The Amaranth Genome

This book describes the development of genetic resources in amaranths, with a major focus on genomics, reverse, and forward genetics tools and strategies that have been developed for crop improvement. Amaranth is an ancient crop native to the New World. Interest in amaranths is being renewed, due to their adaptability, stress tolerance, and nutritional value. There are about 65 species in the genus, including Amaranthus caudatus L., A. cruentus L., and A. hypochondriacus L., which are primarily grown as protein-rich grains or pseudocereals. The genus also includes major noxious weeds (e.g., A. palmeri). The amaranths are within the Caryophyllales order and thus many species (e.g., A. tricolor) produce red (betacyanin) or yellow (betaxanthin) betalain pigments, which are chemically distinct from the anthocyanins responsible for red pigmentation in other plants. A. hypochondriacus, which shows disomic inheritance (2n = 32; n= 466 Mb), has been sequenced and annotated with 23,059 protein-coding genes. Additional members of the genus are now also been sequenced including weedy amaranths, other grain amaranths, and their putative progenitors.

Amaranthus hypochondriacus is an emerging pseudo-cereal native to the New World which has garnered increased attention in recent years due to its nutritional quality, in particular its seed protein, and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleotetraploid that shows amphidiploid inheritance (2n=32), and has an estimated genome size of 466 Mb. Here we present a high-quality draft 377 Mb in 3,518 scaffolds with an N50 of 371 kb. Repetitive element analysis predicted that 48% common classified retrotransposon. A transcriptome, consisting of 66,370 contigs, was assembled from eight different tissue and abiotic stress libraries. Annotation of the genome identified 23,059 genes that were supported by our de novo transcriptome assembly, the RefBeet 1.1 gene index and the Uniprot_sprot database. To describe the genetic diversity within the grain amaranths (A. hypochondriacus. A. caudatus, and A. cruentus) and their putative progenitor (A. hybridus) we re-sequenced seven accessions in the genus Amaranthus (four A. hypochondriacus, and one of each A. caudatus, A. cruentus, and A. hybridus), which identified 7,184,636 and 1,760,433 interspecific and intraspecific single nucleotide polymorphisms, respectively. A phylogeny analysis of the re-sequenced accessions substantiated the classification of A. hybridus hypochondriacus using the BioNano optical mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano optical mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano optical genome maps nearly doubled the N50 of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and Beta vulgaris (sugar beet) and estimated, using Ks analysis, the age of the most recent polyploidization event in amaranth.

This book serves the larger community of plant researchers working on the taxonomy, species delimitation, phylogeny, and biogeography of pseudo-cereals, with a special emphasis on amaranths. It also provides extensive information on the nutritive value of underutilized pseudo-cereals, the goal being to broaden the vegetable list. Amaranthus is a cosmopolitan genus of annual or short-lived perennial plants. Most of the species are summer annual weeds and are commonly referred to as pigweed. Only a few are cultivated as vitamin-rich vegetables and ornamentals. The protein-rich seeds of a handful of species, known as grain amaranths, are consumed as pseudo-cereals. Amaranthusmanifests considerable morphological diversity among and even within certain species, and there is no general agreement on the taxonomy or number of species. Currently the genus Amaranthus is believed to include three recognized subgenera and 70 species. Amatanthus is considered to potentially offer an alternative crop in temperate and tropical climate. The classification of amaranths is ambiguous due to the lack of discrete and quantitative species-defining characteristics and the wide range of phenotypic plasticity, as well as introgression and hybridization involving weedy and crop species. It is a known fact that both vegetable and grain amaranths have evolved from their respective weed progenitors. There are more than 180 different weed species that are herbicide-resistant, and amaranths are considered to be leading members of the resistant biotypes. Amaranth species provide ample scope for investigating herbicide resistance mechanisms. Amaranths also show variability in terms of their mating behavior and germplasm, adaptability to different growing conditions, and wide range of variability in sexual systems, from monoecy to dioecy. A solid grasp of these parameters is essential to the future utilization of amaranths as super crops. There are quite a few amaranth research center and germplasm collections all over the world that maintain and evaluate working germplasms. To date, the genetic improvement of amaranths has primarily involved the application of conventional selection methods. But advances in genomics and biotechnology have dramatically enriched the potential to manipulate the amaranth genome, especially improving the amount and availability of nutrients. In conclusion, the book covers all aspects of amaranths, including their food value, significance as vegetables and pseudo-cereals, taxonomy, phylogeny, germplasm variability, breeding behavior and strategies, cultivation practices, and variability in terms of their sexual systems. It offers a valuable resource for all students, researchers and experts working in the field of plant taxonomy and diversity.

