Preface

Model plants, among all other plant species, are very important for genetic studies to enhance understanding of plant life on our planet. Model plant species help researchers to study the genetics of key biological phenomena, processes, and characteristics. Plant models, as whole plants are grown from seed as well as tissue or cell culture, are used to experimentally investigate the consequences of natural mutations, adaptation of plants to harsh environments or changing climate, plant ecology and evolution, and polyploidization. Model organisms are particularly important when targeted plant species are difficult to study or when there is a lack of data. Because of the simplicity, suitability, and availability of research material for randomized and repeated experiments as well as the speed and precision of laboratory experiments, model plants are the key objects for plant science investigations.

Model plants with emerging new candidate species are widely used to simulate various morphological, physiological, and molecular processes in plants, allowing a more accurate understanding of the mechanisms underlying plant life. Furthermore, knowledge gained in studying model plants for key characteristics of interest can be generally translated to other plant species with the basic understanding that many key cellular and molecular processes are conserved and regulated by 'blueprint' genes inherited from a common ancestor.

*Model Organisms in Plant Genetics* discusses plant models for genetics and breeding research. Chapters describe characteristics of model plants such as *Arabidopsis*, moss, soybean, maize, and cotton, highlighting their advantages and limitations as well as their importance in studies of plant development, plant genome polyploidization, adaptive selection, evolution, and domestication, as well as in the improvement of industrially important traits. This book is a useful resource for students, life science researchers, and other interested readers.

I am thankful to the staff at IntechOpen, especially the Author Service Manager, Ms. Nera Butigan for her help throughout the editing process. I also thank all the chapter authors for their excellent contributions.

> **Ibrokhim Y. Abdurakhmonov** Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan

Section 1 Introduction

#### **Chapter 1**

## Introductory Chapter: Model Plants for Discovering the Key Biological Processes in Plant Research

*Ibrokhim Y. Abdurakhmonov*

#### **1. Introduction**

Model plants for genetic studies are very important among all other plant species living on our planet. Models, as the whole plant is grown from seed as well as tissue or cellular culture, help researchers to study the genetics of key biological phenomena, processes, and characteristics that are useful for understanding the consequences of natural mutations, adaptation of plants to the harsh environment or changing climate, plant ecology and evolution as well as polyploidization. Model organisms are particularly important and required when targeted plant species are very difficult to be easily studied or a needed research material is unavailable to be efficiently analyzed and data is generated; therefore, because of model plant simplicity, suitability, availability of research material for randomized and repeated experiments as well as speed and precision of laboratory experiments, model plants are "stand-in" [1] object for plant science investigations. Moreover, discovered biological and genetic functions of model plant species can be translated to the related plant taxa under the investigation due to orthologous and paralogous gene function and molecular cellular processes that can be extrapolated, explained, and varied by close or distant phylogenetic relationships.

#### **2. Current status**

One of the first model organisms for plant sciences was *Arabidopsis thaliana*, which was recognized as the universal model plant especially for all flowering eudicot plants due to short life cycle, ease of cultivation, relatively small genome size, and having a fully annotated genome sequence [1]. For the first time, studies on Arabidopsis as a model plant have begun to be carried out in the late 1970s. Currently, a search using the **"**plant models" keyword in the PubMed database has revealed more than 300 research publications on various model plants, including *A. thaliana* (**Figure 1**). A sharp increase in the number of publications on this topic has been observed since 2005, reaching a maximum in the last 5 years.

Since 2000, molecular genetic features of such biological processes as plant development, plant evolution, plant response to biotic and abiotic stresses, intracellular signaling, including hormonal signaling, were revealed using *A. thaliana* as a model plant [1]. In addition, *A. thaliana* is used as a model for studying the epigenetic regulation of metabolism [3]. In these studies, it was possible to establish the role

#### **Figure 1.**

*Dynamics of "plant models" keyword-retrieved scientific publications. Source: PubMed [2].*

of chromatin modification in the regulation of metabolism, as well as to identify metabolic pathways involving reactive oxygen species and nitric oxide (NO) in the modulation of chromatin activity under stress conditions [3].

