New estimates of the impacts of germplasm improvement in the major staple crops between 1965 and 2004 on global land-cover change are presented, based on simulations carried out using a global economic model (Global Trade Analysis Project Agro-Ecological Zone), a multicommodity, multiregional computable general equilibrium model linked to a global spatially explicit database on land use. We estimate the impact of removing the gains in cereal productivity attributed to the widespread adoption of improved varieties in developing countries. Here, several different effects—higher yields, lower prices, higher land rents, and trade effects—have been incorporated in a single model of the impact of Green Revolution research (and subsequent advances in yields from crop germplasm improvement) on land-cover change. Our results generally support the Borlaug hypothesis that increases in cereal yields as a result of widespread adoption of improved crop germplasm have saved natural ecosystems from being converted to agriculture. However, this relationship is complex, and the net effect is of a much smaller magnitude than Borlaug proposed. We estimate that the total crop area in 2004 would have been between 17.9 and 26.7 million hectares larger in a world that had not benefited from crop germplasm improvement since 1965. Of these hectares, 12.0–17.7 million would have been in developing countries, displacing pastures and resulting in an estimated 2 million hectares of additional deforestation. However, the negative impacts of higher food prices on poverty and hunger under this scenario would likely have dwarfed the welfare effects of agricultural expansion.
Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject to selection during improvement, we developed a high-throughput array to interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. Using a SNP-based diversity map we characterized the impact of crop improvement on genomic and geographic patterns of genetic diversity. We found evidence of a small population bottleneck and extensive use of ancestral variation often traceable to founders of cultivars from diverse geographic regions. Analyzing genetic differentiation among populations and the extent of haplotype sharing, we identified allelic variants subjected to selection during improvement. Selective sweeps were found around genes involved in the regulation of flowering time and phenology. An introgression of a wild relative-derived gene conferring resistance to a fungal pathogen was detected by haplotype-based analysis. Comparing selective sweeps identified in different populations, we show that selection likely acts on distinct targets or multiple functionally equivalent alleles in different portions of the geographic range of wheat. The majority of the selected alleles were present at low frequency in local populations, suggesting either weak selection pressure or temporal variation in the targets of directional selection during breeding probably associated with changing agricultural practices or environmental conditions. The developed SNP chip and map of genetic variation provide a resource for advancing wheat breeding and supporting future population genomic and genome-wide association studies in wheat.
It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation1. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism.
Scientists of the agency are seeking permission to cultivate a GM wheat suitable for coeliacs on a plot of Córdoba. The harvest, half a ton of grain serve to develop and carry out a clinical trial with patients. Researchers believe that the cereal could reach the market within five years...
CSIC scientists have requested permission to plant there, on a plot of 1,000 square meters, wheat whose genes have been modified so that it can be consumed by people with celiac disease, a currently incurable disease of unknown origin that affects about 1% of the world population.
When people with celiac disease consume gluten - a protein found in wheat, barley and rye - their body's defenses react and damage the intestine. As a result, there are diarrhea, vomiting and unexplained weight loss until it is given to the cause. Their only option now is to eat gluten-free foods that are more expensive. Celiacs spent each year 1,600 euros more on food than the other people. In the U.S. alone, the market for gluten-free foods moved 4,200 billion in 2012.
To remedy this, a team from the Institute of Sustainable Agriculture Cordoba, led by biologist Francisco Barro, has since 2004 investigating transgenic wheat varieties without gluten. In 2011, researchers announced that they had obtained varieties capable of producing in celiacs "a reaction up to 95% less toxic than natural wheat", according to laboratory results.
Now, Barro has asked the National Biosafety Commission for a permit to grow wheat for the first time outdoors. His goal is to harvest half a ton of grain to make crackers that will be used to conduct a clinical trial with celiacs. The test, if all goes as planned, will be held for three months with between 30 and 60 patients, who will be able to taste wheat again, until now forbidden to them, in a trial coordinated by medical Queen Sofía Hospital. The biologist believes his cereal could reach the market within five years.
Barro is aware that its GM wheat "has no chance in Europe", the continent most reluctant to genetically modified organisms. Five countries - USA, Canada, Argentina, Brazil and India - grabbing global GM production, with 152 million hectares.
