High-Throughput Sequencing and Mutagenesis to Accelerate the Domestication of Microlaena stipoides as a New Food Crop

Global food demand, climatic variability and reduced land availability are driving the need for domestication of new crop species. The accelerated domestication of a rice-like Australian dryland polyploid grass, Microlaena stipoides (Poaceae), was targeted using chemical mutagenesis in conjunction with high throughput sequencing of genes for key domestication traits. While M. stipoides has previously been identified as having potential as a new grain crop for human consumption, only a limited understanding of its genetic diversity and breeding system was available to aid the domestication process. Next generation sequencing of deeply-pooled target amplicons estimated allelic diversity of a selected base population at 14.3 SNP/Mb and identified novel, putatively mutation-induced polymorphisms at about 2.4 mutations/Mb. A 97% lethal dose (LD₉₇) of ethyl methanesulfonate treatment was applied without inducing sterility in this polyploid species. Forward and reverse genetic screens identified beneficial alleles for the domestication trait, seed-shattering. Unique phenotypes observed in the M2 population suggest the potential for rapid accumulation of beneficial traits without recourse to a traditional cross-breeding strategy. This approach may be applicable to other wild species, unlocking their potential as new food, fibre and fuel crops.     

Dedicated Energy Crops and Crop Residues for Bioenergy Feedstocks in the Central and Eastern USA

Dedicated energy crops and crop residues will meet herbaceous feedstock demands for the new bioeconomy in the Central and Eastern USA. Perennial warm-season grasses and corn stover are well-suited to the eastern half of the USA and provide opportunities for expanding agricultural operations in the region. A suite of warm-season grasses and associated management practices have been developed by researchers from the Agricultural Research Service of the US Department of Agriculture (USDA) and collaborators associated with USDA Regional Biomass Research Centers. Second generation biofuel feedstocks provide an opportunity to increase the production of transportation fuels from recently fixed plant carbon rather than from fossil fuels. Although there is no “one-size-fits-all” bioenergy feedstock, crop residues like corn (Zea mays L.) stover are the most readily available bioenergy feedstocks. However, on marginally productive cropland, perennial grasses provide a feedstock supply while enhancing ecosystem services. Twenty-five years of research has demonstrated that perennial grasses like switchgrass (Panicum virgatum L.) are profitable and environmentally sustainable on marginally productive cropland in the western Corn Belt and Southeastern USA.     

Plant Domestication and Crop Evolution in the Near East: On Events and Processes

Reconstructing the evolutionary history of crop plants is fundamental for understanding their adaptation profile and the genetic basis of yield-limiting factors, which in turn are critical for future crop improvement. A major topic in this field is the recent claim for a millennia-long ‘protracted’ domestication process. Here we evaluate the evidence for the protracted domestication model in light of published archaeobotanical data, experimental evidence and the biology of the Near Eastern crops and their wild progenitors. The crux of our discussion is the differentiation between events or ‘domestication episodes’ and the later following crop evolutionary processes under domestication (frequently termed ‘crop improvement stage’), which are by definition, still ongoing. We argue that by assuming a protracted millennia-long domestication process, one needlessly opts to operate within an intellectual framework that does not allow differentiating between the decisive (critical) domestication traits and their respective loci, and those that have evolved later during the crop dissemination and improvement following the episodic domestication event. Therefore, in our view, apart from the lack of experimental evidence to support it, the protracted domestication assumption undermines the resolution power of the study of both plant domestication and crop evolution, from the cultural as well as from the biological perspectives.     

Photosynthetic Energy Conversion Efficiency: Setting a Baseline for Gauging Future Improvements in Important Food and Biofuel Crops

