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Rescooped by Neelam Redekar from ESRC press coverage
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Oak health and Phytophthora control projects get £2m

Oak health and Phytophthora control projects get £2m | Research | Scoop.it
Oak health and Phytophthora control projects get £2m - from Horticulture Week

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ESRC's curator insight, March 11, 7:28 AM

ESRC is a co-funder of this prroject

Rescooped by Neelam Redekar from Publications from The Sainsbury Laboratory
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BMC Genomics: The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression (2016)

BMC Genomics: The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression (2016) | Research | Scoop.it
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The Sainsbury Lab's curator insight, May 26, 4:58 AM
Understanding how plants and pathogens modulate gene expression during the host-pathogen interaction is key to uncovering the molecular mechanisms that regulate disease progression. Recent advances in sequencing technologies have provided new opportunities to decode the complexity of such interactions. In this study, we used an RNA-based sequencing approach (RNA-seq) to assess the global expression profiles of the wheat yellow rust pathogen Puccinia striiformis f. sp. tritici (PST) and its host during infection.
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bioRxiv: The potato NLR immune receptor R3a does not contain non-canonical integrated domains (2016)

bioRxiv: The potato NLR immune receptor R3a does not contain non-canonical integrated domains (2016) | Research | Scoop.it

A recent study by Kroj et al. (New Phytologist, 2016) surveyed nucleotide binding-leucine rich repeat (NLR) proteins from plant genomes for the presence of extraneous integrated domains that may serve as decoys or sensors for pathogen effectors. They reported that a FAM75 domain of unknown function occurs near the C-terminus of the potato late blight NLR protein R3a. Here, we investigated in detail the domain architecture of the R3a protein, its potato paralog R3b, and their tomato ortholog I2. We conclude that the R3a, R3b, and I2 proteins do not carry additional domains besides the classic NLR modules, and that the FAM75 domain match is likely a false positive among computationally predicted NLR-integrated domains.


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Nature Biotech: News & Views - Plant immunity switched from bacteria to virus (2016)

Nature Biotech: News & Views - Plant immunity switched from bacteria to virus (2016) | Research | Scoop.it
Each year, staple crops around the world suffer massive losses in yield owing to the destructive effects of pathogens. Improving the disease resistance of crops by boosting their immunity has been a key objective of agricultural biotech ever since the discovery of plant immune receptors in the 1990s. Nucleotide-binding leucine-rich repeat (NLR) proteins, a family of intracellular immune receptors that recognize pathogen molecules, are promising targets for enhancing pathogen resistance. In a recent paper in Science, Kim et al.1 describe a clever twist on this approach in which the host target protein for the pathogen effector is engineered rather than the NLR protein itself.

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Wigwams: identifying gene modules co-regulated across multiple biological conditions

Wigwams: identifying gene modules co-regulated across multiple biological conditions | Research | Scoop.it

Wigwams is a simple and efficient method to identify gene modules showing evidence for co-regulation in multiple time series of gene expression data. Wigwams analyzes similarities of gene expression patterns within each time series (condition) and directly tests the dependence or independence of these across different conditions. The expression pattern of each gene in each subset of conditions is tested statistically as a potential signature of a condition-dependent regulatory mechanism regulating multiple genes. Wigwams does not require particular time points and can process datasets that are on different time scales. Differential expression relative to control conditions can be taken into account. The output is succinct and non-redundant, enabling gene network reconstruction to be focused on those gene modules and combinations of conditions that show evidence for shared regulatory mechanisms. Wigwams was run using six Arabidopsis time series expression datasets, producing a set of biologically significant modules spanning different combinations of conditions.


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Katherine Denby's curator insight, April 14, 2014 9:36 AM

A useful tool for identifying statistically significant sets of genes likely to be co-regulated across multiple time series data sets.

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How to read a scientific paper / How to read a paper in Plant Physiology

How to read a scientific paper / How to read a paper in Plant Physiology | Research | Scoop.it

We posted these last year and have had excellent feedback.

"How to Read a Scientific Paper"

(https://journalaccess.aspb.org/ReadaSciPaper/How%20to%20Read%20a%20Scientific%20Paper%20M%20Williams%20Mar%202013.pdf)

 

"How to read a paper in Plant Physiology"

https://journalaccess.aspb.org/CaseStudy/CaseStudy%20for%20How%20to%20Read%20a%20Sci%20Paper%20M%20Williams%20Mar%202013.pdf


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Lab to Farm: Applying Research on Plant Genetics and Genomics to Crop Improvement - Ronald (2014) - PLoS Biol

Over the last 300 years, plant science research has provided important knowledge and technologies for advancing the sustainability of agriculture... potential for current and future contribution of plant genetic improvement technologies to continue to enhance food security and agricultural sustainability.

 

The Earth's human population is expected to increase from the current 6.7 billion to 9 billion by 2050. To feed the growing population, and the 70% increase in the demand for agricultural production that is expected to accompany this increase, a broad range of improvements in the global food supply chain is needed.

