The Sesame Genome

This book is the first comprehensive compilation of deliberations on whole genome sequencing of sesame including genome assembly, annotation, structure and synteny analysis, and sequencing of its chloroplast genome and also its wild species. It presents narratives on classical genetics and breeding, tissue culture and genetic transformation, molecular mapping and breeding. Other chapters describe the beneficial components in sesame protein and oil, botanical depictions and cytological features. Prospects of designed breeding in the post-genomics era including gene discovery have also been enumerated. Altogether, the book contains 19 chapters authored by globally reputed experts on the relevant field in this crop. This book is useful to the students, teachers, and scientists in the academia and relevant private companies interested in classical and molecular genetics, biotechnology, breeding, biochemistry, traditional and molecular breeding, and structural and evolutionary genomics. The work is also useful to seed and oil industries.

This book is the first comprehensive compilation of deliberations on whole genome sequencing of sesame including genome assembly, annotation, structure and synteny analysis, and sequencing of its chloroplast genome and also its wild species. It presents narratives on classical genetics and breeding, tissue culture and genetic transformation, molecular mapping and breeding. Other chapters describe the beneficial components in sesame protein and oil, botanical depictions and cytological features. Prospects of designed breeding in the post-genomics era including gene discovery have also been enumerated. Altogether, the book contains 19 chapters authored by globally reputed experts on the relevant field in this crop. This book is useful to the students, teachers, and scientists in the academia and relevant private companies interested in classical and molecular genetics, biotechnology, breeding, biochemistry, traditional and molecular breeding, and structural and evolutionary genomics. The work is also useful to seed and oil industries.

The development of new plant varieties is a long and tedious process involving the generation of large seedling populations for the selection of the best individuals. While the ability of breeders to generate large populations is almost unlimited, the selection of these seedlings is the main factor limiting the generation of new cultivars. Molecular studies for the development of marker-assisted selection (MAS) strategies are particularly useful when the evaluation of the character is expensive, time-consuming, or with long juvenile periods. The papers published in the Special Issue “Plant Genetics and Molecular Breeding” report highly novel results and testable new models for the integrative analysis of genetic (phenotyping and transmission of agronomic characters), physiology (flowering, ripening, organ development), genomic (DNA regions responsible for the different agronomic characters), transcriptomic (gene expression analysis of the characters), proteomic (proteins and enzymes involved in the expression of the characters), metabolomic (secondary metabolites), and epigenetic (DNA methylation and histone modifications) approaches for the development of new MAS strategies. These molecular approaches together with an increasingly accurate phenotyping will facilitate the breeding of new climate-resilient varieties resistant to abiotic and biotic stress, with suitable productivity and quality, to extend the adaptation and viability of the current varieties.

The crop plants cater not only to our basic F5 (food, feed, fiber, fuel, and furniture) needs but also provide a number of nutraceuticals with potential nutritional, safety and therapeutic properties. Many crop plants provide an array of minerals, vitamins, and antioxidant-rich bioactive phytochemicals. Increasing incidences of chronic diseases such as cancer, diabetes and HIV, and malnutrition necessitate global attention to health and nutrition security with equal emphasis to food security. This compendium compiles results of researches on biochemical, physiological and genetic mechanisms underlying biosynthesis of the health and nutrition related nutraceuticals. It also explores the precise breeding strategies for augmentation of their content and amelioration of their quality in crop plants under all commodity categories including cereals and millets, oilseeds, pulses, fruits and nuts, and vegetables. The compendium comprise 5 sections dedicated to these 5 commodity groups and presents enumeration on the concepts, strategies, tools and techniques of nutraceutomics. These sections include 50 chapters devoted to even number of major crop plants. These chapters present deliberations on the biochemistry and medicinal properties of the nutracuticals contained; genetic variation in their contents; classical genetics and breeding for their quantitative and qualitative improvement; tissue culture and genetic engineering for augmentation of productivity and quality; and sources of genes underlying their biosynthesis. They also include comprehensive enumeration on genetic mapping of the genes and QTLs controlling the contents and profile of the nutraceuticals and molecular breeding for their further improvement through marker assisted selection and backcross breeding tools. Prospects of post-genomic precise breeding strategies including genome-wide association mapping, genomic selection, allele mining, and genome editing are also discussed. This compendium fills the gap in academia, and research and development wings of the private sector industries interested in an array of subjects including genetics, genomics, tissue culture, genetic engineering, molecular breeding, genomics-assisted breeding, bioinformatics, biochemistry, physiology, pathology, entomology, pharmacognosy, IPR, etc., and will also facilitate understanding of the policy making agencies and people in the socio-economic domain and research sponsoring agencies.

When one is privileged to participate long enough in a professional capacity, certain trends may be observed in the dynamics of how challenges are met or how problems are solved. Agricultural research is no exception in view of how the plant sciences have moved forward in the past 30 years. For example, the once grand but now nearly forgotten art of whole plant physiology has given way almost completely to the more sophisticated realm of molecular biology. What once was the American Society of Plant Physiologists’ is now the American Society of Plant Molecular Biology; a democratic decision to indemnify efforts to go beyond the limits of the classical science and actually begin to understand the underlying biological basis for genetic regulation of metabolic mechanisms in plants. Yet, as new technologies open windows of light on the inner workings of biological processes, one might reminisce with faint nostalgia on days long past when the artisans of plant physiology, biochemistry, analytical chemistry and other scientific disciplines ebbed and waned in prominence. No intentional reference is made here regarding Darwinism; the plant sciences always have been extremely competitive. Technology is pivotal. Those who develop and/or implement innovative concepts typically are regarded as leaders in their respective fields. Each positive incremental step helps bring recognition and the impetus to push a scientific discipline forward with timely approaches to address relevant opportunities.