The conversion efficiency (ε_c) of absorbed radiation into biomass (MJ of dry matter per MJ of absorbed photosynthetically active radiation) is a component of yield potential that has been estimated at less than half the theoretical maximum. Various strategies have been proposed to improve ε_c, but a statistical analysis to establish baseline ε_c levels across different crop functional types is lacking. Data from 164 published ε_c studies conducted in relatively unstressed growth conditions were used to determine the means, greatest contributors to variation, and genetic trends in ε_c across important food and biofuel crop species. ε_c was greatest in biofuel crops (0.049–0.066), followed by C₄ food crops (0.046–0.049), C₃ nonlegumes (0.036–0.041), and finally C₃ legumes (0.028–0.035). Despite confining our analysis to relatively unstressed growth conditions, total incident solar radiation and average growing season temperature most often accounted for the largest portion of ε_c variability. Genetic improvements in ε_c, when present, were less than 0.7% per year, revealing the unrealized potential of improving ε_c as a promising contributing strategy to meet projected future agricultural demand.Substantial increases in yield are needed to feed and fuel the world’s growing human population. With an estimated population of nine billion people by the middle of this century (Lutz and Samir, 2010) and rising affluence resulting in greater consumption of grain-fed animal products (Cirera and Masset, 2010), different studies predict that, by midcentury, global crop production will need to increase 60% to 120% over 2005 levels without the expansion of agricultural land area (Tilman et al., 2011; Alexandratos and Bruinsma, 2012).Doubling yields in major food and fuel crops requires considerable effort, especially as yields are beginning to plateau in many major food crops. Yield increases necessary for doubling productivity by midcentury are estimated at 1.16% to 1.31% each year in all cereals (Hall and Richards, 2013), 1.7% per year in wheat (Triticum aestivum; Rosegrant and Agcaoili, 2010), and 2.4% (noncompounding average per year) across all major grain crops (Ray et al., 2013). However, global mean increases from the past 20 to 30 years suggest that yield gains in rice (Oryza sativa) and wheat are approximately 1% (Lopes et al., 2012; Manès et al, 2012; Ray et al., 2013) and declining in some areas of the world (Cassman et al., 2010; Fischer and Edmeades, 2010; Long and Ort, 2010; Ray et al., 2013). Global yearly increases are estimated at 1.3% in soybean (Glycine max) and 1.6% in maize (Zea mays), with similar concerns that yield trends may also be decreasing in some major growing regions (Lobell and Gourdji, 2012; Ray et al., 2013).Efforts to increase yields in the next few decades must also account for environmental and sustainability goals (Sayer et al., 2013) as well as heightened environmental stresses predicted to occur due to climate change, which are already responsible for some of the stagnation in yield increases. Anthropogenic sources of greenhouse gases have caused an approximately 1°C increase in land surface temperatures since 1900, and global mean surface temperatures are likely to increase by up to 2.4°C to 4.8°C by the end of the century (IPCC, 2013). Drought is also expected to become more frequent and intense in many regions of the world (Dai, 2011; IPCC, 2013). Of the variability present in major food crop yield gains, 30% can be explained by climate change alone (Lobell and Field, 2007), with drastic decreases in barley (Hordeum vulgare), maize, rice, sorghum (Sorghum bicolor), soybean, and wheat yields as average growing season temperatures surpass the temperature optimum for each crop (Lobell and Gourdji, 2012). Current levels of atmospheric CO₂ concentration [CO₂] are the highest they have been in at least 800,000 years (IPCC, 2013). Elevated [CO₂] increases water use efficiency (Ainsworth and Long, 2005, Bernacchi et al., 2007, Leakey et al., 2009), but probably not to an extent that would mitigate the resulting reductions in yield caused by higher temperature and higher vapor pressure deficit (Ort and Long, 2014). Additionally, any fertilization effects on C₃ yields due to elevated [CO₂] would be at least in part negated by drought and temperature stress, leaving yield increases far from optimal (Long et al., 2006a; Lobell and Gourdji, 2012).     

转基因作物及其食品的安全性

对转基因食品存在的潜在危害进行了全面分析,概述了对转基因食品的安全性评价的主要方面及世界各国对转基因食品安全的态度和对转基因食品的管理模式。     

Evaluation of Garden Crop Mercury Uptake and Potential Exposure from Consumption of Garden Crops Grown on Floodplain Soils

ABSTRACT

This study investigated Hg uptake from soil into garden crops to help assess the significance of human consumption of crops as a potential route of exposure to Hg. Locations for both a floodplain and a control garden were identified within the Augusta Forestry Center near Crimora, VA, USA, which is about 16 river-km downstream from the city of Waynesboro, along the South River. The floodplain garden had measured soil Hg concentrations ranging from 4.2 to 78 mg Hg kg^?1 dry weight basis in the surface to 15-cm deep layer. A total of 139 samples from the floodplain garden from 17 different crops were analyzed for Hg. All crop samples (except for nine) had less than 0.1 μg Hg g^?1 wet weight basis (ww). Many samples were less than the method detection limit (MDL) of 0.003 μg Hg g^?1 ww. Based on the measured Hg concentrations and several conservative assumptions (e.g., Hg assumed present when less than MDL; 100% consumption from the geographical area in which study was conducted; and 100% bioavailable Hg as methyl Hg), consumption of crops with these Hg levels is not expected to be a significant route of Hg exposure.     

