Grain yield improvement by genome editing of TaARF12 that decoupled peduncle and rachis development trajectories via differential regulation of gibberellin signalling in wheat

Plant breeding is constrained by trade-offs among different agronomic traits by the pleiotropic nature of many genes. Genes that contribute to two or more favourable traits with no penalty on yield are rarely reported, especially in wheat. Here, we describe the editing of a wheat auxin response factor TaARF12 by using CRISPR/Cas9 that rendered shorter plant height with larger spikes. Changes in plant architecture enhanced grain number per spike up to 14.7% with significantly higher thousand-grain weight and up to 11.1% of yield increase under field trials. Weighted Gene Co-Expression Network Analysis (WGCNA) of spatial-temporal transcriptome profiles revealed two hub genes: RhtL1, a DELLA domain-free Rht-1 paralog, which was up-regulated in peduncle, and TaNGR5, an organ size regulator that was up-regulated in rachis, in taarf12 plants. The up-regulation of RhtL1 in peduncle suggested the repression of GA signalling, whereas up-regulation of TaNGR5 in spike may promote GA response, a working model supported by differential expression patterns of GA biogenesis genes in the two tissues. Thus, TaARF12 complemented plant height reduction with larger spikes that gave higher grain yield. Manipulation of TaARF12 may represent a new strategy in trait pyramiding for yield improvement in wheat.

The effect of water molecules on paraquat salts: from physicochemical properties to environmental impact in the Brazilian Cerrado

Introduction: The green revolution model that is followed in the Brazilian Cerrado is dependent on mechanization, chemical fertilization for soil dressing and correction, and the use of herbicides. Paraquat is a methyl viologen herbicide marketed as bipyridylium dichloride salts and used (in low doses) to combat weeds in their post-emergence stage. It is a non-selective pesticide that causes the peroxidation of the lipids that make up the cell membrane, and when it comes into contact with foliage, it results in the death of the plant. Methods: The effect of water molecules co-crystallized in Paraquat salt structures was analyzed in anhydrous, dihydrate, and trihydrate forms to understand those physicochemical properties in its redox activity. The frontier molecular orbitals were also carried out using DFT to obtain the chemical reactivity of the bipyridylium cation. Finally, the supramolecular arrangements were evaluated to analyze the physicochemical stability and acquire insights on superoxide anions. Results and discussion: The electronic structure indicated that the BP cation presents an acidic character due to its low ELUMO value, while the salt has a more basic character due to its high EHOMO value. For this reason, the BP ion is more susceptible to reduction during the weeds' photosynthesis process. During the process of plant photosynthesis, PQ is reduced to form a stable radical cation. In the supramolecular arrangement, the presence of water molecules increases the number of strong H-bonds, while the weak/moderate H-bonds are stabilized. PQ's toxic effects are observed in wildlife, domesticated animals, human populations, and ecosystems. The influence of PQ on the terrestrial environment is limited because of the soil adsorption capacity associated with good agricultural practices. The current use of good agricultural practices in the Cerrado seems not to prevent the environmental impacts of herbicides like PQ because it aims for the expansion and profitability of large-scale farming based on input-intensive practices instead of sustainable agriculture processes.

Green revolution to genome revolution: driving better resilient crops against environmental instability

Crop improvement programmes began with traditional breeding practices since the inception of agriculture. Farmers and plant breeders continue to use these strategies for crop improvement due to their broad application in modifying crop genetic compositions. Nonetheless, conventional breeding has significant downsides in regard to effort and time. Crop productivity seems to be hitting a plateau as a consequence of environmental issues and the scarcity of agricultural land. Therefore, continuous pursuit of advancement in crop improvement is essential. Recent technical innovations have resulted in a revolutionary shift in the pattern of breeding methods, leaning further towards molecular approaches. Among the promising approaches, marker-assisted selection, QTL mapping, omics-assisted breeding, genome-wide association studies and genome editing have lately gained prominence. Several governments have progressively relaxed their restrictions relating to genome editing. The present review highlights the evolutionary and revolutionary approaches that have been utilized for crop improvement in a bid to produce climate-resilient crops observing the consequence of climate change. Additionally, it will contribute to the comprehension of plant breeding succession so far. Investing in advanced sequencing technologies and bioinformatics will deepen our understanding of genetic variations and their functional implications, contributing to breakthroughs in crop improvement and biodiversity conservation.

