From the 1950s to 1970s, in an effort to combat world hunger, plant breeders at the International Rice Research Institute (IRRI) in the Philippines developed new rice varieties that were, when fertilized, higher yielding than traditional varieties. The new varieties were shorter and less likely to fall over, which made them easier to harvest mechanically. They also ripened sooner, reducing the risk of poor weather affecting yield, and enabling farmers to harvest and replant several times during the growing season. While successful in many areas, the new varieties required more money for fertilizer and chemical pesticides, and in some cases, machines for sowing and harvesting—tools often too costly for peasant farmers. In some areas a single new rice variety replaced diverse, centuries-old varieties adapted to thrive in a particular climate and soil type and with some resistance to local insects and diseases. The new variety was not able to thrive in these areas, and the crop yields were not always greater.
Asian countries produced about 90 percent of the 576 million tons of rice grown worldwide in 2002. Typically, China and India together produce about 50 percent of the world’s rice, and it is a significant agricultural crop in more than 50 other countries. About 96 percent of the rice grown worldwide is consumed in the countries where it is produced, with some exceptions. The United States, for example, exported about 37 percent of the 8.7 million tons it produced in 2000, and Pakistan exported about 28 percent of its 7.2 million tons, according to the FAO. In the same year, Thailand exported significantly more rice than any other country—6.6 million tons, or about 26 percent of its total, while India exported 1.5 million tons, or about 1.1 percent of total production. Major rice-importing countries include Côte d'Ivoire, Nigeria, Philippines, Iran, Saudi Arabia, Brazil, Senegal, Japan, and Indonesia. Some rice-importing countries buy rice on a regular basis, others buy when drought, floods, or other conditions reduce the yield of their own rice crop.
Decades of physiological investigation have resulted in the identification of several distinct ‘response modes’, based on photobiological criteria (for review see Smith, 1995). The classical phytochrome-mediated response, first demonstrated by the pioneering studies of Sterling Hendricks, Harry Borthwick and their colleagues in the 1950s (Borthwick et al., 1952) is the low fluence response (LFR). LFRs (such as the stimulation of seed germination, the inhibition of seedling elongation and the control of flowering by night breaks) are saturated by low fluences of R and reversed by similarly low fluences of FR.All three of these response modes (LFR, VLFR, HIR) can, and often are, involved in the control of germination and de-etiolation. Also, the role of the phytochromes in photoperiodism involves interaction with the circadian rhythms, and can take the form of either an LFR or HIR. Finally, phytochromes regulate growth and flowering in mature plants in the natural environment via a R:FR ratio response. A wide range of phenomena, including elongation growth and the rate of flowering (separately from the induction of flowering), exhibit a direct linear relationship to the proportion of Pfr established by the incident radiation (Smith, 1983, 1995, 2000). These R:FR ratio responses, which are the basis of proximity perception and shade avoidance, may indicate a quite separate response mode, or may represent a sub-set of LFR responses conditioned by acting within the environment of light-grown tissues.
Relating the different response modes to the individual phytochromes became possible with the generation of null mutants that lack functional phytochromes (for review, see Whitelam and Devlin, 1997). The conclusion from many mutant studies is that the VLFR and the FR–HIR are both mediated by phyA, whereas the LFR is mediated predominantly by phyB. Furthermore, the R:FR ratio responses are mediated predominantly by phyB, with supplementary action by phyD and phyE. These discoveries opened the way to exploiting our knowledge of the individual functions of the members of the phytochrome family by transgenic over-expression of the PHY genes. Over-expression has been important for fundamental objectives, to analyse the molecular actions of the phytochromes and to help elucidate signal transduction pathways, but increasingly transgenic methods are being applied towards the improvement of crop plant performance.