 

There are significant opportunities in plant science research. For example, sustainable agricultural intensification will be important because maintaining current per capita food consumption with no increase in yield, and no decrease in post-harvest and food waste, would necessitate a near doubling of the world's cropland area by 2050. However, because most of the Earth's arable land is already in production and what remains is being lost to urbanization, salinization, desertification, and environmental degradation, cropland expansion is not a viable approach to food security.

 

Furthermore, because substantial greenhouse gases are emitted from agricultural systems... the development and deployment of high-yielding crop varieties will make a vital future contribution to sustainable agriculture because it does not rely on expanding cropland.

 

Water systems are also under severe strain across the world... Of the water that is available for use, about 70% is already used for agriculture. Many rivers no longer flow all the way to the sea; 50% of the world's wetlands have disappeared and major groundwater aquifers are being mined unsustainably... Thus, increased food production must largely take place on the same land area while using less water...

 

Compounding the challenges facing agricultural production are the predicted effects of climate change. As the sea level rises and glaciers melt, low lying croplands will be submerged and river systems will experience shorter and more intense seasonal flows. Yields of our most important food, feed, and fiber crops decline precipitously at temperatures much above 30°C, so heat and drought will also increasingly limit crop production.

 

In addition to these environmental stresses, losses to pests and diseases are also expected to increase. Much of the loss caused by these abiotic and biotic stresses, which already result in 30%–60% yield reductions globally each year, occur after the plants are fully grown; a point at which most or all of the land and water required to grow a crop has been invested. For this reason, a reduction in losses to pests, pathogens, and environmental stresses is equivalent to creating more land and more water.

 

Another important opportunity for increasing food availability is to reduce the amount of food wasted before and after it reaches the consumer (estimated at 30%–50% of total global production)... A reduction in meat consumption would contribute to increasing the food supply, because 1 hectare of land can produce rice or potatoes for 19-22 people per year whereas the same area will produce enough meat for only 1-2 people.

 

Augmentation of the nutritional quality of crops is also critical for global food security... Currently, there are 925 million people who are undernourished... The long-term effects of malnutrition include stunted growth, learning disabilities, poor health, and chronic disease in later life... Discoveries in plant genetic and genomics research can be translated to create new crops and cropping systems that more efficiently use finite resources and that can enhance the quality and quantity of food production...

 

For 10,000 years, we have altered the genetic makeup of our crops, first through primitive domestication and, in the last 300 years, using more sophisticated approaches... Mutagenesis—the introduction of random mutations by chemical treatment or radiation, and the interbreeding of related species... Today virtually everything we eat is produced from seeds that have been genetically altered in one way or another using these well-established approaches of genetic improvement... 

 

Over the last 20 years, scientists and breeders have used new genetic technologies to develop modern crop varieties. These include marker assisted selection (MAS) and genetic engineering (GE), which have both already led to the development of new crop varieties... 

 

To understand why some farmers have embraced GE crops and how they benefit the environment, consider Bt cotton, which contains a bacterial protein called Bt that kills pests, such as the cotton bollworm, without harming beneficial insects and spiders. Bt is benign to humans, which is why organic farmers have used Bt sprays and other formulations as their primary method of pest control for 50 years. Although Bt insecticides are permitted in organic farming, Bt crops are not, because the National Organic Program standards in the US and other countries prohibit the use of GE crops in organic agriculture.

 

In 2012, 70%–90% of American, Indian, and Chinese farmers grew Bt cotton... Widespread planting of Bt cotton in China drastically reduced the use of synthetic insecticides, increased the abundance of beneficial organisms on farms, and decreased populations of crop-damaging insects. Its cultivation in China has also reduced pesticide poisoning in farmers and their families. US farms that have cultivated Bt cotton have twice the insect biodiversity relative to neighboring conventional farms. In India, farmers growing Bt cotton increased their yields by 24%, their profits by 50%, and raised their living standards by 18%... The economic benefits of planting Bt cotton extend beyond the farm and into the community... 

 

Despite the considerable and continuing breakthroughs in plant genetic and genomic technologies, there has been relatively little global government investment into funding basic plant science and in translating these discoveries into food crops beneficial to farmers in less developed countries. To fill the gap, some foundations and public–private partnerships have launched programs. For example, the Bill and Melinda Gates Foundation is supporting a large program, called Stress-Tolerant Rice for Africa and South Asia... 

 

The Rockefeller Foundation was instrumental in funding the development of Golden Rice, a genetically engineered rice enriched for provitamin A that is expected to be released soon. Worldwide, over 124 million children are vitamin A-deficient; many go blind or become ill from diarrhea, and nearly 8 million preschool-age children die each year as the result of this deficiency... Eating vitamin A rice could prevent the deaths of thousands of young children each year. The positive effects of Golden Rice are predicted to be most pronounced in the lowest income groups at a fraction of the cost of the current supplementation programs...

 

The Water Efficient Maize for Africa (WEMA) project is another important public-private partnership, which aims to develop drought-tolerant and insect-protected maize... The introduction of drought-tolerant maize to Africa, where three-quarters of the world's severe droughts have occurred over the past ten years, is predicted to dramatically increase yields of this staple food crop for local farmers.

