Genome-Wide Analysis of Somatic Embryogenesis-Related Transcription Factors in Cultivated Strawberry (Fragaria × ananassa) and Evolutionary Relationships among Rosaceae Species

Adrián Garrido-Bigotes,Rodrigo Hasbún,Herman Silva

doi:10.3390/agronomy11020356

Adrián Garrido-Bigotes, Rodrigo Hasbún + Show 1 more

Open Access

https://doi.org/10.3390/agronomy11020356

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Abstract

Somatic embryogenesis is a plant regeneration method commonly used in tissue culture. Its molecular mechanisms are well-known in model plants such as Arabidopsis thaliana L. LEAFY COTYLEDON1 (LEC1), LEAFY COTYLEDON2 (LEC2), FUSCA3 (FUS3), ABSCISIC ACID INSENSITIVE3 (ABI3), and BABYBOOM (BBM) genes are considered master regulators in the induction, growth, and maturation of somatic embryos. However, the study of these transcription factors in fruit crops with high agronomic and economic value such as cultivated strawberry (Fragaria × ananassa Duch.) and other Rosaceae species is scarce. The purpose of this study was the in silico characterization of LEC1, ABI3, FUS3, LEC2, and BBM(LAFL-B) genes from F. × ananassa genome and the study of the evolutionary relationships within the Rosaceae family. Synteny analyses and molecular evolutionary rates were performed to analyze the evolution of each transcription factor within the Rosaceae family. Synteny was conserved between F. × ananassa and other Rosaceae genomes, and paralogous genes were selected through negative selection. Additionally, the exon–intron organization and multiple alignments showed that gene structure and DNA-binding domains were conserved in F. × ananassa transcription factors. Finally, phylogenetic trees showed close evolutionary relationships between F. × ananassa and its orthologous proteins in the Rosoideae subfamily. Overall, this research revealed novel insights in the LAFL-B network in F. × ananassa and other species of the Rosaceae family. These results provide useful in silico information and new resources for the establishment of more efficient propagation systems or the study of ploidy effects on somatic embryogenesis.

Highlights

Plants exhibit high plasticity during their developmental stages, and it is a survival strategy to overcome environmental constraints [1]
These results indicate that most positions for LEAFY COTYLEDON1 (LEC1), L1L, LEAFY COTYLEDON2 (LEC2), FUS3, ABI3, and BABY BOOM (BBM) genes are conserved between F. × ananassa and other Rosaceae family genomes
In the case of FaL1L2, syntenic relationships were not detected with any species. These results indicate that most positions for LEC1,9Lo1f L21, LEC2, FUS3, ABI3, and BBM genes are conserved between F. × ananassa and other Rosaceae family genomes

Summary

Introduction

Plants exhibit high plasticity during their developmental stages, and it is a survival strategy to overcome environmental constraints [1]. Somatic embryogenesis (SE) is an alternative regeneration process, for which a new individual is generated from a vegetative cell [3,4], occurring naturally in some Kalanchoe species [5]. It can be manipulated by in vitro tissue culture under appropriate stress signals such as plant growth regulators and wounding, as well as other mechanisms [5,6], offering multiple possibilities to investigate the bases and potential applications of SE in economically important crops. Others have only reported on the developmental and physiological characteristics [14,15,16]

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