CRISPR Scissors Utilized to Break Yield Barrier in Crops

Scientists at Cold Spring Harbor Laboratory (CSHL) have tapped genome editing to improve agricultural crops. Using tomato as an example, they used CRISPR-Cas9 technology to rapidly generate variants of the plant that display a broad continuum of three separate, agriculturally important traits: fruit size, branching architecture, and overall plant shape — components that determine plant yield. The method is designed to work in all food, feed, and fuel crops, including the staples ricemaize, sorghum, and wheat.
The team used CRISPR “scissors” to make multiple cuts within three tomato genome sequences known as promoters — areas of DNA near associated genes which help regulate when, where, and at what level these “yield” genes are active during growth. The scientists were able to induce a wide range of changes in each of the three targeted traits.
By using CRISPR to mutate regulatory sequences, the CSHL team found that a much subtler impact on quantitative traits is possible. Fine-tuning gene expression rather than deleting or inactivating the proteins they encode is most likely to benefit commercial agriculture because of the flexibility such genetic variation provides for improving yield traits.
CSHL Professor Zachary Lippman, who led the research says, “Traditional breeding involves great time and effort to adapt beneficial variants of relevant genes to the best varieties, which must continuously be improved every year. Our approach can help bypass this constraint by directly generating and selecting for the most desirable variants controlling gene activity in the context of other natural mutations that benefit breeding. We can now work with the native DNA and enhance what nature has provided, which we believe can help break yield barriers.”
For more details, read the CSHL News and Features.

CRISPR-Cas9 Genome Editing in MicroRNA of Rice

MicroRNAs (miRNAs) are small non-coding RNAs with roles in plant development and stress responses. Loss-of-function analysis of miRNA genes has been challenging due to the lack of suitable knockout tools. A team of scientists from various universities, led by Jian-Ping Zhou from the University of Electronic Science and Technology of China, aim to study miRNA genes, specifically OsMIR528, in rice using CRISPR-Cas9.

Frequencies of mutants T0 lines ranged from 48% to 89% at all target sites. Three independent guide RNAs (gRNAs) all generated biallelic mutations among mutant lines. This demonstrates that CRISPR-Cas9 is an effective tool for knocking out plant miRNAs. However, single-base pair (bp) mutations in mature miRNA regions were found to lead to the generation of functionally redundant miRNAs, while large deletions were found to abolish miRNA function. Analysis found that OsMIR528 is a positive regulator of salt stress.

This work provides guidelines on targeting miRNAs with CRISPR-Cas9 and also brings new insights into miRNA function in rice.

For more information, read the article in Frontiers in Plant Science.

Fat content in soybean oil modified with CRISPR-Cpf1

A research team from the Center for Genome Engineering, within the Institute for Basic Research (IBS) in South Korea has successfully edited two genes that contribute to the fat content of soybean oil using the new CRISPR-Cpf1 technology. This technology is an alternative to the more widely used gene editing tool CRISPR-Cas9.

IBS scientists have previously used Cpf1 to edit human DNA cells. This time, they introduced the CRISPR-Cpf1 complex into plant cells. The team designed CRISPR-Cpf1 to cut two of the FAD2 genes in soybeans. These genes are part of the pathway that converts oleic acid into the polyunsaturated linoleic acid. By mutating FAD2 genes, the percentage of oleic acid in soybean seeds increases, resulting in healthier soybean oil.

The IBS research team also discovered at least three benefits of CRISPR-Cpf1 over CRISPR-Cas9: CRISPR-Cpf1 technique has shorter CRISPR-RNA (crRNAs), so the RNA can be synthesized chemically; CRISPR-Cpf1 creates larger deletions (7 base pairs) in the target gene, which is good for making the gene completely inoperative; and the type of cleavage left by Cpf1 might help further gene editing processes.

More details are available at the IBS News Center.

-Published in ISAAA’s Crop Biotech Update.  See original article link here.

Why Bioethics Matters in Biotechnology

The last five years have witnessed amazing acceleration of innovation in biotechnology. CRISPR will lead to precision gene editing that could vastly improve food crop yields and provide cures to cancer. Lightning-fast gene sequencing will enable early detection of cancer from a simple blood test. High-speed bulk data transfer allows the entire genomes of millions of people to be compared online in the search for cures to both common and rare diseases. Neuromorphic chips will accelerate the dawn of artificial intelligence, and smart prostheses will allow para- and quadriplegic patients to move, the deaf to hear, and the blind to see.

Discovery of synergies in applications that blur the boundaries of traditional science, technology, engineering, and mathematics will continue to fuel this exponential growth of innovation. In spite of this exuberant trend, it is important to remember that innovation and discovery often outpace the regulatory structures that ensure their best and most ethical use in society.

The bioethics field traditionally is interpreted as pertaining mainly to the medical interests of humans. It has dealt with five key issues: beneficence, non-maleficence, patient autonomy, social justice, and patient confidentiality. However, with the advent of nanotechnology and other technologies that allow inter-kingdom transfer of genetic material, a need exists to establish a broader interpretation. Theologian Brian Edgar1 notes that a more robust definition should comprise six key considerations: respect for the intrinsic value of all life, valuing human uniqueness, preserving organismal integrity, recognizing ecologic holism, minimizing future liability, and producing social benefit. These considerations, while not expected to provide all of the answers to ethical dilemmas faced by technological advancement, create a framework for productive discussion of the most important aspects of biotechnology.