Europe only allows the cultivation of two GM crops: modified corn by the U.S. company Monsanto to be resistant to insect infestation and a starch potato from German chemicals company BASF for paper and textile industries. However, following a hypocritical policy, Brussels does support importing about 40 GM products from other countries.
The CSIC has sold the license to exploit the patent for its GM wheat, to a British company, Plant Bioscience Limited, based in Norwich. "Possibly, their strategy will be to cultivate our wheat in the U.S., Argentina and China, and they will sell the flour to Spain for the price of gold", speculates Barro.
According to preliminary studies, "in the worst case, a celiac can [at least] eat every day three slices of bread made from the modified wheat". Barro team has organized a blind tasting with 11 tasters, who were unable to distinguish the normal wheat bread from the one baked with transgenic cereals.
To prevent the escape of genetically modified wheat from the plot... CSIC scientists impose a safety distance of 200 meters to any other plot with cereal. Barro considered very unlikely that there is a leak, because "wheat pollen is heavy" and cannot travel long distances on the wind.
Wheat suitable for coeliacs has its genes modified to suppress the proteins responsible for the allergic response of celiacs, gliadins. "It would be surprising that this feature gave the GM wheat a competitive advantage over the normal wheat [if it escapes]," says Barro... "There are anti-GMO environmentalists, who are celiacs, who called me to try our wheat," says Barro...
A subset of short genes hidden inside plant genomes may be important in setting plant growth patterns
Although thousands of entire genomes have been sequenced, our understanding of their detailed workings remains far from complete. Researchers continue to find new genes, determine their function, and map how they interact to build organisms. Working on the well-studied model plant Arabidopsis thaliana, Kousuke Hanada and colleagues from the RIKEN Plant Science Center have revealed that a subset of tiny genes scattered through the genome may control the patterning of development1
Despite receiving the seal of approval from scientists, genetically modified food continues to be unpalatable in many parts of the world. As Cyrus Martin reports, a combination of factors, including economics and culture, may help to explain the differences...
Why the difference in the attitude? Keith Lindsey, a plant scientist at Durham University who sits on a panel charged with advising the British government on GMO, points out that the initial reception of GM food in Europe was actually positive, but the relationship quickly soured due to a combination of suspect science and media sensationalism...
“Originally in the UK, in the mid 90s, the first GM product (Flavr Savr tomato) was very popular in the UK and elsewhere — I bought some from the local supermarket, and it sold very well at the time. The turning point was later, with some flawed experiments on GM potatoes, not peer-reviewed but seized on by the popular press, which in turn was seized on by environmentalist campaigners.”
Indeed, this same scenario seems to have played out in the case of the recent Séralini study as the panel of experts appointed by the EFSA have discredited the paper, citing a combination of small sample sizes and inadequate statistics. Unfortunately for proponents of GM food, reporting on the EFSA findings in the popular media has been scant, in contrast to when the story first broke...
The failure of Calgene was followed by a string of successes with GM crops engineered not to improve the quality of the product but to increase yields and lower costs of production. Chief among these developments was the creation of herbicide- and pest-resistant plants... Such crops are planted extensively in the US, and a global survey reveals that they have also been embraced next door in Canada and in certain South American countries. However, as noted above, GM crops are scarcely planted in Europe. [AS: But they are imported at a large scale.]
If the full history of man’s relationship with food is considered, a reasonable question to ask is whether it is rational for the consumer to put GM food in a different category than traditionally cultivated crops. As is clear in the case of the teosinte to maize transformation, our crops have undergone extensive genetic modification over the millennia, long before modern genetic tools emerged. But there seems to have been a line crossed in the consumer’s mind when it comes to transgenic plants, and the media and environmental groups have certainly helped fan these embers of doubt.
But other scientists close to the GM debate feel that, at least in Europe, there may be other mitigating factors — the economy for instance. Hanspeter Naegeli, a toxicology expert who sits on a GM advisory panel for the EFSA, says, “since the end of WWII, there has been no major economic, financial or political crisis in Western Europe and in these countries we have a very high quality of life with prosperity and a well implemented welfare system. The cost of food declined enormously when compared to the overall costs of living such that people are not dependent on a cheap agricultural production and can afford to buy more expensive products (i.e. organic food).”