Economic Analysis of the Potential of Cellulosic Biomass Available in France from Agricultural Residue and Energy Crops

The objective of this research is to evaluate the feasibility and locations of using cellulosic biomass both from crop residues and from dedicated energy crops to supply 200-million-liter-biodiesel plants in France. The estimation of the potential amount of agricultural residue available in 2015 in each region of France is calculated. The residues considered in this study come from cereal straw and corn stover. Results show that eight out of the twenty one French regions have enough agricultural residues available to supply at least one 200 million liter biofuel plant. Region Centre has the largest potential, with enough residues to supply three to five plants. Finally, cost of supplying one biodiesel plant of 200 million liters in the region Centre is estimated. Results show that collection of biomass will be effective in an area with a radius of 58 Km to 168 Km depending of the raw material considered and its abundance. The cost of supplying a plant with miscanthus is much higher than with residues only. Thus, crop residues appear to offer a lower cost to produce biodiesel in the near term compared to a dedicated crop. Results show that production of biofuel from cellulosic biomass should not be limited by the supply of raw material, but costs of conversion to liquid fuels clearly will play a key role in the development of cellulosic biofuels. Energy prices and policies will have a significant impact on second generation biofuel development.     

In Silico Analysis of Crop Science： Report on the First China-UK Workshop on Chips, Computers and Crops

A workshop on ＂Chips, Computers and Crops＂ was held in Hangzhou, China during September 26-27, 2008. The main objective of the workshop was to bring together China and UK scientists from mathematics, bioinformatics and plant molecular biology communities to exchange ideas, enhance awareness of each others＇ fields, explore synergisms and make recommendations on fruitful future directions in crop science. Here we describe the contributions to the workshop, and examine some conceptual issues that lie at the foundations and future of crop systems biology.     

Characteristic Studies on the Pyrolysis Products from Hydrolyzed Canadian Lignocellulosic Feedstocks

Lignocellulosic feedstocks are utilized for the production of fuel ethanol and butanol through dilute acid/enzymatic hydrolysis and fermentation. Hydrolysis residue, a major by-product of biomass hydrolysis, is rich in recalcitrant carbon as majority of cellulosic and hemicellulosic components are released during pretreatment. With the intention of their effective utilization, hydrolysis residues from forestry (pinewood), energy crop system (timothy grass), and agriculture (wheat straw) were pyrolysed in a fixed-bed reactor at 600 °C with slow heating rate of 5 °C/min for 4 h. In order to understand the product (biochar, bio-oil, and gases) properties and advocate their energy and environmental values, chemical characterizations such as carbon–hydrogen–nitrogen–sulfur analysis, inductively coupled plasma-mass spectrometry, pH, electrical conductivity, scanning electron microscopy, porosity analysis, thermogravimetric analysis, X-ray diffraction, Fourier transform infrared (FTIR) and Raman spectroscopy, nuclear magnetic resonance (NMR) and gas chromatography–mass spectrometry (GC-MS) were employed. The yield of biochar, bio-oil and gases was 38.9–41.7, 18.6–22.3, and 24.9–28.8 wt%, respectively. The high pH and electrical conductivity of biochars with substantial amounts of Na, Mg, K, and Ca indicated their alkaline and saline nature, which would necessitate proper agronomical soil applications. Variable intensities of C–C, C–H, C–O, O–H, and C–N functional groups were detected in the FTIR spectra of residues, biochars, and bio-oils. Raman spectroscopy showed the development of graphite (1,580–1,610 cm^?1) and defect (1,325–1,380 cm^?1) carbon structures in biochars. ¹H NMR of bio-oils indicated aromatics, olefinics, and aliphatics, whereas ¹³C NMR indicated carbonyls, aromatics, carbohydrates, alkyls, methoxy, and hydroxy carbon. GC studies of pyrolysis gases identified chiefly H₂ and CO with traces of CH₄, CO₂, and C₂+ components.     

Genetic Engineering of Energy Crops: A Strategy for Biofuel Production in China

Biomass utilization is increasingly considered as a practical way for sustainable energy supply and long-term environment care around the world.In concerns with food security in China,starch or sugar-based bioethanol and edible-oil-derived biodiesel are harshly restricted for large scale production.However,conversion of lignocellulosic residues from food crops is a potential alternative.Because of its recalcitrance,current biomass process is unacceptably expensive,but genetic breeding of energy crops is a p...     