The phytochromes are a family of photoreceptors that absorb radiation across the 600–800 nm waveband. The 600–700 nm band is conventionally referred to as red light (R) while the 700–800 nm band as far-red (FR). Each phytochrome can exist in two photoconvertible conformers: Pr has an absorption maximum at ca. 665 nm and is converted to Pfr, which absorbs maximally at ca. 730 nm, being thereby converted back to Pr. The overall scheme, first worked out by Sterling Hendricks and Harry Borthwick, with their colleagues at Beltsville in the 1940s and 1950s on the basis of supremely elegant physiological experiments, is as follows:
Both Pr and Pfr have relatively broad absorption bands and these overlap below ca. 700 nm; this means that in broad-band irradiation, such as daylight, Pr and Pfr are continually being inter-converted resulting in a dynamic equilibrium, known as the phytochrome photoequilibrium, which is a quantitative function of the relative amounts of R and FR incident upon the plant. The photoequilibrium is conventionally expressed numerically as a proportion of the total phytochrome present as Pfr, or Pfr/P. The roles and mechanisms of Pr and Pfr have been investigated almost entirely by reductionist approaches, growing plants in darkness and exposing them to brief or prolonged irradiation from narrow-beam sources. For over fifty years this research has been and continues to be a tour de force of modern biology, and the knowledge accrued can now be applied to the infinitely more complex situations where plants growing in a natural environment are subject to continuous and often rapid fluctuations in light signals over a wide wavelength range.
The phytochromes are encoded by a small multi-gene family comprising five genes in Arabidopsis but possibly only three in the cereals (Mathews et al., 1996). The five Arabidopsis phytochromes are known as phytochrome A (phyA) to phytochrome E (phyE). Prior to molecular characterisation, phytochromes were classified into two main pools, based on their biochemical and kinetic characteristics as determined from in vivo and in vitro spectrophotometry. The so-called type I phytochrome is the predominant phytochrome present in etiolated seedlings, the first to be identified and still the most completely characterised. It is described as being ‘light-labile’, although it is only the Pfr form which is labile; thus type I phytochromes are also labile in the dark as long as Pfr has been previously generated.
Degradation half-lives of Pfr are typically around 20–45 minutes, and thus Pfr is essentially absent from plants exposed to more than ca. 24 hours of white light. Phytochrome A (phyA) is the only known representative of the type I phytochrome pool. In etiolated seedlings and dark-grown tissues phyA accumulates to relatively high levels in the Pr form. Exposure to light causes rapid loss of phyA, not only through degradation of Pfr
In contrast, type II phytochromes are present in low steady-state concentrations in both dark-grown and light-grown plants because the Pfr forms are relatively stable (Furuya and Schäfer, 1996). All other members of the phytochrome family, that is, phyB to phyE, have these characteristics and are thus regarded as type II phytochromes. PhyB to phyE are synthesised slowly and appear not to be under such strict transcriptional regulation as phyA. In most cases studied, phyB is the predominant phytochrome in light-grown plants. As phytochrome action is a function of the concentration of Pfr, regulation of the rates of synthesis and degradation of the individual phytochromes is clearly crucial in determining the physiological response. It follows that attempts to regulate development by the transgenic expression of phytochrome genes must take account of the rates of synthesis and degradation of the transgene products.
Plant Biotechnology Field of DreamsThe field of plant biotechnology is concerned with developing ways to improve theproduction of plants in order to supply the world’s needs for food, fiber and fuel. Inaddition, plants provide us with many pharmaceuticals and industrial compounds. As ourpopulation grows, our needs also grow.
Nicoletta Rascioa, 
, 
and Flavia Navari-IzzobThe term “hyperaccumulator” describes a number of plants that belong to distantly related families, but share the ability to grow on metalliferous soils and to accumulate extraordinarily high amounts of heavy metals in the aerial organs, far in excess of the levels found in the majority of species, without suffering phytotoxic effects. Three basic hallmarks distinguish hyperaccumulators from related non-hyperaccumulating taxa: a strongly enhanced rate of heavy metal uptake, a faster root-to-shoot translocation and a greater ability to detoxify and sequester heavy metals in leaves. An interesting breakthrough that has emerged from comparative physiological and molecular analyses of hyperaccumulators and related non-hyperaccumulators is that most key steps of hyperaccumulation rely on different regulation and expression of genes found in both kinds of plants. In particular, a determinant role in driving the uptake, translocation to leaves and, finally, sequestration in vacuoles or cell walls of great amounts of heavy metals, is played in hyperaccumulators by constitutive overexpression of genes encoding transmembrane transporters, such as members of ZIP, HMA, MATE, YSL and MTP families. Among the hypotheses proposed to explain the function of hyperaccumulation, most evidence has supported the “elemental defence” hypothesis, which states that plants hyperaccumulate heavy metals as a defence mechanism against natural enemies, such as herbivores. According to the more recent hypothesis of “joint effects”, heavy metals can operate in concert with organic defensive compounds leading to enhanced plant defence overall.
