Preface

**Section 3 Regulation of Plant Genes and Genomes by Small RNAs 101**

**Understanding Gene Downregulation Mechanism**

Chapter 8 **Genomic Approaches to Developing Molecular Markers Linked to Grey Leaf Spot Resistance Loci in Ryegrasses 145**

> Abdul Qayyum Rao, Salah ud Din, Sidra Akhtar, Muhammad Bilal Sarwar, Mukhtar Ahmed, Bushra Rashid, Muhammad Azmat Ullah Khan, Uzma Qaisar, Ahmad Ali Shahid, Idrees Ahmad Nasir and

Chapter 9 **Advances in Plant Tolerance to Abiotic Stresses 167**

Chapter 10 **Advances in Plant Tolerance to Biotic Stresses 229** Geoffrey Onaga and Kerstin Wydra

Geoffrey Onaga and Kerstin Wydra

Chapter 11 **Genomics of Salinity Tolerance in Plants 273**

Jorge Ricaño-Rodríguez, Jacel Adame-García, Silvia Portilla-Vázquez, José M. Ramos-Prado and Enrique Hipólito-Romero

Christopher A. Cedillo-Jiménez, Marcelo Hernández–Salazar, Tania Escobar-Feregrino, Juan Caballero-Pérez, Mario Arteaga-Vázquez, Alfredo Cruz-Ramírez, Irineo Torres-Pacheco, Ramón Guevara-

Chapter 6 **MicroRNAs Sequencing for Understanding the Genetic**

**Regulation of Plant Genomes 103**

González and Andrés Cruz-Hernández

Chapter 7 **The Extraordinary Nature of RNA Interference in**

**Section 4 Genomics of Plant Stress Response 143**

**in Plants 119**

**VI** Contents

Wataru Takahashi

Tayyab Husnain

Plants are the backbones of food chain for all living matters on Earth, which supply the hu‐ mankind with food, feed products, and clothing and housing materials; balance agrobiose‐ nosis and earth ecology; provide a medicine and cure for many diseases; and produce energy and biofuels. Plants are models to investigate and understand the life in our planet. All of these have been the main driving factors to care about plants, domesticate wild spe‐ cies with important properties, select and breed the best genotypes, and grow them for needs of humanity. This has consequently shaped plant sciences, genetics, and breeding. Furthermore, the advances made in understanding the genetics of phenotypic variations, equipped with optimized, targeted, and efficient selection, phenotyping, and statistical methods as well as agrotechnologies in past centuries, have revolutionized plant sciences and crop breeding.

The "Green Revolution" has significantly increased agricultural production for the past cen‐ turies because of success in conventional breeding and genetics and agro/chemical technolo‐ gies. Even further, plant researchers have attempted to decipher the molecular basis of genetic diversities by cloning and sequencing the genes conditioning of the trait of interest and utilizing them in plant breeding as tools in vertical (i.e., hybridization) or even via revo‐ lutionizing horizontal (i.e., genetic engineering) transfers. There is no doubt that these ef‐ forts have significantly contributed to increase agricultural productions worldwide and enriched the diet of human well-beings. However, humanity still suffers with food deficien‐ cy that could be even more evident with a global human population increase, which is pro‐ jected to reach ~9 billion by 2050. Moreover, current global climate changes with increased biosecurity threats could generate even worsened scenarios of more complex challenges for sustained agriculture and food security in the era of the societal globalization and advances of technologies in the twenty-first century and beyond.

There are needs to find better ways and solutions to mitigate the future challenges, which require enrichment and change of methodologies, technologies, and scientific views of the past. Here comes *Plant genomics*— a newly evolved discipline of plant sciences — targeting to decode, characterize, and study the genetic compositions, structures, organizations, func‐ tions, and interactions/networks of all plant genes in a genome-wide scale. Being evolved from plant molecular genetics, biology, and biotechnology, *Plant genomics* represent the key sub-divisions of structural, functional, comparative, evolutionary, physiological, and geneti‐ cal genomics. Its development and advances, however, are tightly interconnected with plant science sub-disciplines such as proteomics, metabolomics, epigenomics, phenomics, metage‐ nomics, transgenomics, breeding-assisted genomics, bioinformatics, and system biology as well as modern instrumentation and robotics sciences.

