Crop Genomics, NGS and Bioinformatics
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Genome Biology | Full text | Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

Brassica oleracea is a valuable vegetable species that has contributed to human health and nutrition for hundreds of years and comprises multiple distinct cultivar groups with diverse morphological and phytochemical attributes. In addition to this phenotypic wealth, B. oleracea offers unique insights into polyploid evolution, as it results from multiple ancestral polyploidy events and a final Brassiceae-specific triplication event. Further, B. oleracea represents one of the diploid genomes that formed the economically important allopolyploid oilseed, Brassica napus. A deeper understanding of B. oleracea genome architecture provides a foundation for crop improvement strategies throughout the Brassica genus.
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Genome editing of crops may be restricted by EU rules, warn scientists - The Guardian

Genome editing of crops may be restricted by EU rules, warn scientists - The Guardian | Crop Genomics, NGS and Bioinformatics | Scoop.it
The Guardian Genome editing of crops may be restricted by EU rules, warn scientists The Guardian Genome editing is different to genetic modification, because it does not usually involve transplanting genes from one plant or species to another, but...
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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

 


Via Alexander J. Stein
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CRISPR: the next generation of genome editing tools

CRISPR: the next generation of genome editing tools | Crop Genomics, NGS and Bioinformatics | Scoop.it

An arms race has been waged between bacteria and bacteriophage that would bring a satisfactory tear to Sun Tzu’s eye. Scientists have recently recognized that countermeasures developed by bacteria (and archaea) in response to phage infections can be retooled for use within molecular biology. In 2013, large strides have been made to co-opt this system (specifically and most commonly from Streptococcus pyogenes) for use in mammalian cells. This countermeasure, CRISPR (clustered regularly interspaced short palindromic repeats), has brought about another successive wave of genome engineering initiated by recombineering and followed more recently by zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs).

 

ZFNs and TALENs perform a similar function yet the learning curve appears to be more difficult for development due to the use of protein-DNA contacts rather than the simplicity of designing RNA-DNA homology contacts. Although the potential for CRISPR in regards to genome editing within mammalian cells will be of greatest interest to the reader, the CRISPR backstory is equally compelling. Just as we have evolved immune responses to pathogens, so too have bacteria. CRISPR is an adapted immune response evolved by bacteria to create an immunological memory to ward off future phage infections. When a phage infects and injects its DNA within a bacterium, the DNA commandeers bacterial proteins and enzymes for use towards lytic or lysogenic phases. However, exposure of phage DNA allows the bacterium to copy and insert snippets (called spacers) of phage DNA into its genomic DNA between direct repeats (DR). These snippets can later be expressed as an operon (pre-CRISPR RNA, pre-crRNA) alongside a trans-activating CRISPR RNA (tracrRNA) and an effector CRISPR associated nuclease (Cas). Together these components surveil for foreign crRNA cognate sequence and cleave the targeted sequence.

 

Although hallmarks of CRISPR have been known since the late 80’s (CRISPR timeline) and was acronymed in 2002, Jinek et al. in August 2012 were the first to suggest the suitability of CRISPR towards genome editing. In February of 2013, Feng Zhang’s and George Church’s labs simultaneously published the first papers describing the use long oligos/constructs for editing via CRISPR in mammalian cells and made their plasmids readily available on Addgene. Zhang’s lab went one step further and has supplemented their papers with a helpful website and user forum. They have even gone so far as to publish a methods paper to streamline the use of their plasmids towards a plug-and-play, modular cloning approach with your target sequence of interest.

 

CRISPR works fairly well out of the box yet still has some imperfections that are being addressed. For example, CRISPR relies upon a protospacer adjacent motif (PAM; S. pyogenes sequence: NGG) 3’ to the targeting sequence to permit digestion. Although the ubiquity of NGG within the genome may seem advantageous, it may be limiting in some regions. Other species make use of different PAM sites that can be considered when choosing a cut sites of interest. Since double-stranded cuts could potentially create DNA lesions (a byproduct of the cell using non-homologous end joining [NHEJ] instead of homologous recombination) some labs are choosing to use modified Cas enzymes that nick DNA, instead of creating a double-strand break. This potential weakness of CRISPR to create DNA lesions via NHEJ, however, has been exploited by Eric Lander’s and Zhang’s lab this month (Jan. 2014). They have capitalized on the cell’s use of NHEJ to manufacture DNA lesions (frameshift mutations) at cut sites within genes on a large scale as a means to perform large genetic screens. Using this technique knocks out a gene and has the obvious advantage of fully ablating a gene’s expression compared to RNAi where some residual expression can be expected.

 

The advantages of CRISPR lends itself to future therapies. High efficiency, low-to-no background mutagenesis and easy construction put CRISPR front and center as the tool de jour for gene therapy. In combination with induced pluripotent stem cells (iPSCs), one can imagine the creation of patient-specific iPSCs created with non-integrative iPSC vectors and modified by CRISPR, devoid of any residual DNA footprint left behind by the iPSC vector or CRISPR correction. In conjunction with whole genome sequencing, genetically clean cell lines can be selected that are suitable for differentiation towards the germ layer of interest for subsequent autologous transplantation. Proof of principle experiments have already been published in models of cystic fibrosis and cataracts.

 

For better or worse, CRISPR is catching on like wildfire with young investigators, as noted recently by Michael Eisen. What may be looming in the future and not as openly discussed at this time is the potential for CRISPR to open up the genome to large scale editing. We tend to think of any particular genome as fairly static with slight variations between any two individuals and increased variation down the evolutionary line. However, CRISPR has proven to be a fantastic multitasker, capable of modifying multiple loci in one fell swoop as demonstrated by the Jaenisch lab (five loci). With the creation of Caribou Biosciences and a surprising round of venture capital raised by a powerhouse team at Editas Medicine in November ($43 million), CRISPR appears to also have sparked an interest in the private sector. With large sums of money at their disposal, these companies can now begin to look at the genome, not as a static entity, but more akin to operating system, a code that now has a facile editing tool. George Church, an Editas co-founder, has speculated in the past about the potential use of the human genome as the backbone for recreating the Neanderthal genome in his recent book and interview with "Der Spiegel". In an era where the J. Craig Venter Institute can create an organism’s genome de novo and a collaboration between Synthetic Genomics and Integrated DNA Technologies has proposed to synthesize DNA upwards of 2Mbp, the combination of CRISPR, synthetic DNA and some elbow grease will make the genome more accessible and Church’s speculations a potential reality.


Via Dr. Stefan Gruenwald
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The Camelina sativa genome. : The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure : Nature Communications : Nature Publishing Group

The Camelina sativa genome. : The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure : Nature Communications : Nature Publishing Group | Crop Genomics, NGS and Bioinformatics | Scoop.it
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Peter Enyeart presents his PhD thesis on genome editing to middle school students.

Peter Enyeart, University of Texas at Austin PhD candidate, presents his PhD thesis on his new methodology which allows him to radically modify the genomes o...
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