Breeding confusion: hybrid seeds and histories of agriculture

Since the 1970s 'hybrid seeds' have been linked to many perceived perils of industrialized agriculture. This essay revisits the scholarship that helped produce a dominant critical assessment of hybrid seeds, situating its emergence in a series of events and interventions of the late twentieth century. It explores how the singular history of F1 hybrid corn inflected understandings of crop breeding and seed production in general, contributing to effective political mobilization against agroindustry as well as lasting confusion about the promises and pitfalls of distinct approaches to crop development and the nature of hybrid seeds.

Genetic improvement toward nitrogen-use efficiency in rice: Lessons and perspectives

The indispensable role of nitrogen fertilizer in ensuring world food security together with the severe threats it poses to the ecosystem makes the usage of nitrogen fertilizer a major challenge for sustainable agriculture. Genetic improvement of crops with high nitrogen-use efficiency (NUE) is one of the most feasible solutions for tackling this challenge. In the last two decades, extensive efforts toward dissecting the variation of NUE-related traits and the underlying genetic basis in different germplasms have been made, and a series of achievements have been obtained in crops, especially in rice. Here, we summarize the approaches used for genetic dissection of NUE and the functions of the causal genes in modulating NUE as well as their applications in NUE improvement in rice. Strategies for exploring the variants controlling NUE and breeding future crops with "less-input-more-output" for sustainable agriculture are also proposed.

CRISPR for accelerating genetic gains in under-utilized crops of the drylands: Progress and prospects

Technologies and innovations are critical for addressing the future food system needs where genetic resources are an essential component of the change process. Advanced breeding tools like "genome editing" are vital for modernizing crop breeding to provide game-changing solutions to some of the "must needed" traits in agriculture. CRISPR/Cas-based tools have been rapidly repurposed for editing applications based on their improved efficiency, specificity and reduced off-target effects. Additionally, precise gene-editing tools such as base editing, prime editing, and multiplexing provide precision in stacking of multiple traits in an elite variety, and facilitating specific and targeted crop improvement. This has helped in advancing research and delivery of products in a short time span, thereby enhancing the rate of genetic gains. A special focus has been on food security in the drylands through crops including millets, teff, fonio, quinoa, Bambara groundnut, pigeonpea and cassava. While these crops contribute significantly to the agricultural economy and resilience of the dryland, improvement of several traits including increased stress tolerance, nutritional value, and yields are urgently required. Although CRISPR has potential to deliver disruptive innovations, prioritization of traits should consider breeding product profiles and market segments for designing and accelerating delivery of locally adapted and preferred crop varieties for the drylands. In this context, the scope of regulatory environment has been stated, implying the dire impacts of unreasonable scrutiny of genome-edited plants on the evolution and progress of much-needed technological advances.

Bioinoculants-Natural Biological Resources for Sustainable Plant Production

Agricultural sustainability is of foremost importance for maintaining high food production. Irresponsible resource use not only negatively affects agroecology, but also reduces the economic profitability of the production system. Among different resources, soil is one of the most vital resources of agriculture. Soil fertility is the key to achieve high crop productivity. Maintaining soil fertility and soil health requires conscious management effort to avoid excessive nutrient loss, sustain organic carbon content, and minimize soil contamination. Though the use of chemical fertilizers have successfully improved crop production, its integration with organic manures and other bioinoculants helps in improving nutrient use efficiency, improves soil health and to some extent ameliorates some of the constraints associated with excessive fertilizer application. In addition to nutrient supplementation, bioinoculants have other beneficial effects such as plant growth-promoting activity, nutrient mobilization and solubilization, soil decontamination and/or detoxification, etc. During the present time, high energy based chemical inputs also caused havoc to agriculture because of the ill effects of global warming and climate change. Under the consequences of climate change, the use of bioinputs may be considered as a suitable mitigation option. Bioinoculants, as a concept, is not something new to agricultural science, however; it is one of the areas where consistent innovations have been made. Understanding the role of bioinoculants, the scope of their use, and analysing their performance in various environments are key to the successful adaptation of this technology in agriculture.