Investigating the Efficacy of Integrating Energy Crops into Non-Profitable Subfields in Iowa

Within-field spatial variability reduces growers’ return on investment and overall productivity while potentially increasing negative environmental impacts through increased soil erosion, nutrient runoff, and leaching. The hypothesis that integrating energy crops into non-profitable segments of agricultural fields could potentially increase grain yield and biomass feedstock production was tested in this study using a statewide analysis of predominantly corn- and soy-producing counties in Iowa. Basic and rigorous controls on permissible soil and soil-carbon losses were imposed on harvest of crop residues to enhance year-to-year sustainability of crop and residue production. Additional criteria limiting harvesting costs and focus on large-area subfields for biomass production were imposed to reduce the impacts of energy crop integration on grain production. Model simulations were conducted using 4 years (2013–2016) of soil, weather, crop yield, and management practice data on all counties in Iowa. Miscanthus (Miscanthus x giganteus), switchgrass (Panicum virgatum), and crop-residue-based bioenergy feedstock systems were evaluated as biomass. Average energy crop and plant residue harvesting efficiencies were estimated at 50 and 60%, respectively. Because of higher potential yields, average logistics costs for miscanthus-based biomass production were 15 and 23% lower than switchgrass-based and crop residue-based biomass productions, respectively, under basic sustainability controls, and 17 and 26% lower under rigorous sustainability controls. Subfield shape, size, area, and harvest equipment size were the dominant factors influencing harvesting cost and efficiency suggesting that in areas where subfields are predominantly profitable or harvesting efficiencies low, other options such as prairie strips, buffer zones around fields, and riparian areas should be investigated for more profitable biomass production and sustainable farming systems.     

Topography Mediates the Influence of Cover Crops on Soil Nitrate Levels in Row Crop Agricultural Systems

Supplying adequate amounts of soil N for plant growth during the growing season and across large agricultural fields is a challenge for conservational agricultural systems with cover crops. Knowledge about cover crop effects on N comes mostly from small, flat research plots and performance of cover crops across topographically diverse agricultural land is poorly understood. Our objective was to assess effects of both leguminous (red clover) and non-leguminous (winter rye) cover crops on potentially mineralizable N (PMN) and NO3--N levels across a topographically diverse landscape. We studied conventional, low-input, and organic managements in corn-soybean-wheat rotation. The rotations of low-input and organic managements included rye and red clover cover crops. The managements were implemented in twenty large undulating fields in Southwest Michigan starting from 2006. The data collection and analysis were conducted during three growing seasons of 2011, 2012 and 2013. Observational micro-plots with and without cover crops were laid within each field on three contrasting topographical positions of depression, slope and summit. Soil samples were collected 4–5 times during each growing season and analyzed for NO3--N and PMN. The results showed that all three managements were similar in their temporal and spatial distributions of NO₃ ^—N. Red clover cover crop increased NO3--N by 35% on depression, 20% on slope and 32% on summit positions. Rye cover crop had a significant 15% negative effect on NO3--N in topographical depressions but not in slope and summit positions. The magnitude of the cover crop effects on soil mineral nitrogen across topographically diverse fields was associated with the amount of cover crop growth and residue production. The results emphasize the potential environmental and economic benefits that can be generated by implementing site-specific topography-driven cover crop management in row-crop agricultural systems.     

Domestication of plants in the Americas: insights from Mendelian and molecular genetics

BACKGROUND: Plant domestication occurred independently in four different regions of the Americas. In general, different species were domesticated in each area, though a few species were domesticated independently in more than one area. The changes resulting from human selection conform to the familiar domestication syndrome, though different traits making up this syndrome, for example loss of dispersal, are achieved by different routes in crops belonging to different families. GENETIC AND MOLECULAR ANALYSES OF DOMESTICATION: Understanding of the genetic control of elements of the domestication syndrome is improving as a result of the development of saturated linkage maps for major crops, identification and mapping of quantitative trait loci, cloning and sequencing of genes or parts of genes, and discoveries of widespread orthologies in genes and linkage groups within and between families. As the modes of action of the genes involved in domestication and the metabolic pathways leading to particular phenotypes become better understood, it should be possible to determine whether similar phenotypes have similar underlying genetic controls, or whether human selection in genetically related but independently domesticated taxa has fixed different mutants with similar phenotypic effects. CONCLUSIONS: Such studies will permit more critical analysis of possible examples of multiple domestications and of the origin(s) and spread of distinctive variants within crops. They also offer the possibility of improving existing crops, not only major food staples but also minor crops that are potential export crops for developing countries or alternative crops for marginal areas.     