The grain amaranths (Amaranthus hypochondriacus L., A. cruentus L., and A. caudatus L.) are important pseudocereals native to the Americas that have received increased attention for their nutritional content, specifically their balance of amino acids. The objective of this project was to produce and characterize a set of highly informative, reproducible microsatellite markers for the grain amaranths. A total of 1457 clones were sequenced from three genomic libraries enriched for the microsatellite motifs AAC, AAT and AC. Of these, 353 (24%) contained unique microsatellites. An additional 29 microsatellite loci were identified among 728 BAC-end sequences of a newly developed amaranth BAC library. Flanking primers were designed for 319 of the microsatellite loci and all were screened on a panel of diverse amaranths, including grain and weedy Amaranthus species. A total of 179 (56%) microsatellites were polymorphic across accessions from the three grain amaranths. Among these polymorphic microsatellite loci, a total of 731 alleles were identified with average of four alleles per locus. Heterozygosity values ranged from 0.14 to 0.83 with a mean value of 0.62. Thirty-seven (21%) of the markers were polymorphic between the parents of a segregating population and were shown to be inherited in a normal Mendelian fashion based on chi-squared analysis, demonstrating the utility of these markers for linkage mapping of the amaranth genome. Phylogenetic analysis using the marker data showed A. hybridus accessions in two of the three major grain amaranth clades, suggesting the polyphyletic evolution of the three cultivated species from different A. hybridus ancestors. The microsatellite markers reported here will be useful for further evaluating the relationships among the grain amaranths and their relatives and are an ideal resource for use in marker-assisted breeding programs, germplasm analysis and varietal identification. The transferability of these markers to A. hybridus, A. powellii, and A. retroflexus as reported here suggests that the markers may be useful to other species with the genus Amaranthus, including economically important weeds, vegetable amaranths, and ornamentals.

The Helix was meant to be a revolution, but even the most pure of intentions can spawn terrible evil, and the revolution of information and innovation they hoped for may not be the one they get.

This book is devoted to amaranth, a plant to which 45 species are indigenous to the Mesoamerican region and 10 others originated in Africa, Asia, and Europe. Amaranth was the foundation of the extensive North and South American ancient civilizations and is still important in the agriculture of more recent Indian cultures. However, this plant nearly disappeared after the Spanish conquest. In view of the outstanding agronomic performance of the plant and the high nutritional value of the grain, it is now becoming an important crop in various regions of the world. Progress in the utilization of amaranth is directly related to scientific and technical information on its biological, physical, and chemical properties. Amaranth: Biology, Chemistry, and Technology begins with a chapter on the use of tissue culture, molecular biology, and genetic engineering techniques for crop improvement. The next few chapters deal with classical genetics, traditional plant breeding, and plant physiology. Following chapters review the properties of storage and leaf proteins, carbohydrates (especially starch), and seed oil. The potential of amaranth for new food products and popping is discussed, and commercialization and marketing of amaranth and its products are described. The book also emphasizes the outstanding nutritional properties of amaranth.

This report is the second in a series of three evaluating underexploited African plant resources that could help broaden and secure Africa's food supply. The volume describes the characteristics of 18 little-known indigenous African vegetables (including tubers and legumes) that have potential as food- and cash-crops but are typically overlooked by scientists and policymakers and in the world at large. The book assesses the potential of each vegetable to help overcome malnutrition, boost food security, foster rural development, and create sustainable landcare in Africa. Each species is described in a separate chapter, based on information gathered from and verified by a pool of experts throughout the world. Volume I describes African grains and Volume III African fruits.

Characterisation of the Amaranth Genetic Resources in the Czech Gene Bank.

Research on gene drive systems is rapidly advancing. Many proposed applications of gene drive research aim to solve environmental and public health challenges, including the reduction of poverty and the burden of vector-borne diseases, such as malaria and dengue, which disproportionately impact low and middle income countries. However, due to their intrinsic qualities of rapid spread and irreversibility, gene drive systems raise many questions with respect to their safety relative to public and environmental health. Because gene drive systems are designed to alter the environments we share in ways that will be hard to anticipate and impossible to completely roll back, questions about the ethics surrounding use of this research are complex and will require very careful exploration. Gene Drives on the Horizon outlines the state of knowledge relative to the science, ethics, public engagement, and risk assessment as they pertain to research directions of gene drive systems and governance of the research process. This report offers principles for responsible practices of gene drive research and related applications for use by investigators, their institutions, the research funders, and regulators.

The impact of global climate change on crop production has emerged as a major research priority during the past decade. Understanding abiotic stress factors such as temperature and drought tolerance and biotic stress tolerance traits such as insect pest and pathogen resistance in combination with high yield in plants is of paramount importance to counter climate change related adverse effects on the productivity of crops. In this multi-authored book, we present synthesis of information for developing strategies to combat plant stress. Our effort here is to present a judicious mixture of basic as well as applied research outlooks so as to interest workers in all areas of plant science. We trust that the information covered in this book would bridge the much-researched area of stress in plants with the much-needed information for evolving climate-ready crop cultivars to ensure food security in the future.