Coupled to a favourable economic climate in which the consumer can afford to turn their nose up at a genetically modified potato, Naegeli senses an anti-big business current running through Europe, explaining, “there is also a negative attitude against large multinational companies. The economies of Western European countries are traditionally built upon small and medium-sized enterprises and larger international companies are considered suspicious.” Ironically, Naegeli thinks that the stranglehold that big business enjoys is also a product of the reforms environmentalists lobbied for, explaining that, “because of the extensive experimental testing required for approval, GM crops are mainly a domain of such large multinationals.” ...
As with any technology, at some point there has to be a cost/benefit analysis done. While all of the food safety scares surrounding GM food continue to be debunked as fast as they materialize, there are no doubt potential risks that are not yet fully understood, as can be seen in the ecology aspect of the debate. And there is nothing to say that new varieties of GM food could, in principle, potentially be harmful. On the other side of the ledger, however, we have the enormous challenge of feeding the world’s population, which is rapidly growing on a planet with finite resources. Of course, malnourishment has many causes, including local politics and war, but agricultural technology will certainly factor importantly.
And GM food has lived up to its promise of providing increased yields with less pesticide use and at a lower cost to the consumer. Not only this, but genetic engineering has the potential to provide much needed micronutrients (i.e., vitamins) to the malnourished of the world. A case in point is the recent development of an engineered form of rice that produces a precursor of vitamin A, dubbed ‘golden rice’. This remarkable and easily implementable technology has the potential to mitigate hundreds of thousands of cases of blindness in the developing world, and yet it remains shelved due to unsubstantiated health concerns.
Many western consumers can afford to stock their refrigerators with organic produce, but can the rest of the world? Do the potential risks really trump malnourishment and starvation? While the interested parties continue to debate, science marches on. On the horizon are GM crops that can grow in inhospitable corners of the earth, such as the dry and salty environs. And we are now seeing the application of GM technology to animals, such as salmon engineered to reach market weight more quickly through the expression of genes encoding growth hormones. Whether these technologies are taken up or left to gather dust on the shelf will likely depend on the ability of scientists and the government to make a convincing case to the public. If they fail, we potentially handcuff ourselves and will be forced to rely on 20th century technology to solve 21st century problems.
An international team, led by Dr. Zhangjun Fei at the Boyce Thompson Institute for Plant Research, Dr. Yongsheng Liu at Hefei University of Technology and Dr. Hongwen Huang at South China Botanical Garden, has sequenced and assembled a draft genome of kiwifruit (Actinidia chinensis). A heterozygous diploid Chinese kiwifruit variety, called Hongyang, was used to generate the draft genome sequence, which is accessible at the online Kiwifruit Genome Database (http://bioinfo.bti.cornell.edu/kiwi).
Improving the efficiency of root systems should result in crop varieties with better yields, requiring fewer chemical inputs, and that can grow in harsher environments. Little is known about the genetic factors that condition root growth because of roots’ complex shapes, the opacity of soil, and environmental influences. We designed a 3D root imaging and analysis platform and used it to identify regions of the rice genome that control several different aspects of root system growth. The results of this study should inform future efforts to enhance root architecture for agricultural benefit.
The Conifer Genomics Learning Modules are a series of presentations and supporting materials that describe the field of conifer genomics. The series includes genetics foundation materials as well as more advanced materials on topics of tree genomics. Modules in this series are meant to be integrated into genetics curricula for high school, college, and post-graduate learners.
The relationship between solar radiation capture and potential plant growth is of theoretical and practical importance. The key processes constraining the transduction of solar radiation into phyto-energy (i.e. free energy in phytomass) were reviewed to estimate potential solar-energy-use efficiency. Specifically, the out-put : input stoichiometries of photosynthesis and photorespiration in C3 and C4 systems, mobilization and translocation of photosynthate, and biosynthesis of major plant biochemical constituents were evaluated. The maintenance requirement, an area of important uncertainty, was also considered. For a hypothetical C3 grain crop with a full canopy at 30°C and 350 ppm atmospheric [CO2], theoretically potential efficiencies (based on extant plant metabolic reactions and pathways) were estimated at c. 0.041 J J−1 incident total solar radiation, and c. 0.092 J J−1 absorbed photosynthetically active radiation (PAR). At 20°C, the calculated potential efficiencies increased to 0.053 and 0.118 J J−1 (incident total radiation and absorbed PAR, respectively). Estimates for a hypothetical C4 cereal were c. 0.051 and c. 0.114 J J−1, respectively. These values, which cannot be considered as precise, are less than some previous estimates, and the reasons for the differences are considered. Field-based data indicate that exceptional crops may attain a significant fraction of potential efficiency.