Evaluation of Three Antimicrobial Peptides Mixtures to Control the Phytopathogen Responsible for Fire Blight Disease

Fire blight is a severe bacterial plant disease that affects important chain-of-value fruit trees such as pear and apple trees. This disease is caused by Erwinia amylovora, a quarantine phytopathogenic bacterium, which, although highly distributed worldwide, still lacks efficient control measures. The green revolution paradigm demands sustainable agriculture practices, for which antimicrobial peptides (AMPs) have recently caught much attention. The goal of this work was to disclose the bioactivity of three peptides mixtures (BP100:RW-BP100, BP100:CA-M, and RW-BP100:CA-M), against three strains of E. amylovora representing distinct genotypes and virulence (LMG 2024, Ea 630 and Ea 680). The three AMPs' mixtures were assayed at eight different equimolar concentrations ranging from 0.25 to 6 μM (1:1). Results showed MIC and MBC values between 2.5 and 4 μM for every AMP mixture and strain. Regarding cell viability, flow cytometry and alamarBlue reduction, showed high reduction (>25%) of viable cells after 30 min of AMP exposure, depending on the peptide mixture and strain assayed. Hypersensitive response in tobacco plants showed that the most efficient AMPs mixtures and concentrations caused low to no reaction of the plant. Altogether, the AMPs mixtures studied are better treatment solutions to control fire blight disease than the same AMPs applied individually.

Genetic improvement of nitrogen use efficiency in crops

Nitrogen (N) is an essential mineral nutrient for plant growth and development. N deficiency is the major factor limiting plant growth and crop production in most natural and agricultural soils. The green revolution of the 1960's boosted crop yields through cultivation of semi-dwarf plant varieties. However, green revolution wheat and rice varieties have relatively poor nitrogen use efficiency (NUE), require a high N fertilizer supply to achieve maximum yield potential, and this leads to an increase in production costs and environmental problem. Therefore, a major challenge for sustainable agriculture is whether improvement of NUE through the reduction of N fertilizer supply can be achieved without yield penalty. In this review, we summarize the recent advances in understanding of molecular mechanisms underlying the regulation of N-responsive plant growth, utilization and possibility for improvements of NUE in crops, and new breeding strategies through modulation of N-responsive growth-metabolism coordination for future sustainable agriculture.

Lessons From the Aftermaths of Green Revolution on Food System and Health

Food production has seen various advancements globally in developing countries, such as India. One such advancement was the green revolution. Notably, the World Bank applauds the introduction of the green revolution as it reduced the rural poverty in India for a certain time. Despite the success of the green revolution, the World Bank reported that health outcomes have not been improved. During the post-green revolution period, several notable negative impacts arose. Exclusive studies were not conducted on the benefits and harms before the introduction of the green revolution. Some of such interventions deviate from the natural laws of balance and functioning and are unsustainable practices. To avoid the adverse effects of some of these developments, a review of these interventions is necessary.

Impact of Historical Changes in Coarse Cereals Consumption in India on Micronutrient Intake and Anemia Prevalence

BACKGROUND

Production of rice and wheat increased dramatically in India over the past decades, with reduced proportion of coarse cereals in the food supply.

OBJECTIVE

We assess impacts of changes in cereal consumption in India on intake of iron and other micronutrients and whether increased consumption of coarse cereals could help alleviate anemia prevalence.

METHODS

With consumption data from over 800 000 households, we calculate intake of iron and other micronutrients from 84 food items from 1983 to 2011. We use mixed-effect models to relate state-level anemia prevalence in women and children to micronutrient consumption and household characteristics.

RESULTS

Coarse cereals reduced from 23% to 6% of calories from cereals in rural households (10% to 3% in urban households) between 1983 and 2011, with wide variations across states. Loss of iron from coarse cereals was only partially compensated by increased iron from other cereals and food groups, with a 21% (rural) and 11% (urban) net loss of total iron intake. Models indicate negative association between iron from cereals and anemia prevalence in women. The benefit from increased iron from coarse cereals is partially offset by the adverse effects from antinutrients. For children, anemia was negatively associated with heme-iron consumption but not with iron from cereals.

CONCLUSIONS

Loss of coarse cereals in the Indian diet has substantially reduced iron intake without compensation from other food groups, particularly in states where rice rather than wheat replaced coarse cereals. Increased consumption of coarse cereals could reduce anemia prevalence in Indian women along with other interventions.