Heavy metal contaminated soils pose an increasing problem to human and animal health. Using plants that hyperaccumulate specific metals in cleanup efforts appeared over the last 20 years. Metal accumulating species can be used for phytoremediation (removal of contaminant from soils) or phytomining (growing plants to harvest the metals). In addition, as many of the metals that can be hyperaccumulated are also essential nutrients, food fortification and phytoremediation might be considered two sides of the same coin. An overview of literature discussing the phytoremediation capacity of hyperaccumulators to clean up soils contaminated with heavy metals and the possibility of using these plants in phytomining is presented.
'Being able to understand and ultimately control seasonal flowering will enable more predictable flowering, better scheduling and reduced wastage of crops', explained Dr Jackson.
Whilst the relationship between CONSTANS and flowering time in response to day length is well established, the mechanism controlling the expression of CONSTANS is still not fully understood.
The scientists present their work at the Society for Experimental Biology Annual Meeting in Prague on Wednesday 30th June 2010.
Many plants control when they flower to coincide with particular seasons by responding to the length of the day, a process known as photoperiodism. A flowering mutant of Arabidopsis, which had an altered response to photoperiod, was used in the study led by Dr Stephen Jackson.
In the study funded by the BBSRC, the team identified the defective gene in the mutant plant that caused its abnormal flowering time.
They then cloned a working version of the gene, known as DAY NEUTRAL FLOWERING (DNF), from a normal Arabidopsis plant and introduced it into the mutant plant to restore its normal flowering response to day length.
The role of DNF in normal plant flowering is to regulate the CONSTANS gene. CONSTANS is activated only in the light and the plant is triggered to flower when CONSTANS levels rise above a certain threshold level during the daytime.
In normal plants, DNF represses the levels of CONSTANS until the day length is long enough and conditions are favourable for the survival of their seedlings. In mutant plants without an active DNF gene, CONSTANS is not repressed and they are able to flower earlier in the year, when days are still short.
The presence of the DNF gene has not yet been identified in species other than Arabidopsis but the scientists believe their on-going work may prove to have a wider significance for other species.
Scientists can override complex pathways that control flowering by artificially inducing or inhibiting key flowering genes such as DNF and CONSTANS. This can already be done in the laboratory by spraying an 'inducing agent' onto plants, stimulating them to flower early.
This could be used to extend the length of the harvesting season or to co-ordinate flowering or fruit production to a specific time. Growers already regulate the flowering of a few plants such as Chrysanthemum and Poinsettia, the latter specifically for Christmas and Easter.
Unravelling the complex pathways that control plant flowering will help scientists to understand and influence flowering patterns more effectively and in many different species.
Provided by Society for Experimental Biology
"Global reserves of phosphate are critically low, and because the demand for phosphate goes hand in hand with human population expansion, it is predicted that there will be major shortages in the next few decades," said Ian Sanders of the University of Lausanne in Switzerland. "Unfortunately, most of our important crop plants do not respond strongly, if at all, to inoculation with these fungi. This is especially so for rice, the most globally important food plant. There are no clear reports that rice benefits from inoculation with mycorrhizal fungi."
That is, until now. In fact, the researchers started with a strain of mycorrhizal fungus of the species Glomus intraradices that clearly didn't benefit rice. They then took advantage of the fungus's unusual genetics. A single fungal filament can contain genetically distinct nuclei. Those distinct nuclei can fuse together, mixing genes up in different combinations, and fungal spores can also end up with different complements of genes, the new research shows. As such, the supposedly clonal fungi maintain a degree of genetic variation that had been overlooked.
"It turns out we can very simply manipulate their genetics to produce fungi that induce up to a five-fold growth increase in this globally important food plant," Sanders said.
The genetic changes that the researchers produced in the fungi led to changes in the activity of important genes in the rice, they report. Those affected genes are known to be involved in establishing the mutually beneficial relationship between plant and fungus and in the transport of phosphate at the interface between fungus and plant.
