Genetic and Genomic Resources of Small Millets

Small millets are very promising agricultural entity to ensure global food security. They gained remarkable importance in agriculture due to their resilience to climatic changes and increasing demand for nutritious food and feed. The genetic variability in the core and mini-core germplasm of small millets was characterized for nutritional composition and capacity to tolerate abiotic stresses that can be infused in breeding programs. Other than the foxtail millet, availability of genomic information in small millets is far below the mark for use in marker-assisted breeding and other genetic improvement programs. The genome sequence of foxtail millet has recently triggered a plethora of post-genomic analysis and envisaged foxtail millet as a model organism for the C₄ grasses and bioenergy research. Recent developments in the next-generation sequencing technologies enabled us, with the simultaneous discovery of high-throughput markers and multiplexed genotyping of germplasm, to speedup marker-assisted breeding. In this context, an in-depth analysis of the wealth of diverse germplasm resources and future perspectives of integrating genomics in genome-wide marker-trait association and breeding in small millets is worthy.     

Genetic engineering of millets: current status and future prospects

This review summarizes progress on the genetic transformation of millets and discusses the future prospects for the development of improved varieties. Only a limited number of studies have been carried out on genetic improvement of millets despite their nutritional importance in supplying minerals, calories and protein. Most genetic transformation studies of millets have been restricted to pearl millet and bahiagrass and most studies have been limited to the assessment of reporter and marker gene expression. Biolistic-mediated gene delivery has been frequently used for the transformation of millets but Agrobacterium-mediated transformation is still lagging. Improved transformation of millets, allied to relevant gene targets which may offer, for example, improved nutritional quality, resistance to abiotic and biotic stresses, and resistance to fungal infection will play important roles in millet improvement.     

Improvement of small seed for big nutritional feed

Exploding global population, rapid urbanization, salinization of soils, decreasing arable land availability, groundwater resources, and dynamic climatic conditions pose impending damage to our food security by reducing the grain quality and quantity. This issue is further compounded in arid and semi-arid regions due to the shortage of irrigation water and erratic rainfalls. Millets are gluten (a family of proteins)-free and cultivated all over the globe for human consumption, fuel, feed, and fodder. They provide nutritional security for the under- and malnourished. With the deployment of strategies like foliar spray, traditional/marker-assisted breeding, identification of candidate genes for the translocation of important minerals, and genome-editing technologies, it is now tenable to biofortify important millets. Since the bioavailability of iron and zinc has been proven in human trials, the challenge is to make such grains accessible. This review encompasses nutritional benefits, progress made, challenges being encountered, and prospects of enriching millet crops with essential minerals.     

Millet-inspired systems metabolic engineering of NUE in crops

The use of nitrogen (N) fertilizers in agriculture has a great ability to increase crop productivity. However, their excessive use has detrimental effects on the environment. Therefore, it is necessary to develop crop varieties with improved nitrogen use efficiency (NUE) that require less N but have substantial yields. Orphan crops such as millets are cultivated in limited regions and are well adapted to lower input conditions. Therefore, they serve as a rich source of beneficial traits that can be transferred into major crops to improve their NUE. This review highlights the tremendous potential of systems biology to unravel the enzymes and pathways involved in the N metabolism of millets, which can open new possibilities to generate transgenic crops with improved NUE.     

Food consumption trends and drivers

A picture of food consumption (availability) trends and projections to 2050, both globally and for different regions of the world, along with the drivers largely responsible for these observed consumption trends are the subject of this review. Throughout the world, major shifts in dietary patterns are occurring, even in the consumption of basic staples towards more diversified diets. Accompanying these changes in food consumption at a global and regional level have been considerable health consequences. Populations in those countries undergoing rapid transition are experiencing nutritional transition. The diverse nature of this transition may be the result of differences in socio-demographic factors and other consumer characteristics. Among other factors including urbanization and food industry marketing, the policies of trade liberalization over the past two decades have implications for health by virtue of being a factor in facilitating the ‘nutrition transition’ that is associated with rising rates of obesity and chronic diseases such as cardiovascular disease and cancer. Future food policies must consider both agricultural and health sectors, thereby enabling the development of coherent and sustainable policies that will ultimately benefit agriculture, human health and the environment.     