Aiming to develop genome-wide scaled high-throughput technologies and methodologies for plant science research and application, *Plant genomics* has significantly advanced over the past three decades in the land of inexpensive, high-throughput, and automated new-genera‐ tion DNA sequencing methodologies and platforms. This resulted in decoding of more than 100 plant genomes of 64 megabases to 23 gigabases in lengths within past 10 years. These advances made have broad implications for every aspects of plant biology while generating many unexpected challenges and grand tasks ahead. The grand tasks ahead require more extended collaborations and integrated approaches as well as better computing and data storage/systematization capacity, ways to handle data with improved or novel analytical/ bioinformatics tools, extended training and education of well-qualified new-generation re‐ searchers, and larger investments and funding.

This book, *Plant genomics*, aiming to provide updated discussions on current advances, chal‐ lenges, and future perspectives of plant genomics research and application, has compiled 10 chapters from the plant researchers worldwide, including results of the first draft of full ge‐ nome sequencing and assembly of a leaf chicory plant. Chapters also have reviewed and discussed strategies for plant genome sequencing, assembly, and its challenges, new-genera‐ tion sequencing platforms for comparative genomics of cereal crops and non-model cactus plants, and the characterization of small RNA/micro-RNA world of plant genomes. Several chapters have covered the advances toward plant resistance genomics and molecular breed‐ ing of bacterial diseases in ryegrasses, RNA interference technology in plants, and some as‐ pects of salinity tolerance genomics in agricultural crops. I trust that these chapter materials will be additional reading sources for scientist, students, and readers interested with the plant science development.

I greatly acknowledge the efforts of all authors of the book chapters for their timely re‐ sponse to our book project invitation, chapter proposal development, and writing and revi‐ sing full chapters per my editorial requests. I also thank the InTech book department for giving me the opportunity to work on this book project, and Ms. Sandra Bakic and Ms. Iva Simcic, InTech's Publishing Process Managers, for their overwhelming efforts with publish‐ ing of this book.

**Ibrokhim Y. Abdurakhmonov**

Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan **Introduction to Plant Genomics**

Aiming to develop genome-wide scaled high-throughput technologies and methodologies for plant science research and application, *Plant genomics* has significantly advanced over the past three decades in the land of inexpensive, high-throughput, and automated new-genera‐ tion DNA sequencing methodologies and platforms. This resulted in decoding of more than 100 plant genomes of 64 megabases to 23 gigabases in lengths within past 10 years. These advances made have broad implications for every aspects of plant biology while generating many unexpected challenges and grand tasks ahead. The grand tasks ahead require more extended collaborations and integrated approaches as well as better computing and data storage/systematization capacity, ways to handle data with improved or novel analytical/ bioinformatics tools, extended training and education of well-qualified new-generation re‐

This book, *Plant genomics*, aiming to provide updated discussions on current advances, chal‐ lenges, and future perspectives of plant genomics research and application, has compiled 10 chapters from the plant researchers worldwide, including results of the first draft of full ge‐ nome sequencing and assembly of a leaf chicory plant. Chapters also have reviewed and discussed strategies for plant genome sequencing, assembly, and its challenges, new-genera‐ tion sequencing platforms for comparative genomics of cereal crops and non-model cactus plants, and the characterization of small RNA/micro-RNA world of plant genomes. Several chapters have covered the advances toward plant resistance genomics and molecular breed‐ ing of bacterial diseases in ryegrasses, RNA interference technology in plants, and some as‐ pects of salinity tolerance genomics in agricultural crops. I trust that these chapter materials will be additional reading sources for scientist, students, and readers interested with the

I greatly acknowledge the efforts of all authors of the book chapters for their timely re‐ sponse to our book project invitation, chapter proposal development, and writing and revi‐ sing full chapters per my editorial requests. I also thank the InTech book department for giving me the opportunity to work on this book project, and Ms. Sandra Bakic and Ms. Iva Simcic, InTech's Publishing Process Managers, for their overwhelming efforts with publish‐

**Ibrokhim Y. Abdurakhmonov**

Tashkent, Uzbekistan

Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan,

searchers, and larger investments and funding.

plant science development.

ing of this book.

VIII Preface