Predicting Greenhouse Gas Emissions and Soil Carbon from Changing Pasture to an Energy Crop

Bioenergy related land use change would likely alter biogeochemical cycles and global greenhouse gas budgets. Energy cane (Saccharum officinarum L.) is a sugarcane variety and an emerging biofuel feedstock for cellulosic bio-ethanol production. It has potential for high yields and can be grown on marginal land, which minimizes competition with grain and vegetable production. The DayCent biogeochemical model was parameterized to infer potential yields of energy cane and how changing land from grazed pasture to energy cane would affect greenhouse gas (CO₂, CH₄ and N₂O) fluxes and soil C pools. The model was used to simulate energy cane production on two soil types in central Florida, nutrient poor Spodosols and organic Histosols. Energy cane was productive on both soil types (yielding 46–76 Mg dry mass⋅ha⁻¹). Yields were maintained through three annual cropping cycles on Histosols but declined with each harvest on Spodosols. Overall, converting pasture to energy cane created a sink for GHGs on Spodosols and reduced the size of the GHG source on Histosols. This change was driven on both soil types by eliminating CH₄ emissions from cattle and by the large increase in C uptake by greater biomass production in energy cane relative to pasture. However, the change from pasture to energy cane caused Histosols to lose 4493 g CO₂ eq⋅m⁻² over 15 years of energy cane production. Cultivation of energy cane on former pasture on Spodosol soils in the southeast US has the potential for high biomass yield and the mitigation of GHG emissions.     

Leaf Spot of Alternanthera sessilis and Its Implications for Food Crops

A leaf spot of Alternanthera sessilis caused by Fusarium pallidoroseum (syn. F. semitectum) is described. During pathogenicity tests, the fungus caused leaf spots of Amarantbus sp. Abelmoschus esculentus (okra), Celosia sp. and Sorghum bicolor. It also caused rots of tubers of Dioscorea rotundata, D. alata, Solanum tuberosum, corms of Colocasia esculenta, bulbs of Allium cepa and roots of Daucus carota when wounded. Unwounded tubers, corms, bulbs and roots of these named plants were not infected except roots of Daucus carota which disintegrated between 4 and 6 days after inoculation.     

Ecosystem-Service Tradeoffs Associated with Switching from Annual to Perennial Energy Crops in Riparian Zones of the US Midwest

Integration of energy crops into agricultural landscapes could promote sustainability if they are placed in ways that foster multiple ecosystem services and mitigate ecosystem disservices from existing crops. We conducted a modeling study to investigate how replacing annual energy crops with perennial energy crops along Wisconsin waterways could affect a variety of provisioning and regulating ecosystem services. We found that a switch from continuous corn production to perennial-grass production decreased annual income provisioning by 75%, although it increased annual energy provisioning by 33%, decreased annual phosphorous loading to surface water by 29%, increased below-ground carbon sequestration by 30%, decreased annual nitrous oxide emissions by 84%, increased an index of pollinator abundance by an average of 11%, and increased an index of biocontrol potential by an average of 6%. We expressed the tradeoffs between income provisioning and other ecosystem services as benefit-cost ratios. Benefit-cost ratios averaged 12.06 GJ of additional net energy, 0.84 kg of avoided phosphorus pollution, 18.97 Mg of sequestered carbon, and 1.99 kg of avoided nitrous oxide emissions for every $1,000 reduction in income. These ratios varied spatially, from 2- to 70-fold depending on the ecosystem service. Benefit-cost ratios for different ecosystem services were generally correlated within watersheds, suggesting the presence of hotspots – watersheds where increases in multiple ecosystem services would come at lower-than-average opportunity costs. When assessing the monetary value of ecosystem services relative to existing conservation programs and environmental markets, the overall value of enhanced services associated with adoption of perennial energy crops was far lower than the opportunity cost. However, when we monitized services using estimates for the social costs of pollution, the value of enhanced services far exceeded the opportunity cost. This disparity between recoverable costs and social value represents a fundamental challenge to expansion of perennial energy crops and sustainable agricultural landscapes.