Biotic stresses cause yield loss of 31-42% in crops in addition to 6-20% during post-harvest stage. Understanding interaction of crop plants to the biotic stresses caused by insects, bacteria, fungi, viruses, and oomycetes, etc. is important to develop resistant crop varieties. Knowledge on the advanced genetic and genomic crop improvement strategies including molecular breeding, transgenics, genomic-assisted breeding and the recently emerging genome editing for developing resistant varieties in oilseed crops is imperative for addressing FPNEE (food, health, nutrition. energy and environment) security. Whole genome sequencing of these crops followed by genotyping-by-sequencing have facilitated precise information about the genes conferring resistance useful for gene discovery, allele mining and shuttle breeding which in turn opened up the scope for 'designing' crop genomes with resistance to biotic stresses. The eight chapters each dedicated to an oilseed crop in this volume elucidate on different types of biotic stress agents and their effects on and interaction with the crop plants; enumerate on the available genetic diversity with regard to biotic stress resistance among available cultivars; illuminate on the potential gene pools for utilization in interspecific gene transfer; present brief on the classical genetics of stress resistance and traditional breeding for transferring them to their cultivated counterparts; depict the success stories of genetic engineering for developing biotic stress resistant varieties; discuss on molecular mapping of genes and QTLs underlying biotic stress resistance and their marker-assisted introgression into elite varieties; enunciate on different emerging genomics-aided techniques including genomic selection, allele mining, gene discovery and gene pyramiding for developing resistant crop varieties with higher quantity and quality of yields; and also elaborate some case studies on genome editing focusing on specific genes for generating disease and insect resistant crops.

Sesame (Sesamum indicum L.) belongs to the Pedaliaceae family. It is an important oil seed crop which is cultivated in tropical and subtropical areas of Asia and Africa. China is the largest producer of sesame seed in the world while Turkey ranks seventh and produces 21036 tonnes of sesame seed in a year. Although sesame's edible seed and high quality seed oil are important for both humans and the economy, there is not enough information about the sesame genome in the literature. Our aim was to determine the diversity of 158 Turkish sesame accessions by using the AFLP marker system and to design a new set of sesame-specific SSR markers from genomic sequence of S. indicum. The Turkish sesame accessions were tested with five AFLP primer combinations, as a result, 148 polymorphic fragments were obtained. The maximum similarity was 57% for the accessions and a good level of diversity was present in the sesame germplasm. Secondly, a genomic library of sesame was constructed. A total of 1.094.317 reads were obtained and 702.371 of them were clustered to 140.669 reads containing 93.365 nucleotides. A total of 3101 primer pairs were developed from flanking regions of SSRs with primers for dinucleotide (36,4%), tetranucleotide (29,3%), trinucleotide (23,1%), pentanucleotide (7,1%), and hexanucleotide (4,2%) repeats. These primers are the first genomic-SSR markers developed for sesame cultivars. SSRs have good reproducibility, high genome coverage, co-dominant inheritance, good transferability to close species and are multiallelic. The designed genomic-SSRs should be very useful for sesame mapping and diversity studies.

This book highlights modern strategies and methods to improve oilseed crops in the era of climate change, presenting the latest advances in plant molecular breeding and genomics-driven breeding. Spectacular achievements in the fields of molecular breeding, transgenics and genomics in the last three decades have facilitated revolutionary changes in oilseed- crop-improvement strategies and techniques. Since the genome sequencing of rice, as the first crop plant, in 2002, the genomes of about one dozen oilseed crops have been sequenced and more are to follow. This has made it possible to decipher the exact nucleotide sequence and chromosomal positions of agroeconomic genes. Most importantly, comparative genomics and genotyping-by-sequencing have opened up new vistas for exploring available biodiversity, particularly of wild crop relatives, for identifying useful donor genes.

This book deliberates on the concept, strategies, tools, and techniques of allele mining in oilseed crops and its application potential in genome elucidation and improvement, including studying allele evolution, discovery of superior alleles, discerning new haplotypes, assessment of intra- and interspecific similarity, and studies of gene expression and gene prediction. Available gene pools in global germplasm collections, specifically consisting of wild allied species and local landraces for almost all major crops, have facilitated allele mining. The development of advanced genomic techniques, including PCR-based allele priming and Eco-TILLING-based allele mining, is now widely used for mining superior alleles. Allele's discovery has become more relevant now for employing molecular breeding to develop designed crop varieties matching consumer needs and with genome plasticity to adapt to climate change scenarios. All these concepts and strategies, along with precise success stories, are presented in the chapters dedicated to the major oilseed crops. 1. This is the first book on the novel strategy of allele mining in oilseed crops for precise breeding. 2. This book presents genomic strategies for mining superior alleles underlying agronomic traits from genomic resources. 3. This book depicts case studies of PCR-based allele priming and Eco-TILLING based allele mining. 4. This book elaborates on gene discovery and gene prediction in major oilseed crops. This book will be useful to students and faculties in various plant science disciplines, including genetics, genomics, molecular breeding, agronomy, and bioinformatics; scientists in seed industries; and policymakers and funding agencies interested in crop improvement.