The imperative for regenerative agriculture

A review is made of the current state of agriculture, emphasising issues of soil erosion and dependence on fossil fuels, in regard to achieving food security for a relentlessly enlarging global population. Soil has been described as "the fragile, living skin of the Earth", and yet both its aliveness and fragility have all too often been ignored in the expansion of agriculture across the face of the globe. Since it is a pivotal component in a global nexus of soil-water-air-energy, how we treat the soil can impact massively on climate change - with either beneficial or detrimental consequences, depending on whether the soil is preserved or degraded. Regenerative agriculture has at its core the intention to improve the health of soil or to restore highly degraded soil, which symbiotically enhances the quality of water, vegetation and land-productivity. By using methods of regenerative agriculture, it is possible not only to increase the amount of soil organic carbon (SOC) in existing soils, but to build new soil. This has the effect of drawing down carbon from the atmosphere, while simultaneously improving soil structure and soil health, soil fertility and crop yields, water retention and aquifer recharge - thus ameliorating both flooding and drought, and also the erosion of further soil, since runoff is reduced. Since food production on a more local scale is found to preserve the soil and its quality, urban food production should be seen as a significant potential contributor to regenerative agriculture in the future, so long as the methods employed are themselves 'regenerative'. If localisation is to become a dominant strategy for dealing with a vastly reduced use of fossil fuels, and preserving soil quality - with increased food production in towns and cities - it will be necessary to incorporate integrated ('systems') design approaches such as permaculture and the circular economy (which minimise and repurpose 'waste') within the existing urban infrastructure. In addition to growing food in urban space, such actions as draught-proofing and thermally insulating existing building stock, and living/ working on a more local scale, would serve well to cut our overall energy consumption. In order to curb our use of fossil fuels, methods for reducing overall energy use must be considered at least equally important to expanding low-carbon energy production. In synopsis, it is clear that only by moving from the current linear, 'take, make, dispose (waste-creation)' model for resource-consumption, to the systemic, circular alternative of 'reduce, reuse, recycle, regenerate', are we likely to meet demands for future generations.

Crop Diversity: An Unexploited Treasure Trove for Food Security

The prediction is that food supply must double by 2050 to cope with the impact of climate change and population pressure on global food systems. The diversification of staple crops and the systems in which they grow is essential to make future agriculture sustainable, resilient, and suitable for local environments and soils.

The changing nutrition scenario

The past seven decades have seen remarkable shifts in the nutritional scenario in India. Even up to the 1950s severe forms of malnutrition such as kwashiorkar and pellagra were endemic. As nutritionists were finding home-grown and common-sense solutions for these widespread problems, the population was burgeoning and food was scarce. The threat of widespread household food insecurity and chronic undernutrition was very real. Then came the Green Revolution. Shortages of food grains disappeared within less than a decade and India became self-sufficient in food grain production. But more insidious problems arising from this revolution were looming, and cropping patterns giving low priority to coarse grains and pulses, and monocropping led to depletion of soil nutrients and 'Green Revolution fatigue'. With improved household food security and better access to health care, clinical manifestations of severe malnutrition virtually disappeared. But the decline in chronic undernutrition and "hidden hunger" from micronutrient deficiencies was slow. On the cusp of the new century, an added factor appeared on the nutritional scene in India. With steady urban migration, upward mobility out of poverty, and an increasingly sedentary lifestyle because of improvements in technology and transport, obesity rates began to increase, resulting in a dual burden. Measured in terms of its performance in meeting its Millennium Development Goals, India has fallen short. Despite its continuing high levels of poverty and illiteracy, India has a huge demographic potential in the form of a young population. This advantage must be leveraged by investing in nutrition education, household access to nutritious diets, sanitary environment and a health-promoting lifestyle. This requires co-operation from all the stakeholders, including governments, non government organizations, scientists and the people at large.

Peak phosphorus - peak food? The need to close the phosphorus cycle

The peak in the world production of phosphorus has been predicted to occur in 2033, based on world reserves of rock phosphate (URR) reckoned at around 24,000 million tonnes (Mt), with around 18,000 Mt remaining. This figure was reckoned-up to 71,000 Mt, by the USGS, in 2012, but a production maximum during the present century is still highly probable. There are complex issues over what the demand will be for phosphorus in the future, as measured against a rising population (from 7 billion to over 9 billion in 2050), and a greater per capita demand for fertiliser to grow more grain, in part to feed animals and meet a rising demand for meat by a human species that is not merely more populous but more affluent. As a counterweight to this, we may expect that greater efficiencies in the use of phosphorus - including recycling from farms and of human and animal waste - will reduce the per capita demand for phosphate rock. The unseen game changer is peak oil, since phosphate is mined and recovered using machinery powered by liquid fuels refined from crude oil. Hence, peak oil and peak phosphorus might appear as conjoined twins. There is no unequivocal case that we can afford to ignore the likelihood of a supply-demand gap for phosphorus occurring sometime this century, and it would be perilous to do so.

