Genomics Era for Plants and Crop Species – Advances Made and Needed Tasks Ahead

Abstract

Historically, unintentional plant selection and subsequent crop domestication, coupled with the need and desire to get more food and feed products, have resulted in the continuous development of plant breeding and genetics efforts. The progress made toward this goal elucidated plant genome compositions and led to decoding the full DNA sequences of plant genomes controlling the entire plant life. Plant genomics aims to develop highthroughput genome-wide-scale technologies, tools, and methodologies to elucidate the basics of genetic traits/characteristics, genetic diversities, and by-product production; to understand the phenotypic development throughout plant ontogenesis with genetic by environmental interactions; to map important loci in the genome; and to accelerate crop improvement. Plant genomics research efforts have continuously increased in the past 30 years due to the availability of cost-effective, high-throughput DNA sequencing platforms that resulted in fully sequenced 100 plant genomes with broad implications for every aspect of plant biology research and application. These technological advances, however, also have generated many unexpected challenges and grand tasks ahead. In this introductory chapter, I aimed briefly to summarize some advances made in plant genomics studies in the past three decades, plant genome sequencing efforts, current state-of-the-art technological developments of genomics era, and some of current grand challenges and needed tasks ahead in the genomics and post-genomics era. I also highlighted the related book chapters contributed by different authors in this book.

Recent Developments in Fiber Genomics of Tetraploid Cotton Species

“…Similar to the plastid genome analysis, the phylogenetic analysis of mt genomes revealed Brassicales were closely related to Malvales in the rosids clades [1]. Sequencing and characterization of both nuclear and cytoplasmic genomes of the Gossypium species will enrich the knowledge used to identify fiber-related genes for the improvement of cotton fiber quality trait using modern genetic engineering tools [58,59].…”

Genome Editing in Plants: An Overview of Tools and Applications

“…After first successful exploitation in mammalian systems, oligonucleotide-directed mutagenesis (ODM) has become another novel gene editing tool for plants [7,64]. ODM, a tool for targeted mutagenesis, uses a specific 20-to 100-base long oligonucleotide, the sequence of which is identical to the target sequence in the genome except that it contains a single base pair change (intended mutation to be inserted in the genome) towards achieving site-directed editing of gene/sequence of interest (Table 1) [65].…”

“…This produces the desired targeted single nucleotide or base editing in the plant genome that confers novel function or trait while the plant cell degrades the repair template oligonucleotide. Using tissue culture methods, cells with edited sequences are subsequently regenerated and genome edited novel varieties with improved traits/characteristics are developed through traditional breeding (Table 2) [7,64,65].…”

Introductory Chapter: Introduction to Cotton Research Highlights

“…This has not only accelerated the development of superior cotton cultivars with reduced cost and time, but it also helped in widening the "conventionally-narrow" genetic base of novel cultivars via introducing 'yet-unexploited' genetic diversities from cotton germplasm resources [8,14,[20][21][22][23]28]. Further, molecular marker technology has helped to establish and genetically differentiate 13 homeologous chromosome pairs accelerating cotton cytogenetics and genetics studies [29].…”

“…This opened a new paradigm for the development of fine-tuned innovations for cotton breeding and farming with the integration of knowledge gained from "omics" sciences, system biology, and chemical genomics as well as from the translation of the concept of "personalized agriculture" [28], which should increase cotton production worldwide [14].…”