Sanders emphasized that the genetic manipulation the researchers undertook didn't involve any insertion of new genes into the fungal genome. It rather relied on the same biological processes of genetic exchange and segregation that normally take place in the fungus. "What we have done with these fungi is not much different from what plant breeders, and farmers before them, have done to improve crops," he said. "The only difference is that the genetics of these fungi is a little bit more unusual, and no one thought it worth doing."
On a cautionary note, Sanders did emphasize that the plants they studied were grown in a greenhouse in Switzerland under conditions that only mimicked those found in the tropics. "This is clearly not at all the same environment as a rice plant growing in a real paddy field," he said. It remains to be seen whether the same growth benefits will apply in practice.
"However," Sanders said, "our study clearly shows that the potential is there to manipulate the genetics of the fungus to achieve greater crop yields."
More information: Angelard et al.: “Report: Segregation in a Mycorrhizal Fungus Alters Rice Growth and Symbiosis-Specific Gene Transcription.” Publishing in Current Biology 20, 13, July 13, 2010. DOI 10.1016/j.cub.2010.04.043
Provided by Cell Press
University of Illinois researchers are studying the impact of elevated carbon dioxide, elevated ozone and higher atmospheric temperatures on plant diseases that could challenge crops in these changing conditions.
Darin Eastburn, U of I associate professor of crop sciences, evaluated the effects of elevated carbon dioxide and ozone on three economically important soybean diseases under natural field conditions at the soybean-free air-concentrating enrichment (SoyFACE) facility in Urbana.
The diseases downy mildew, Septoria brown spot, and sudden death syndrome were observed from 2005 to 2007 using visual surveys and digital image analysis. While changes in atmospheric composition altered disease expression, the responses of the three pathosystems varied considerably, Eastburn said.
Elevated carbon dioxide levels are more likely to have a direct effect on plant diseases through changes to the plant hosts rather than the plant pathogens.
"Plants growing in a high carbon dioxide environment tend to grow faster and larger, and they have denser canopies," Eastburn said. "These dense plant canopies favor the development of some diseases because the low light levels and reduced air circulation allow higher relative humidity levels to develop, and this promotes the growth and sporulation of many plant pathogens."
At the same time, plants grown in high carbon dioxide environments also close their stomata, pores in the leaves that allow the plant to take in carbon dioxide and release oxygen, more often. Because plant pathogens often enter the plant through the stomata, the more frequent closing of the stomata may help prevent some pathogens from getting into the plant.
In elevated ozone, plant growth is inhibited and results in shorter plants with less dense canopies. This can slow the growth and reproduction of certain pathogens. However, ozone also damages plant tissues that can help pathogens infect the plant more easily.
"Elevated levels of carbon dioxide and ozone can make a plant more susceptible to some diseases, but less susceptible to others," Eastburn said. "This is exactly what we've observed in our climate change experiments."U of I's SoyFACE was the first facility to expose plants to elevated ozone under completely open-air conditions within an agricultural field.
"The SoyFACE facility allowed us to evaluate the influence of natural variability of meteorological factors such as drought and temperature in conjunction with imposed atmospheric composition (elevated carbon dioxide and ozone) on naturally occurring soybean diseases across several growing seasons," Eastburn said.
He believes rising temperatures and changes in rainfall patterns will also affect development of plant disease epidemics.
"In some cases, changes of only a few degrees have allowed plant diseases to become established earlier in the season, resulting in more severe disease epidemics," Eastburn said. "The ranges of some diseases are expanding as rising temperatures are allowing pathogens to overwinter in regions that were previously too cold for them."
For example, warmer winters may allow kudzu to expand its range northward. Because kudzu is an alternate host for the soybean rust pathogen, one result of rising temperatures may be that soybean rust arrives in Illinois earlier in the soybean growing season, Eastburn said.
"Information derived from climate change studies will help us prepare for the changes ahead by knowing which diseases are most likely to become more problematic," he said. "Now is the time for plant pathologists, plant breeders, agronomists and horticulturalists to adapt disease management strategies to the changing environment."
Eastburn's soybean research, "Elevated atmospheric carbon dioxide and ozone alter soybean diseases at SoyFACE," was recently published in Global Change Biology. Researchers also included Melissa DeGennaro and Evan DeLucia of the U of I, Orla Dermody of Pioneer Hi-Bred Switzerland, and Andrew McElrone of the University of California - Davis.