The phytohormone auxin regulates virtually every aspect of plant development. To identify new genes involved in auxin activity, a genetic screen was performed for Arabidopsis mutants with altered expression of the auxin responsive reporter DR5rev:GFP. One of the mutants recovered in the screen, designated as weak auxin response 3 (wxr3), exhibits much lower DR5rev:GFP expression when treated with the synthetic auxin, 2,4-D, and displays severe defects in root development. The wxr3 mutant decreases polar auxin transport and results in a disruption of the asymmetric auxin distribution. The level of the auxin transporters, AUX1 and PINs, is dramatically reduced in the wxr3 root tip. Molecular analyses demonstrate that WXR3 is ROOT UV-B SENSITIVE1 (RUS1), a member of the conserved DUF647 protein family found in diverse eukaryotic organisms. Our data suggests that RUS1/WXR3 plays an essential role in the regulation of polar auxin transport by maintaining the proper level of auxin transporters on the plasma membrane.
Sixty seven pages, twenty seven figures, but still very readable. If you ever teach about transport or homeostasis, add this comprehensive update to your folder.
As the title indicates, this big review pulls together the latest information on the evolution, development and functions of the plant vascular system (including its role as an effective long-distance communication system).
Colorado State University will offer a one-credit online course in Plant Breeding for Drought Tolerance August 26 to December 13, 2013. Course instructor is Dr. Patrick Byrne, Department of Soil and Crop Sciences.
This distance course is targeted to graduate students in the plant sciences, as well as to professionals in the public and private sectors who want to increase their knowledge in this area. It will provide one transferable graduate-level credit.
The course will focus on plant breeding strategies and practices directed toward improving plant performance under drought stress. Concepts for this intensive, one-credit graduate level course include: • Analyzing the target environment • Understanding plant response to drought stress and plant adaptation strategies • Using wild species and landraces as sources of drought tolerance • Determining which phenotypic traits to use in selection practices • Detecting marker-trait associations for relevant traits • Understanding transgenic approaches to drought tolerance • Learning from successful examples of improving drought tolerance in a variety of crops
The 15-week curriculum is divided into 15 lessons. Each lesson's content will be delivered via a voice-over PowerPoint presentation, a video, a reading assignment, or combinations of these media. Some lessons will require student participation in an online discussion, completion of an online quiz, or submission of a homework assignment. The compiled homework assignments will comprise a portfolio of documents describing an analysis and breeding strategy for a specific crop and environment. There will be a comprehensive final exam administered during the week of December 16.
Participants should have a basic understanding of genetics, plant breeding, and plant physiology. Prior to the beginning of the course, students will review online material on these topics to provide a common background in breeding and physiology concepts.
PROGRAM COSTS AND REQUIREMENTS
The cost of student tuition is US $549 plus a $20 technology fee. Word processing, spreadsheet, and presentation software (e.g., Microsoft Word, Excel, and PowerPoint) is required, as is Adobe Reader. Students are required to have access to a computer and Internet access that meet the general CSU recommendations.
Figure 1: Mutant rice plants without the CYP714B1 andCYP714B2 genes (right) show enhanced uppermost node lengths, indicating that these genes are negative regulators of growth.
Andres Zurita's insight:
Finding the missing genes in a hormone-biosynthesis pathway hints at subtle control of growth in rice
The plant hormones known as gibberellins (GAs) are growth promoters that are involved in a wide range of processes from seed germination to flower development. The details of the biosynthesis of GAs, however, have yet to be fully clarified. Hiroshi Magome and colleagues of the Gene Discovery Research Group at the RIKEN Center for Sustainable Resource Science have now identified genes for two ‘cytochrome P450’ enzymes involved in GA biosynthesis in rice1. 1. Magome, H., Nomura, T., Hanada, A., Takeda-Kamiya, N., Ohnishi, T., Shinma, Y., Katsumata, T., Kawaide, H., Kamiya, Y. & Yamaguchi, S. CYP714B1 and CYP714B2 encode gibberellin 13-oxidases that reduce gibberellin activity in rice. Proceedings of the National Academy of Sciences USA 110, 1947–1952 (2013).