 

Another exciting development is... Bt eggplant that is resistant to fruit and shoot borers. Bt eggplant was recently made available on a royalty-free basis to smallholder farmers in Bangladesh. Researchers estimate that farmers growing the new Bt eggplant varieties could obtain yield increases of 30%-45% while reducing insecticide use... 

 

These examples demonstrate the success of non-profit and public–private partnerships in translating basic research discoveries into benefits at the farm. Well-funded, long-term, multinational, multidisciplinary collaborations are vital if we are to continue making significant progress in developing new crop varieties to enhance food security in the developing world... 

 

Despite the scientific consensus that the genetically engineered crops on the market are safe to eat, have massively reduced the use of sprayed insecticides, and have benefited the environment, they are still viewed with skepticism by some consumers. Without public support for genetic technologies, regulatory costs will continue to climb. The end result may be that only multinational corporations can afford to develop and license such crops. This exclusivity places constraints on broad access to genetic technologies because large corporations have little incentive to develop subsistence (e.g., cassava and banana) and specialty crops (e.g., strawberries, apples, lettuce)—for poor farmers that need them. Costly regulations also hinder the creation of small businesses that wish to translate discoveries in plant genetics into commercially viable enterprises...

 

A related issue, which applies to most seed developed by corporations (conventional or genetically engineered), is that intellectual property rights constrain sharing of genetic resources. Whereas seeds protected by the plant variety protection act include exemptions for farmers to save seed for next year's planting and for breeders to include the variety in breeding programs, certain plant varieties, including GE crops, can be protected by patents, which are much more restrictive and prohibit seed saving by farmers and breeders...

 

Although ~25% of the patented inventions in agricultural biotechnology were made by public sector researchers (e.g., public universities), many of these inventions are exclusively licensed to private companies. Five firms... produce the majority of the world's seeds and control many of the older technologies such as Bt and transformation. Fortunately, the business landscape is changing as many of the earlier patents expire or as alternatives to enabling technologies controlled by corporations emerge in the public sector and as more countries use genetic engineering to create a greater variety of crops...

 

University scientists have also been active in reversing the trend of exclusively licensing genetic technologies... Establish the Public Intellectual Property Resource for Agriculture (PIPRA). PIPRA helps universities to retain rights of their technologies for humanitarian purposes and for crops that are vital to small-acreage farmers...

 

Ultimately, the continued translation of basic research into tangible crop improvement will rely not only on the research itself but also in communicating the vital role that agriculture and plant genetics plays in all of our lives. In the developed world where less than 2% of the population are farmers, the challenges of producing food in a sustainable manner is far removed from the average consumer... Plant biologists can promote agricultural literacy through... highlight the social, economic, biological, environmental, and ethical aspects of food production.

 

We can more fully engage with the policy makers, non-governmental organizations, and journalists by providing science-based information in more creative ways... An engaged, informed public will help us to attain an agricultural system that can produce safe food in a secure, sustainable, and equitable manner.

 

http://dx.doi.org/10.1371/journal.pbio.1001878

 


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Transgenic Crops, Production Risk, and Agrobiodiversity - Krishna &al (2014) - ZEF

Do transgenic crops cause agrobiodiversity erosion? We hypothesize that they increase productivity and reduce production risk and may therefore reduce farmer demand for on-farm varietal diversity, especially when only a few transgenic varieties are available. We also hypothesize that varietal diversity can be preserved when more transgenic varieties are supplied. These hypotheses are tested and confirmed with panel data for the case of transgenic cotton in India. Cotton varietal diversity in India, with of over 90% adoption of transgenic technology, is now at the same level than it was before the introduction of this technology... 

 

During the Green Revolution it was observed that many local crop varieties were replaced with a few high-yielding ones in large parts of the developing world. There are widespread concerns that such agrobiodiversity erosion may continue and be accelerated through

transgenic crop technologies. However, transgenic crops differ... 


From the private perspective of farmers, varietal diversity can have productivity-enhancing and risk-reducing effects... transgenic crops can also increase productivity and reduce production risk and may therefore substitute for on-farm varietal diversity. Yet, a transgenic technology is not only one new variety; the same genes coding for desirable traits can be introgressed into many varieties that are well adapted to various soil and climate conditions. If many transgenic varieties with the same traits are developed and adopted, agrobiodiversity can be preserved. These hypotheses were confirmed in the empirical analysis... 

 

In the early phase of Bt technology diffusion, the Indian regulatory authorities had only approved a very small number of Bt varieties, while in later years many more Bt varieties became available in the seed market. indeed, farmers that fully adopted Bt cotton in the early years, reduced their varietal diversity. In later years, with more Bt varieties available, these same technology adopters restored varietal diversity.

 

These results underline that a combination of transgenic technology and high levels of varietal diversity is possible, and is even further increasing productivity and reducing production risk. Overall, cotton varietal diversity in India with a Bt adoption rate of over 90% is now at the same level or even higher than it was before the introduction of this transgenic technology.


Interestingly, even in the early phase of technology diffusion, with only a few Bt varieties available in the market, average diversity did not decline significantly, because many farmers adopted Bt only partially and maintained varietal diversity through growing conventional varieties on the same farm... Yet we have shown that full adoption would have been economically advantageous for many even with only a few Bt varieties available. Hence, we suppose that the observed partial adoption in the early phase was also a reflection of typical smallholder cautiousness... 