Salt Stress Threshold in Millets: Perspective on Cultivation on Marginal Lands for Biomass

Millets hold an immense assurance for food safety and nourishment amid ever-rising agricultural expenses and climate alterations. They are healthful, have supplementary wellbeing profit and need remarkably fewer effort overheads for crop growing. These characters draw attention to millets as a plant of preference for the humankind in the course of emergent alarm about environmental changes. Millets have the prospect to provide biomass and thus bioenergy, reduced carbon emission, carbon footprint and sustainable modern agriculture. As the rate of expansion in budding countries is increasing day by day, the scarcity of energy is a big panic and there is a mounting turn in the direction and rehearsal of waste and biomass as an energy source. Globally, at least 20% of total irrigated land has been injured by salt and 1.5 million hectares is taken away of cultivation every year. Thus, in future, we will have a requirement of efficient crops and utilisation of marginal lands for agriculture. Millet is an answer to the efficient crop. Plants are subjected to various environmental pressures (high/low temperature, heavy metal, salinity, pesticides, etc.) as well as biotic stresses (virus, bacteria, fungi, etc.) and millets are not an exception to it. Millets are categorised as glycophytes and can tolerate average salt threshold of about 6 (EC_e) (dS/m) with some variation from specie to specie. Increase in the salt concentrations can lead to retarded growth and development, thus need for mitigants arise to reduce such stresses. Some mitigants to overcome the stress levels include proline, polyamine and betaines, Na₂SeO₃, H₂S, KNO₃, Mg(NO₃)₂, etc.

     

Microbial and genetically engineered oils as replacements for fish oil in aquaculture feeds

As the global population grows more of our fish and seafood are being farmed. Fish are the main dietary source of the omega-3 (n-3) long-chain polyunsaturated fatty acids (LC-PUFA), eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids, but these cannot be produced in sufficient quantities as are now required for human health. Farmed fish have traditionally been fed a diet consisting of fishmeal and fish oil, rich in n-3 LC-PUFA. However, the increase in global aquaculture production has resulted in these finite and limited marine ingredients being replaced with sustainable alternatives of terrestrial origin that are devoid of n-3 LC-PUFA. Consequently, the nutritional value of the final product has been partially compromised with EPA and DHA levels both falling. Recent calls from the salmon industry for new sources of n-3 LC-PUFA have received significant commercial interest. Thus, this review explores the technologies being applied to produce de novo n-3 LC-PUFA sources, namely microalgae and genetically engineered oilseed crops, and how they may be used in aquafeeds to ensure that farmed fish remain a healthy component of the human diet.     

Diversifying crops for food and nutrition security – a case of teff

There are more than 50000 known edible plants in the world, yet two‐thirds of global plant‐derived food is provided by only three major cereals – maize (Zea mays), wheat (Triticum aestivum) and rice (Oryza sativa). The dominance of this triad, now considered truly global food commodities, has led to a decline in the number of crop species contributing to global food supplies. Our dependence on only a few crop species limits our capability to deal with challenges posed by the adverse effects of climate change and the consequences of dietary imbalance. Emerging evidence suggests that climate change will cause shifts in crop production and yield loss due to more unpredictable and hostile weather patterns. One solution to this problem is through the wider use of underutilised (also called orphan or minor) crops to diversify agricultural systems and food sources. In addition to being highly nutritious, underutilised crops are resilient in natural and agricultural conditions, making them a suitable surrogate to the major crops. One such crop is teff [Eragrostis tef (Zucc.) Trotter], a warm‐season annual cereal with the tiniest grain in the world. Native to Ethiopia and often the sustenance for local small farmers, teff thrives in both moisture‐stressed and waterlogged soil conditions, making it a dependable staple within and beyond its current centre of origin. Today, teff is deemed a healthy wheat alternative in the West and is sought‐after by health aficionados and those with coeliac disease or gluten sensitivity. The blooming market for healthy food is breathing new life into this underutilised crop, which has received relatively limited attention from mainstream research perhaps due to its ‘orphan crop’ status. This review presents the past, present and future of an ancient grain with a potential beyond its size.     

Recent patents in plant biotechnology: impact on global health

Agricultural biotechnology offers a robust series of tools by which to address global concerns such as food security, crop protection, and fuel/energy requirements. A number of advances made recently in plant molecular biology also have resulted in applications which largely focus on improving global human health. This review describes some of the recent innovations in plant biotechnology that have come to the forefront over the past year. Included are novel techniques by which plants can be improved as platforms for biopharmaceutical protein production, a growing field also referred to as 'molecular pharming'. The metabolic engineering of plants to produce compounds which have additional nutritional benefits is also outlined. The review concludes with a discussion of the future impact that these innovations may have both on global health and on the development of our future intellectual property landscape.     