The introduction of the first transgenic plant 30 years ago heralded the start of a second green revolution, providing food to the starving, profits to farmers and environmental benefits to boot. Many GM crops fulfilled the promise. But their success has been mired in controversy with many questioning their safety, their profitability and their green credentials. A polarized debate has left little room for consensus. In this special issue, Nature explores the hopes, the fears, the reality and the future.
SummaryDeficiency of abscisic acid (ABA) in the sitiens mutant of tomato (Solanum lycopersicum) culminates in increased resistance to Botrytis cinerea through a rapid epidermal hypersensitive response (HR) and associated phenylpropanoid pathway-derived cell wall fortifications. This study focused on understanding the role of primary carbon : nitrogen (C : N) metabolism in the resistance response of sitiens to B. cinerea. How alterations in C : N metabolism are linked with the HR-mediated epidermal arrest of the pathogen has been also investigated.Temporal alterations in the γ-aminobutyric acid (GABA) shunt, glutamine synthetase/glutamate synthase (GS/GOGAT) cycle and phenylpropanoid pathway were transcriptionally, enzymatically and metabolically monitored in both wild-type and sitiens plants. Virus-induced gene silencing, microscopic analyses and pharmacological assays were used to further confirm the data.Our results on the sitiens–B. cinerea interaction favor a model in which cell viability in the cells surrounding the invaded tissue is maintained by a constant replenishment of the tricarboxylic acid (TCA) cycle through overactivation of the GS/GOGAT cycle and the GABA shunt, resulting in resistance through both tightly controlling the defense-associated HR and slowing down the pathogen-induced senescence.Collectively, this study shows that maintaining cell viability via alterations in host C : N metabolism plays a vital role in the resistance response against necrotrophic pathogens.
Yijun Ruan and colleagues report the draft genome of the sweet orange, Citrus sinensis. Their data suggests sweet orange originated from a cross between pummelo and mandarin.
Andres Zurita's insight:
Oranges are an important nutritional source for human health and have immense economic value. Here we present a comprehensive analysis of the draft genome of sweet orange (Citrus sinensis). The assembled sequence covers 87.3% of the estimated orange genome, which is relatively compact, as 20% is composed of repetitive elements. We predicted 29,445 protein-coding genes, half of which are in the heterozygous state. With additional sequencing of two more citrus species and comparative analyses of seven citrus genomes, we present evidence to suggest that sweet orange originated from a backcross hybrid between pummelo and mandarin. Focused analysis on genes involved in vitamin C metabolism showed that GalUR, encoding the rate-limiting enzyme of the galacturonate pathway, is significantly upregulated in orange fruit, and the recent expansion of this gene family may provide a genomic basis. This draft genome represents a valuable resource for understanding and improving many important citrus traits in the future.
Molecular, genetic, and electrophysiological evidence indicates that at least one of the plant Glu receptor-like molecules, GLR3.4, functions as an amino acid–gated Ca2+ channel at the plasma membrane. The aspect of plant physiology, growth, or development to which GLR3.4 contributes is an open question. Protein localization studies performed here provide important information. In roots, GLR3.4 and the related GLR3.2 protein were present primarily in the phloem, especially in the vicinity of the sieve plates. GLR3.3 was expressed in most cells of the growing primary root but was not enriched in the phloem, including the sieve plate area. GLR3.2 and GLR3.4 physically interacted with each other better than with themselves as evidenced by a biophotonic assay performed in human embryonic kidney cells and Nicotiana benthamiana leaf cells. GLR3.3 interacted poorly with itself or the other two GLRs. Mutations in GLR3.2, GLR3.4, or GLR3.2and GLR3.4 caused the same and equally severe phenotype, namely, a large overproduction and aberrant placement of lateral root primordia. Loss of GLR3.3did not affect lateral root primordia. These results support the hypothesis that apoplastic amino acids acting through heteromeric GLR3.2/GLR3.4 channels affect lateral root development via Ca2+ signaling in the phloem.
Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala × Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r2 = 24-37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops.