaches. In this study, the establishment of efficient and reproducible
in vitro
regeneration followed by predicting and optimizing through machine learning (ML) models, such as artificial neural network algorithms, was performed. Mature embryos of common bean were pretreated with 5, 10, and 20 mg/L benzylaminopurine (BAP) for 20 days followed by isolation of plumular apice for
in vitro
regeneration and cultured on a post-treatment medium containing 0.25, 0.50, 1.0, and 1.50 mg/L BAP for 8 weeks. Plumular apice explants pretreated with 20 mg/L BAP exerted a negative impact and resulted in minimum shoot regeneration frequency and shoot count, but produced longer shoots. All output variables (shoot regeneration frequency, shoot counts, and shoot length) increased significantly with the enhancement of BAP concentration in the post-treatment medium. Interaction of the pretreatment × post-treatment medium revealed the need for a specific combination for inducing a high shoot regeneration frequency. Higher shoot count and shoot length were achieved from the interaction of 5 mg/L BAP × 1.00 mg/L BAP followed by 10 mg/L BAP × 1.50 mg/L BAP and 20 mg/L BAP × 1.50 mg/L BAP. The evaluation of data through ML models revealed that
R
2
values ranged from 0.32 to 0.58 (regeneration), 0.01 to 0.22 (shoot counts), and 0.18 to 0.48 (shoot length). On the other hand, the mean squared error values ranged from 0.0596 to 0.0965 for shoot regeneration, 0.0327 to 0.0412 for shoot count, and 0.0258 to 0.0404 for shoot length from all ML models. Among the utilized models, the multilayer perceptron model provided a better prediction and optimization for all output variables, compared to other models. The achieved results can be employed for the prediction and optimization of plant tissue culture protocols used for biotechnological approaches in a breeding program of common beans.