Understanding the development of roots exposed to contaminants and the potential of plant-associated bacteria for optimization of growth

BACKGROUND AND SCOPE

Plant responses to the toxic effects of soil contaminants, such as excess metals or organic substances, have been studied mainly at physiological, biochemical and molecular levels, but the influence on root system architecture has received little attention. Nevertheless, the precise position, morphology and extent of roots can influence contaminant uptake. Here, data are discussed that aim to increase the molecular and ecological understanding of the influence of contaminants on root system architecture. Furthermore, the potential of plant-associated bacteria to influence root growth by their growth-promoting and stress-relieving capacities is explored.

METHODS

Root growth parameters of Arabidopsis thaliana seedlings grown in vertical agar plates are quantified. Mutants are used in a reverse genetics approach to identify molecular components underlying quantitative changes in root architecture after exposure to excess cadmium, copper or zinc. Plant-associated bacteria are isolated from contaminated environments, genotypically and phenotypically characterized, and used to test plant root growth improvement in the presence of contaminants.

KEY RESULTS

The molecular determinants of primary root growth inhibition and effects on lateral root density by cadmium were identified. A vertical split-root system revealed local effects of cadmium and copper on root development. However, systemic effects of zinc exposure on root growth reduced both the avoidance of contaminated areas and colonization of non-contaminated areas. The potential for growth promotion and contaminant degradation of plant-associated bacteria was demonstrated by improved root growth of inoculated plants exposed to 2,4-di-nitro-toluene (DNT) or cadmium.

CONCLUSIONS

Knowledge concerning the specific influence of different contaminants on root system architecture and the molecular mechanisms by which this is achieved can be combined with the exploitation of plant-associated bacteria to influence root development and increase plant stress tolerance, which should lead to more optimal root systems for application in phytoremediation or safer biomass production.

The 'Green Revolution' dwarfing genes play a role in disease resistance in Triticum aestivum and Hordeum vulgare

The Green Revolution dwarfing genes, Rht-B1b and Rht-D1b, encode mutant forms of DELLA proteins and are present in most modern wheat varieties. DELLA proteins have been implicated in the response to biotic stress in the model plant, Arabidopsis thaliana. Using defined wheat Rht near-isogenic lines and barley Sln1 gain of function (GoF) and loss of function (LoF) lines, the role of DELLA in response to biotic stress was investigated in pathosystems representing contrasting trophic styles (biotrophic, hemibiotrophic, and necrotrophic). GoF mutant alleles in wheat and barley confer a resistance trade-off with increased susceptibility to biotrophic pathogens and increased resistance to necrotrophic pathogens whilst the converse was conferred by a LoF mutant allele. The polyploid nature of the wheat genome buffered the effect of single Rht GoF mutations relative to barley (diploid), particularly in respect of increased susceptibility to biotrophic pathogens. A role for DELLA in controlling cell death responses is proposed. Similar to Arabidopsis, a resistance trade-off to pathogens with contrasting pathogenic lifestyles has been identified in monocotyledonous cereal species. Appreciation of the pleiotropic role of DELLA in biotic stress responses in cereals has implications for plant breeding.

Elevating optimal human nutrition to a central goal of plant breeding and production of plant-based foods

High-yielding cereals and other staples have produced adequate calories to ward off starvation for much of the world over several decades. However, deficiencies in certain amino acids, minerals, vitamins and fatty acids in staple crops, and animal diets derived from them, have aggravated the problem of malnutrition and the increasing incidence of certain chronic diseases in nominally well-nourished people (the so-called diseases of civilization). Enhanced global nutrition has great potential to reduce acute and chronic disease, the need for health care, the cost of health care, and to increase educational attainment, economic productivity and the quality of life. However, nutrition is currently not an important driver of most plant breeding efforts, and there are only a few well-known efforts to breed crops that are adapted to the needs of optimal human nutrition. Technological tools are available to greatly enhance the nutritional value of our staple crops. However, enhanced nutrition in major crops might only be achieved if nutritional traits are introduced in tandem with important agronomic yield drivers, such as resistance to emerging pests or diseases, to drought and salinity, to herbicides, parasitic plants, frost or heat. In this way we might circumvent a natural tendency for high yield and low production cost to effectively select against the best human nutrition. Here we discuss the need and means for agriculture, food processing, food transport, sociology, nutrition and medicine to be integrated into new approaches to food production with optimal human nutrition as a principle goal.