 

One general conclusion can be drawn nevertheless: transgenic technology can help to preserve crop varietal diversity, but the concrete outcome depends on various institutional factors that determine how many transgenic varieties are available in the market... 

 

Policy implications. 

 

First, the biosafety regulatory framework matters. In India, the regulatory authorities were slow in the beginning to approve additional transgenic varieties, mainly due to the public debate... However, once a transgenic event has been tested and deregulated, introgressing that same event into other varieties cannot reasonably be expected to lead to new risks. Hence, a complex regulatory process for each new transgenic variety jeopardizes agrobiodiversity without increasing safety levels.

 

Second, local breeding capacities in a country play an important role. India has a strong public and private breeding sector for cotton. Hence, many companies were technically able to introgress a transgenic trait into their varieties and breeding lines. Such introgression of an available transgenic trait is less complicated than identifying the trait and developing the transformation event, but it still requires some capacity that may not be available in many poorer countries in Africa. Public support through development organizations or international agricultural research centers may be required... Innovative models of public-private partnership may also be an interesting approach...

 

Third, IPRs may play an important role. Many of the transgenic technologies available so far are not patented in developing countries, so that local organizations can use these technologies for free or with relatively simple licensing agreements for introgression into their own varieties and breeding lines. Stronger IPRs may involve more complex licensing agreements. If many local organizations can obtain a license from the IPR holder, agrobiodiversity could be preserved. Restricted licenses to only one or a few organizations, however, could contribute to agrobiodiversity erosion. Such institutional aspects should be considered when designing national policies and regulatory frameworks for transgenic technologies.

 

http://www.zef.de/fileadmin/webfiles/downloads/zef_dp/zef_dp_186.pdf

 


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Benefits of Organic Farming

Benefits of Organic Farming | Research | Scoop.it

Benefits of Organic Farming

The benefits of organic farming are manifold. First, organic farming benefits people directly by producing safe, nutritious foods that are free from the potentially harmful chemicals used in synthetic fertilizers and pesticides. Second, organic farming also benefits the environment by utilizing methods that help preserve biodiversity and conserve natural resources such as soil, water, and energy.

Given the relatively higher cost of operating organic farms and gardens, more and more people are still turning to the practice of organic farming. Incidentally, more and more people are also consuming organically grown products. Obviously, both are due in large part to the fact that the perceived benefits of producing and consuming organic products far outweigh the disadvantages.

So why do many farmers insist on practicing organic agriculture techniques when conventional methods and practices are currently more profitable?

By working in harmony with nature, organic farming delivers long-term benefits to people and the environment. Compared with conventional agriculture, it preserves soil fertility more effectively. Organic farming also uses methods for controlling pests and diseases that do not harm the environment. By not using synthetic chemicals, organic farming ensures that the local water supply remains safe and clean. By utilizing only readily available resources, organic farmers get to save the money that will otherwise be spent for additional farming inputs.

The benefits of organic farming are highlighted when considered in the context of conventional agriculture’s negative effects. In conventional agriculture, synthetic chemicals from pesticides, herbicides, and fungicides gets easily transported from the soil to the water system, polluting rivers, lakes, and other water courses. Prolonged exposure to synthetic fertilizers depletes the soil’s organic matter content, which in turn reduces the soil’s resistance to erosion. Prolonged use of synthetic fertilizers also makes soils too dependent on the chemicals such that more amounts of fertilizer are needed every year just to harvest the same yield level. Synthetic pesticides and fertilizers destroy most microorganisms in the soil—even the beneficial ones—resulting to poor soil structure and deficient nutrient content. Synthetic and health-damaging chemicals tend to stay in the soil, eventually entering the food chain to be consumed by humans.

To effectively deliver the potential benefits of organic farming, farmers rely heavily on sustainable agricultural techniques such as green manure, composting, crop rotation, and natural methods of weed, pest, and fungus control. While employing these techniques, organic farmers also strictly restrict the use of genetically-modified organisms (GMO’s) and synthetic chemicals, thereby ensuring the harvesting of healthy, nutritious produce.

To conserve and enhance soil quality, organic farmers use recycled and composted crop wastes and manure. Organic farmers also practice crop rotation. To control pests, diseases and weeds, organic farmers plan crop sequence and use resistant varieties. Farmers also allow natural predators to control plant pests first before seriously using organic pesticides.

Given these benefits, there are also downsides to organic farming, however. For one thing, organic produce costs considerably more than their commercial counterparts simply because organic farming is costlier to operate. Nonetheless, given the consistently demonstrated environmental benefits of organic crops, at least trying them out is good choice, especially for people who can afford them or who care deeply for the environment and biodiversity.


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Climate Change's Big Winners: Pests and weeds

Climate Change's Big Winners: Pests and weeds | Research | Scoop.it
Count weeds and insect pests among the beneficiaries of climate change. Meanwhile, the crops we need will have fewer nutrients that make them beneficial, scientists revealed this week.