The impacts of Japanese food losses and food waste on global natural resources and greenhouse gas emissions

Japan depends heavily on imports for its food supply. Since 2000, the food self‐sufficiency ratio has remained approximately 40% on a caloric basis. Japanese food wastage (i.e., food losses and food waste) is estimated to have been 6.42 million tonnes (50 kg per capita of wastage) in 2012. These values indicate that food wastage leads to wasted natural resources and excessive greenhouse gas (GHG) emissions both in Japan and in countries that export to Japan. This study estimates Japanese food wastage by food item to evaluate impacts on land and water resources and global GHG emissions during the processing, distribution, and consumption phases of the food supply chain while also considering the feed crops needed for livestock production. Despite uncertainties due to data limitations, in 2012, 1.23 million hectares of harvested land were used to produce food that was eventually wasted, and 413 million m³ of water resources were wasted due to Japanese food wastage in agricultural production. Furthermore, unnecessary GHG emissions were 3.51 million tonnes of CO₂ eq. in agricultural production and 0.49 million tonnes of CO₂ eq. in international transportation. The outcomes of the present study can be used to develop countermeasures to food wastage in industrializing Asian countries where food imports are projected to increase and food wastage issues in the consumption stage are expected to become as serious as they currently are in Japan.     

Nutritional supremacy of pearl- and foxtail millets: assessing the nutrient density,protein stability and shelf-life of flours in millets and cereals for developing nutri-stable foods

Journal of Plant Biochemistry and Biotechnology - Flour of millets is nutritionally better, as compared to cereals, but has problem of low shelf-life. Here, we analyzed the nutritional density, and...     

Domestication, cultivation and utilization of two small millets, brachiaria ramosa and Setaria glauca (Poaceae), in South India

Brachiaria ramosa is cultivated in pure stands. Its grains are used in preparing at least nine traditional foods in South India. Setaria glauca is cultivated in mixed stands along with little millet (Panicum sumatrense). In Orissa state and in Southern India the grains are used to make at least six traditional foods as a supplementary ingredient. The weedy forms of these were found growing with upland rice and some millets in diverse agro-ecological niches, and are identified by various vernacular names by local farmers. Explorations were conducted to gather information on the evolutionary trends, domestication and ethnobotany of these minor food crops. These findings substantiate the belief that domestication process may have passed through three distinct phases: (i) an associated mimic weed with upland rice and some millets; (ii) a secondary crop mixed with little millet or kodo millet; and (iii) as an independent crop. Also, this process has been promoted as a means of imparting adaptation to an arid climate and in turn related to the diversification of the agriculture basic complex.     

Insect-resistant biotech crops and their impacts on beneficial arthropods

With a projected population of 10 billion by 2050, an immediate priority for agriculture is to achieve increased crop yields in a sustainable and cost-effective way. The concept of using a transgenic approach was realized in the mid-1990s with the commercial introduction of genetically modified (GM) crops. By 2010, the global value of the seed alone was US $11.2 billion, with commercial biotech maize, soya bean grain and cotton valued at approximately US $150 billion. In recent years, it has become evident that insect-resistant crops expressing δ-endotoxin genes from Bacillus thuringiensis have made a significant beneficial impact on global agriculture, not least in terms of pest reduction and improved quality. However, because of the potential for pest populations to evolve resistance, and owing to lack of effective control of homopteran pests, alternative strategies are being developed. Some of these are based on Bacillus spp. or other insect pathogens, while others are based on the use of plant- and animal-derived genes. However, if such approaches are to play a useful role in crop protection, it is desirable that they do not have a negative impact on beneficial organisms at higher trophic levels thus affecting the functioning of the agro-ecosystem. This widely held concern over the ecological impacts of GM crops has led to the extensive examination of the potential effects of a range of transgene proteins on non-target and beneficial insects. The findings to date with respect to both commercial and experimental GM crops expressing anti-insect genes are discussed here, with particular emphasis on insect predators and parasitoids.     

Reproductive System and Molecular Phylogenetic Relationships of Fonio Millets (Digitaria spp., Poaceae) with Some Polyploid Wild Relatives

Fonio millets (Digitaria exilis, D. iburua) are minor but important indigenous cereals in the semiarid areas of West-Africa. Recent interest in breeding strategies for these crops requires a better understanding of their biology and genetics. Amplified Fragment Length Polymorphism (AFLP) markers were employed to assess the phylogenetic relationships among cultivated fonio species and some polyploid wild relatives and examine proposed hypotheses on fonio ancestry. The AFLP analysis was found quite suitable for identifying each species. A very strong genetic affinity (over 92% similarity) was detected between the wild D. longiflora and D. ternata and the cultivated D. exilis and D. iburua, respectively. These data provided additional molecular evidence supporting the previous view of direct domestication of fonio millets from these two wild species. High genetic divergences were expectedly found between fonio species and the other taxonomically distant Digitaria taxa investigated. The results also revealed D. ciliaris and D. sanguinalis as separate species sharing close ancestry. Selfing experiments and subsequent progeny analyses using three isozymes supplemented by AFLPs were further conducted to determine the reproductive system in fonio millets. The results revealed apomixis as absolute mode of reproduction of these crops, except D. exilis in which 2% residual sexuality was detected. Additional data documented on seed set and pollen viability suggested that apomixis in fonio would be of pseudogamous type. The data also revealed fonio crops as highly self-compatible and of allopolyploid origin. This study adds new information about the reproductive system and the evolution of fonio, contributing to the knowledge on their biology, and thus providing useful subsides for future genetic improvement of these valuable crops.     