However, the using of *A. thaliana* as a model plant is limited to Monocots and nonflowering plants due to strong differences in morphology, physiology, and genetics. Therefore, *A. thaliana* cannot be directly used to model studies on symbiotic interactions with soil microorganisms [1, 4]. All this prompted researchers to search for other model plants. So, at present, *Brachypodium distachyon* is used as a model for studying Monocots, mosses - *Physcomitrella patens*, legumes - *Medicago truncatula*, trees - *Populus trichocarpa* [1]. In addition, *Setaria viridis* is used to study C4 photosynthesis, the evolution of terrestrial plants – *Marchantia polymorpha* [1].

Additionally, currently, attention is being increasingly focused on the study of genomic multi-tissue metabolic models that allow to identify the metabolic interactions between tissues and organs [5]. Such models are developed for *Arabidopsis*, barley, soybean, and *Setaria*. Moreover, Arabidopsis-based models for metabolic pathways studies allow predicting the metabolic phenotype under genetic modifications, the course of metabolic reaction of plant tissues under changing environmental conditions [5]. Moreover, soybean-based multi-tissue models are used to study nutrient mobilization during seed germination. In addition, the model of using mesophyll and bundle sheath cells in *S. viridis* allows revealing the metabolic features of C4 photosynthesis [5].

Another interesting area of application of plant models is the study of allelopathy at the level of interaction both between individual plants and between organisms belonging to different kingdoms (plants, insects, fungi, and bacteria) [6]. Allelopathic plants (i.e., producing chemicals that inhibit the growth and development of other organisms) include wheat (*Triticum* sp.), rye (*Secale cereale*), corn (*Zea mays*), barley (*Hordeum vulgare*), rice (*Oryza sativa*), and sorghum (*Sorghum bicolor*). Of these plants, maize (Z. mays) is most often used as a model for studying allelopathy [6]. The use of allelopathic models made it possible to reveal the mechanism of stability and synergy of allelochemical substances, the dependence of their effect on biotic (soil bacteria) and abiotic (temperature, soil moisture, etc.) environmental factors.

Also, to study the synergistic or antagonistic interaction between organisms belonging to different kingdoms (plants, soil fungi, and bacteria), a system consisting of soybeans, rhizobacteria, and soil fungi are used as a model [7]. Such multicomponent modeling made it possible to reveal the mechanisms of interaction

*Introductory Chapter: Model Plants for Discovering the Key Biological Processes in Plant Research DOI: http://dx.doi.org/10.5772/intechopen.103759*

between these organisms, including changes in the level of gene expression [7]. These results later can be used in agriculture to reduce the level of invasion by weeds and yield increase potential [6, 7].

Practical application in agriculture has received data on the features of the plants architecture and growth obtained using the so-called agent-based modeling [8–10]. These data made it possible to obtain plants with desired architecture and height and were used for such plants as kiwi (*Actinidia deliciosa*), apple (*Malus domestica*), avocado (*Persea americana* 'Hass'), peach (*Prunus persica*), grape (*Vitis vinifera*) [8–10]. *In silico* programs and platforms specially developed are used to process and optimize such numerical simulation models [11, 12].

#### **3. Chapter topics**

In this *Model Organisms in Plant Genetics* book, together with a group of international plant researchers, we successfully compiled the current status and view on the advance of plant models for genetics and breeding research. Chapter topics, presented herein, described advances on plant models characteristics of the mostly used plant Arabidopsis with its limitations and need for other types of model plants, views on how mosses are used for plant development studies. Several chapters describe how crops such as soybean, maize, and cotton can be a model for studying a group of industrially important traits such as oil production and plant genome polyploidization, adaptive selection, evolution, and domestication as well as crop improvement.

#### **4. Conclusions**

Thus, the last-five years' literature review, highlighted above, and new advances presented in chapters of this book, collectively highlight the importance and future key role of plant models for the development of plant sciences research, leading to novel discoveries. Model plants with emerging new candidate species will be widely used to simulate various morphological, physiological, and molecular processes in plants, allowing a more accurate understanding of the mechanisms explaining the plant ontogenesis.

#### **Author details**

Ibrokhim Y. Abdurakhmonov Center of Genomics and Bioinformatics, Academy of Science of Republic of Uzbekistan, Tashkent, Uzbekistan

\*Address all correspondence to: i.y.abdurakhmonov@gmail.com

© 2022 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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[2] PubMed database [Internet]. 2021. Available from: http://www.ncbi.nlm. nih.gov/pubmed (Accessed: January 28, 2022).

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Section 2