At the root of the problem: Rising carbon dioxide levels, warm...

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Darin Hoagland's curator insight, May 9, 2014 2:54 PM

Unfortunately this result of climate change is not surprising.

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Genetic Engineering and Breeding of Drought-Resistant Crops - Annual Review of Plant Biology, 65(1):

Genetic Engineering and Breeding of Drought-Resistant Crops - Annual Review of Plant Biology, 65(1): | Research | Scoop.it

Drought is one of the most important environmental stresses affecting the productivity of most field crops. Elucidation of the complex mechanisms underlying drought resistance in crops will accelerate the development of new varieties with enhanced drought resistance. Here, we provide a brief review on the progress in genetic, genomic, and molecular studies of drought resistance in major crops. Drought resistance is regulated by numerous small-effect loci and hundreds of genes that control various morphological and physiological responses to drought. This review focuses on recent studies of genes that have been well characterized as affecting drought resistance and genes that have been successfully engineered in staple crops. We propose that one significant challenge will be to unravel the complex mechanisms of drought resistance in crops through more intensive and integrative studies in order to find key functional components or machineries that can be used as tools for engineering and breeding drought-resistant crops.


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Legume genomics: understanding biology through DNA and RNA sequencing

Legume genomics: understanding biology through DNA and RNA sequencing | Research | Scoop.it

Good review for teaching  - shows how the power of next-gen sequencing methods inform our understanding of plant physiology and diversity


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Box plot, Fisher’s style

Box plot, Fisher’s style | Research | Scoop.it
In a recent issue of Significance, I discovered an interesting – and amuzing – figure, about some box & beard plot, in Dr Fisher’s casebook: Beard the statistician in his den. In French, the box plot (introduced by John Tukey, not George Box, as discussed in a previous post) is popular under the name boîte à moustaches (box with a mustache, for a simple translation). > set.seed(2) > x=rnorm(500) > boxplot(x,horizontal=TRUE,axes=FALSE) > axis(1) I was wondering if it was possible to reproduce that Fisher’s style […]

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Mol Plant Path: Bacterial pathogenesis of plants: Future challenges from a microbial perspective (2016)

Mol Plant Path: Bacterial pathogenesis of plants: Future challenges from a microbial perspective (2016) | Research | Scoop.it

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The Sainsbury Lab's curator insight, May 16, 4:03 AM
Plant infection is a complicated process. Upon encountering a plant, pathogenic microorganisms must first adapt to life on the epiphytic surface, and survive long enough to initiate an infection. Responsiveness to the environment is critical throughout infection, with intracellular and community-level signal transduction pathways integrating environmental signals and triggering appropriate responses in the bacterial population. Ultimately, phytopathogens must migrate from the epiphytic surface into the plant tissue using motility and chemotaxis pathways. This migration is coupled to overcoming the physical and chemical barriers to entry into the plant apoplast. Once inside the plant, bacteria use an array of secretion systems to release phytotoxins and protein effectors that fulfil diverse pathogenic functions (Fig. 1)(Phan Tran et al., 2011, Melotto & Kunkel, 2013).
The Pub Club's curator insight, May 17, 8:23 AM
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Rakesh Yashroy's curator insight, May 18, 9:54 PM
Host-pathogen interface is the real battle field of survival against odds both for animals and plant infections @ https://en.wikipedia.org/wiki/Host-pathogen_interface
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Nature Microbiology: Fungal pathogenesis: Host modulation every which way (2016)

Nature Microbiology: Fungal pathogenesis: Host modulation every which way (2016) | Research | Scoop.it

The plant pathogenic fungus Fusarium oxysporum secretes an effector that is similar to a plant peptide hormone, underscoring the variety of mechanisms that plant pathogens have evolved to tamper with host physiology.

 

Plant pathogens cause devastating diseases of crop plants and threaten food security in an era of continuous population growth. Annual losses due to fungal and oomycete diseases amount to enough food calories to feed at least half a billion people. Understanding how plant pathogens infect and colonize plants should help to develop disease-resistant crops. It appears that plant pathogens are sophisticated manipulators of their hosts. They secrete effector molecules that alter host biological processes in a variety of ways, generally promoting the pathogen lifestyle. A new study by Masachis, Segorbe and colleagues describes a new mechanism by which plant pathogens interfere with plant physiology. They discovered that the root-infecting fungus F. oxysporum secretes a peptide similar to the plant regulatory peptide RALF (rapid alkalinization factor) to induce host tissue alkalinization and enhance plant colonization. This study demonstrates that in addition to secreting classical plant hormones (or mimics thereof), fungi have also evolved functional homologues of plant peptides to alter host cellular processes.


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Nature Biotech: News & Views - Plant immunity switched from bacteria to virus (2016)

Nature Biotech: News & Views - Plant immunity switched from bacteria to virus (2016) | Research | Scoop.it
Each year, staple crops around the world suffer massive losses in yield owing to the destructive effects of pathogens. Improving the disease resistance of crops by boosting their immunity has been a key objective of agricultural biotech ever since the discovery of plant immune receptors in the 1990s. Nucleotide-binding leucine-rich repeat (NLR) proteins, a family of intracellular immune receptors that recognize pathogen molecules, are promising targets for enhancing pathogen resistance. In a recent paper in Science, Kim et al.1 describe a clever twist on this approach in which the host target protein for the pathogen effector is engineered rather than the NLR protein itself.