Removing politics from innovations that improve food security

Genetically modified (GM) organisms and crops have been a feature of food production for over 30 years. Despite extensive science-based risk assessment, the public and many politicians remain concerned with the genetic manipulation of crops, particularly food crops. Many governments have addressed public concern through biosafety legislation and regulatory frameworks that identify and regulate risks to ensure human health and environmental safety. These domestic regulatory frameworks align to international scientific risk assessment methodologies on a case-by-case basis. Regulatory agencies in 70 countries around the world have conducted in excess of 4400 risk assessments, all reaching the same conclusion: GM crops and foods that have been assessed provide no greater risk to human health or the environment than non-GM crops and foods. Yet, while the science regarding the safety of GM crops and food appears conclusive and societal benefits have been globally demonstrated, the use of innovative products have only contributed minimal improvements to global food security. Regrettably, politically-motivated regulatory barriers are currently being implemented with the next genomic innovation, genome editing, the implications of which are also discussed in this article. A decade of reduced global food insecurity was witnessed from 2005 to 2015, but regrettably, the figure has subsequently risen. Why is this the case? Reasons have been attributed to climate variability, biotic and abiotic stresses, lack of access to innovative technologies and political interference in decision making processes. This commentary highlights how political interference in the regulatory approval process of GM crops is adversely affecting the adoption of innovative, yield enhancing crop varieties, thereby limiting food security opportunities in food insecure economies.

     

A chromosome-level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop

Traditional crops have historically provided accessible and affordable nutrition to millions of rural dwellers but have been neglected, with most modern agricultural systems over-reliant on a small number of internationally traded crops. Traditional crops are typically well-adapted to local agro-ecological conditions and many are nutrient-dense. They can play a vital role in local food systems through enhanced nutrition (particularly where diets are dominated by starch crops), food security and livelihoods for smallholder farmers, and a climate-resilient and biodiverse agriculture. Using short-read, long-read and phased sequencing technologies, we generated a high-quality chromosome-level genome assembly for Amaranthus cruentus, an under-researched crop with micronutrient- and protein-rich leaves and gluten-free seed, but lacking improved varieties, with respect to productivity and quality traits. The 370.9 Mb genome demonstrates a shared whole genome duplication with a related species, Amaranthus hypochondriacus. Comparative genome analysis indicates chromosomal loss and fusion events following genome duplication that are common to both species, as well as fission of chromosome 2 in A. cruentus alone, giving rise to a haploid chromosome number of 17 (versus 16 in A. hypochondriacus). Genomic features potentially underlying the nutritional value of this crop include two A. cruentus-specific genes with a likely role in phytic acid synthesis (an anti-nutrient), expansion of ion transporter gene families, and identification of biosynthetic gene clusters conserved within the amaranth lineage. The A. cruentus genome assembly will underpin much-needed research and global breeding efforts to develop improved varieties for economically viable cultivation and realization of the benefits to global nutrition security and agrobiodiversity.     

Molecular breeding strategies for the modification of lipid composition

Summary Lipids are key components of all living cells. Acyl lipids and sterols provide the matrix of the biological membranes that both define the boundaries of cells and organelles, and act as sites for the trafficking of molecules within and into/out of cells. Lipids are also important metabolic intermediates and the most efficient form of energy storage that is available to a cell. It is the latter, energy-storing function that is of most relevance to this review. Storage lipids are accumulated in abundance in many of our most important crops, including maize, soybean, rapeseed, and oil palm, giving rise to a commerical sector valued at over $50 billion/year. Because the storage lipids of the major global oil crops have a relatively restricted composition, there is great interest in using all available breeding technologies, whether traditional or modern, to enhance the variation in lipid quality in existing crops and/or to domesticate new crops that already accumulate useful novel lipids. Over the past few decades, there has been a great deal of effort to manipulate fatty acid composition in order to produce novel lipids, especially for industrial applications. However, these attempts, many based on genetic engineering, have met with only limited commercial success-to date. More recently, there has been a resurgence of interest in the modification of both acyl and non-acyl lipids to enhance the nutritional quality of plant oils. In this review, we will examine the background to plant lipid modification and some of the latest developments, with a particular focus on edible oils.     

Global agricultural intensification during climate change: a role for genomics

Agriculture is now facing the ‘perfect storm’ of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic‐assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.