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Nature Biotech: Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture (2016)

Nature Biotech: Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture (2016) | Research | Scoop.it

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The Sainsbury Lab's curator insight, April 26, 4:14 AM
Wild relatives of domesticated crop species harbor multiple, diverse, disease resistance (R) genes that could be used to engineer sustainable disease control. However, breeding R genes into crop lines often requires long breeding timelines of 5–15 years to break linkage between R genes and deleterious alleles (linkage drag). Further, when R genes are bred one at a time into crop lines, the protection that they confer is often overcome within a few seasons by pathogen evolution1. If several cloned R genes were available, it would be possible to pyramid R genes2 in a crop, which might provide more durable resistance1. We describe a three-step method (MutRenSeq)-that combines chemical mutagenesis with exome capture and sequencing for rapid R gene cloning. We applied MutRenSeq to clone stem rust resistance genes Sr22 and Sr45 from hexaploid bread wheat. MutRenSeq can be applied to other commercially relevant crops and their relatives, including, for example, pea, bean, barley, oat, rye, rice and maize.
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A Legume Genetic Framework Controls Infection of Nodules by Symbiotic and Endophytic Bacteria

A Legume Genetic Framework Controls Infection of Nodules by Symbiotic and Endophytic Bacteria | Research | Scoop.it
by Rafal Zgadzaj, Euan K. James, Simon Kelly, Yasuyuki Kawaharada, Nadieh de Jonge, Dorthe B. Jensen, Lene H. Madsen, Simona Radutoiu
Legumes have an intrinsic capacity to accommodate both symbiotic and endophytic bacteria within root nodules.

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A faster Rubisco with potential to increase photosynthesis in crops

A faster Rubisco with potential to increase photosynthesis in crops | Research | Scoop.it

In photosynthetic organisms, D-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the major enzyme assimilating atmospheric CO2 into the biosphere1. Owing to the wasteful oxygenase activity and slow turnover of Rubisco, the enzyme is among the most important targets for improving the photosynthetic efficiency of vascular plants2, 3. It has been anticipated that introducing the CO2-concentrating mechanism (CCM) from cyanobacteria into plants could enhance crop yield4, 5, 6. However, the complex nature of Rubisco’s assembly has made manipulation of the enzyme extremely challenging, and attempts to replace it in plants with the enzymes from cyanobacteria and red algae have not been successful7, 8. Here we report two transplastomic tobacco lines with functional Rubisco from the cyanobacterium Synechococcus elongatus PCC7942 (Se7942). We knocked out the native tobacco gene encoding the large subunit of Rubisco by inserting the large and small subunit genes of the Se7942 enzyme, in combination with either the corresponding Se7942 assembly chaperone, RbcX, or an internal carboxysomal protein, CcmM35, which incorporates three small subunit-like domains9, 10. Se7942 Rubisco and CcmM35 formed macromolecular complexes within the chloroplast stroma, mirroring an early step in the biogenesis of cyanobacterial β-carboxysomes11, 12. Both transformed lines were photosynthetically competent, supporting autotrophic growth, and their respective forms of Rubisco had higher rates of CO2 fixation per unit of enzyme than the tobacco control. These transplastomic tobacco lines represent an important step towards improved photosynthesis in plants and will be valuable hosts for future addition of the remaining components of the cyanobacterial CCM, such as inorganic carbon transporters and the β-carboxysome shell proteins


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Climate-Smart Agriculture: Global Science Conference 20-22 March at UC Davis

Climate-Smart Agriculture: Global Science Conference 20-22 March at UC Davis | Research | Scoop.it

General Registration - $150
Student Registration - $75

Registration includes:

• Lunch on March 20, 21 and 22
• Reception on March 19 and 21
• Dinner on March 20

Please be sure to book your travel reservations.  Click here for a list of conference hotels and information on ground transportation.

Refunds:

• Registration refunds will not be issued but substitutions are allowed. Send substitution requests to Louise Uota atclimatesmart@ucdavis.edu

Questions? Contact Louise Uota at climatesmart@ucdavis.edu or telephone 530-754-2007

The conference will include two blocks of parallel science sessions. In order to gauge interest and plan for the correct room sizes, please indicate your first and second choices within each block of six when registering. Please note that your selections here will not be binding and will not guarantee admission to a particular session.

Parallel Session Block I

1. Crop physiology and genetics under climate change: implications for breeding and dissemination strategies.
2. Livestock management, animal health and policies for climate change impacts on disease.
3. Nitrogen management: balancing agricultural growth, GHG accounting, GHG mitigation + adaptation.
4. Farmer decision making under climate change and barriers to the adoption of climate smart agriculture practices.
5. Energy and biofuels: production and technologies to cut emissions without interfering with food production.
6. Climate risk management (financial mechanisms, insurance, or climate services for farmers).

Parallel Session Block II

7. Using GCM-based regional scenarios of development, deforestation, climate change and food security to design and test adaptive strategies for uncertain future climates.
8. Soil quality, organic matter and water use across landscapes: achieving multifunctionality through adaptation, mitigation and GHG accounting.
9. Water management related to food and fisheries systems under climate change: implementing strategies, technologies and institutions.
10. Managing and conserving agrobiodiversity to increase ecosystem services and resilience to climate change (e.g. REDD+ in mosaics of forest+cultivated systems, agroforestry, genetic resources)
11. Rural-urban connections that promote climate change resilience for agriculture (e.g. rural outmigration, peri-urban agriculture, avoiding urban sprawl into valuable farmlands)
12. Metrics for vulnerability assessment, mitigation, adaptation, food security and ecosystem services in agricultural landscapes.


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Nobel laureate, former Texas A&M professor Norman Borlaug to be honored with Capitol statue

Nobel laureate, former Texas A&M professor Norman Borlaug to be honored with Capitol statue | Research | Scoop.it

WASHINGTON—Congress will unveil a statue of Norman Borlaug Tuesday, enshrining the “Father of the Green Revolution” in the U.S. Capitol.

Borlaug, who died in 2009 in Dallas, earned the moniker after he developed a disease-resistant, high-yielding wheat strain that helped feed more than one billion starving people across the globe. That accomplishment won him the Nobel Peace Prize in 1970, along with the U.S. Presidential Medal of Freedom and the Congressional Gold Medal. The two medals are the highest civilian awards in the country.

The statue will be dedicated on Borlaug’s 100th birthday by congressional leaders and Iowa lawmakers.

“Dr. Borlaug’s efforts to advance biotechnology and agronomy vastly improved the levels of food security in nations around the world,” Iowa Republican Sen. Chuck Grassley said in a statement. “He was an extraordinary man, with a brilliant vision, and the common sense and commitment to turn his dreams into reality.”

Although Borlaug was born in Iowa, he had strong ties to the Lone Star State. He joined the faculty at Texas A&M University in 1984 and the university’s Office of International Agricultural Programs now bears his name. Borlaug spent the later years of his life in Dallas.

The statue will join the collection that adorns the halls of the Capitol. By law, each state can have two statues in the building to represent it. Borlaug’s statue will replace one of James Harlan, secretary of the interior under President Andrew Johnson. Harlan’s statue had resided in the Capitol for more than 100 years.

Texas is represented by statues of Sam Houston and Stephen F. Austin.


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WHAT HAPPENS TO SOYBEANS WHEN THEY GET FROSTED!

WHAT HAPPENS TO SOYBEANS WHEN THEY GET FROSTED! | Research | Scoop.it

Various areas in the province received frost in September and there continues to be concern the impact subsequent frost will have on the soybean crop. The extent of injury will depend on the stage of development as well as the length of exposure to frost. 

 MECHANISM

 Low temperatures injure plants primarily by inducing ice formation between or within cells.  The water that surrounds the plant cells freezes first (at about 0 C), while the water within the cell contains dissolved substances that depress the freezing point of water by several degrees.  Furthermore, when the water around the cells becomes ice, water vapour moves out of the cells and into the spaces around the cell, where it becomes ice.  The reduced water content of the cells depresses further the freezing point of the intracellular water.  This can continue to a point without damaging the cell, but below a certain point, ice crystals form within the cell, disrupt the cell membrane, and cause injury to the cell. 

 LATE-SEASON FROST INJURY

Studies indicate that soybeans are easily injured by frost until they reach physiological maturity which is attained at the R7 stage. Frost after physiological maturity (maximum dry weight) generally does not damage soybean plants if pods remain intact. Prior to this stage, soybeans will be injured both for grain and seed purposes.  Soybean reproductive development can be divided into eight stages (Table 1). 

 Table 1 – Stage of development descriptions for soybeans.

 R1 (Beginning flower) – One open flower on any node on main stem.

R2 (Full flower) - Open flower at one of the two uppermost nodes.

R3 (Beginning pod) - Green 0.5cm (1/4″) long pod at one of the                                              four upper nodes.

R4 (Full pod) – Green pod 2cm (3/4″) long at one of the four upper                       nodes.

R5 (Beginning seed) – Beans beginning to develop 0.25cm (1/8″) seed                                    in at one of the four upper nodes.

R6 (Full seed) – Green seed fills pod cavity at one of the four                                           uppermost nodes.

R7 (Beginning maturity) – One normal pod on main stem has reached its mature colour (brown or tan); 50% of leaves yellow.

R8 (Full maturity) – 95% of pods are mature brown colour.  Harvest           moisture is reached within 1-2 weeks.              

Freezing during earlier development (the green pod stage, R6) will result in a severely damaged bean with a greenish “candied” appearance.  But even moderately frosted beans with a greenish colour and slightly wrinkled seedcoat are considered as damaged soybeans and will be discounted if present in excess of limits (3%) for No. 2 Canada soybeans.  The seed will eventually dry down with a wrinkled seedcoat and germination will be severely affected.  The Canadian Grain Commission classifies frost damaged soybeans as those “soybeans whose cotyledons, when cut, are green or greenish-brown in colour with a glassy wax-like appearance”.

Besides affecting seed quality, an early frost can also significantly reduce seed yield.  See table #3. 

 Table 3 – Soybean Yield Response to Freeze Damage

 Growth Stage                                                   Yield Reduction

 R4      Full Pod                                                            70-80%

R5      Beginning Seed                                                50-70%

R6      Full Seed                                                          15-30%

R7      Beginning Maturity                                            0-5%

R8      Full Maturity                                                     0%

 What is the impact on seed quality?  It has been determined that temperatures required to cause reductions in seed germination and vigour decrease as seed maturation progresses (Table 4).

 Table 4 – Effect of freezing temperature on the standard germination of seed

 Temp.           Exposure                           PERCENT GERMINATION

 C                 Time                       Green           Yellow           Brown

 Control                                         12.2              84.2                        83.2

 -2                  1 Hr                        7.2               —-                          —-

                     2                             12.2              78.5                        —-

                     4                             9.2               72.8                        —-

                     8                             10.0              79.0                        —-

                     16                           9.0               74.0                        —-

                     32                           —-                75.8                        —-

 -7                  1                             7.0               —-                          —-

                     2                             0.8               63.0                        77.2

                     4                             0.2               61.0                        82.5

                     8                             0.0               50.8                        82.5

                     16                           0.0               34.2                        80.8

                     32                           —                10.2                        58.0

 -12                1                             0.0               42.8                        73.8

                     2                             0.0               34.2                        77.8

                     4                             0.0               23.5                        58.0

 Therefore, seed producers and growers should be especially cautious about using soybean seedlots that have been frosted before maturity.  Although some of the severely wrinkled and shrunken seed can be eliminated during cleaning, slightly injured seed may remain which would be expected to have less seedling vigour, storability and field performance capacity.

 Frosted plants will reach harvest maturity earlier but should have the same level of seed moisture as non-frosted soybeans. Seed protein should not be affected by frost, but the oil concentration will be lower if the frost occurred before the seed grew to full size. In soybeans grown for seed, germination and vigour may be reduced in cases where the seed contained more than 55 percent moisture at the time of the frost.

 Points to consider when assessing a field:

 1)     If all the seed has turned yellow (physiologically mature) there are no yield or quality  impacts due to frost.  However since even R7 fields have not completely turned yellow some green beans will remain green at harvest.  Yield impact is minimal. (0-5% Yield reduction)

2)     If some pods had turned yellow or brown before the frost these pods should be opened up to determine if the seed is detached from the pod.  If the beans have not detached from the white membrane inside the pod the beans will stay green.  If the seed has detached from the pod the seed will likely turn yellow if given enough time.

3)     If all the pods were green before the frost a large percentage of the seed will remain green even after dry-down. (frosted pods may turn black due to frost)

4)     Even if the stem is still green once the temperature gets below –2 C essentially no translocation occurs from the stem to the pods.  The majority of the seed will stay green.

Albert Tenuta, Field Crop Plant Pathologist, OMAFRA, Ridgetown

and

Horst Bohner, Soybean Specialist, OMAFRA, Stratford

- See more at: http://fieldcropnews.com/2013/09/what-happens-to-soybeans-when-they-get-frosted/#sthash.tjPi79F7.dpuf


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How to draw venn pie-agram (multi-layer pie chart) in R?

How to draw venn pie-agram (multi-layer pie chart) in R? | Research | Scoop.it
I was wondering how to draw a venn diagram like pie chart in R, to show the distribution of my RNA-seq reads mapped onto different annotation regions (e.g. intergenic, intron, exons etc.). A google search returns several options, including the nice one...

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Molecular Genetics of Nodulation Control in Legumes

Professor Peter M. Gresshoff
QAAFI Science Seminar -- 27 May 2014
http://www.uq.edu.au/agriculture/pete...

Most legume plants, such as soybean, are capable of nodulation, that is development of de novo organs called nodules in which the inducing bacterium, broadly called Rhizobium, is captured to allow complex differentiation of both plant and bacterium to facilitate symbiotic nitrogen fixation. This has immense economic as well as ecological and environmental benefits, as nitrogen fertiliser demand is significantly reduced.

The main questions are: how are these structures induced by the bacterium? What genes do legumes possess to facilitate that process? What genes does the plant use to control the development of these nodule structures?

We have used diverse genetic, molecular and physiological methods to generate a functional impression of these overall processes. The seminar will high-light discoveries made by the speaker's research effort over the last 30 years, leading to an in-depth understanding of key processes. Sadly, as in all science, this is just a beginning, and future insights are hoped to elucidate the inability of non-legumes to enter this nitrogen fixation symbiosis.

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Jean-Michel Ané's curator insight, May 28, 2014 2:09 AM

Great lecture from Peter Gresshoff

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Putting Up Resistance (to wheat stem rust fungus Ug99). The Scientist Magazine®

Putting Up Resistance (to wheat stem rust fungus Ug99). The Scientist Magazine® | Research | Scoop.it
Will the public swallow science’s best solution to one of the most dangerous wheat pathogens on the planet?

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