As Christians, we must also acknowledge that we are made in the image of God2, and have the unique ability, of all created things, to have a relationship with our Creator. In thoughtfully considering the implications of having been thus created, we have the responsibility of honoring Him by not only valuing human life, but by valuing and caring for His creation as well. If we actively and consistently apply this principle to guide us in making decisions about the application of biotechnology, the benefits to ourselves and to our world will be tremendous.


  1. Edgar, B. 2009. Biotheology: Theology, Ethics and the New Biotechnologies. Christian Perspectives on Science and Technology. ISCAST Online Journal 2009.
  2. Genesis 1:26-27; 5:1-3; 9:5-6; 1 Corinthians 11:7; James 3:9

-Written by David Dyer, Ph.D. in Asuza Pacific University.  See original article link here.  David Dyer, Ph.D., is executive director of Azusa Pacific’s M.S. in Biotechnology program.

There’s no need to fear gene-edited food: CRSPR democratizes food technology

Not since Alice in Wonderland’s hookah-smoking caterpillar doled out his weird wisdom atop a ­psychedelic-looking mushroom has the lowly fungus so upstaged the action. At most dinner tables, mushrooms are ancillary characters. But this past spring, the food and agriculture worlds became obsessed with one mushroom in particular: Agaricus bisporus, known as the white button mushroom—that all-purpose fungus you jam by the fistful into a plastic bag at the market and abandon in the fridge, only to find it slimy and brown several days later. Science has now found a way to delay that browning, using the buzzy genome-editing tool CRISPR, which can trigger changes in the DNA of plants, humans, and other animals with unprecedented precision and speed.

The name—Clustered Regularly Interspaced Short Palindromic Repeats—refers to a system that targets genetic code. The makers of the nonbrowning mushroom, at Pennsylvania State University, used the CRISPR enzyme Cas9, which can delete base pairs, changing a gene and altering its expression.

But that’s not the part that got people talking. In April, the U.S. Department of Agriculture said that it would not regulate the CRISPR-altered mushroom. To organic purists and eco-watchdogs, a genetically modified organism (GMO) had been given a green light to go to market without oversight: no warnings about what was in our food and no investigations into its environmental impact.

The outcry from food warriors was swift: How had a genetically tweaked food evaded regulation?

It hadn’t, exactly. “The USDA simply decided that, legally, the mushroom didn’t fall within their regulatory system,” says Greg Jaffe, the biotechnology director at the Center for Science in the Public Interest.

The USDA regulates genetically modified (GM) plants only for their potential to be “plant pests”—whether they can infect other crops. If there’s that chance, it can require further testing and a permit before the crop is planted. A handful of modified GM plants have previously managed to escape regulation for various reasons. But the CRISPR process itself is what helped push the mushroom past the red tape. While most GM crops use bacteria or viruses to introduce new genes into a plant, CRISPR needed only a few snips to the genetic code. Since the CRISPR’ed mushroom contained no plant-pest DNA, the USDA decided it was out of their hands. (The Food and Drug Administration still may weigh in before the ’shroom goes to market.)

Still, consumers are wary. Ever since federal regulators approved GM seed crops 20 years ago, we’ve been a nation torn—and often misinformed—over so-called Frankenfoods. The organic-food lobby and environmentalists vigilantly warn us about potentially harmful side effects to our health and to the ­planet. The issue has created a hothouse split between ­science and the public. A 2015 Pew Research survey found that more than 57 percent of Americans believe GMOs are “generally unsafe.” Meanwhile, 88 percent of scientists surveyed say they are “generally safe.”

The biggest mistake we can make, as a curious and concerned public, is to vilify CRISPR and the food it makes. We should instead push for informed, science-based evaluation.

But we’ve come a long way since the early days of GMO projects, when herbicide-resistant crops led to “superweeds” immune to chemical treatment. Such stories make us justifiably wary of playing God with our food. But nearly everything we eat is genetically modified. (See freshman biology: Gregor Mendel). The real superweeds today have grown up around, and are choking, our legal-approval apparatus. Oversight has become part of the problem; our biotech regulatory framework is outdated and ill-equipped to deal with rapidly evolving tech. (The White House has promised to change that.)

The biggest mistake we can make, as a curious and concerned public, is to prematurely vilify CRISPR and the food it makes. We should instead push for ­informed, science-based evaluation. It could help improve the global food supply. The whole reason for a tweaked mushroom is that it resists bruising during harvest and browning in your fridge. That means you’re more likely to eat it instead of tossing it—no small success in a country where 40 percent of food ends up in a landfill. And CRISPR itself opens up a new world of food development, since it’s cheap and easy to use, making it accessible to smaller labs and breaking Big Ag’s GMO monopoly.

So let’s not stall this science at a time when better, hardier, more efficiently grown food is a rising need. Gene editing requires funding and research—but it also requires public support to make it viable. There is great potential for smaller companies to make food that can nourish a growing population without harming the planet. Traditional bioengineering has a very high bar for entry. CRISPR lowers it: It democratizes the technology so engineered plants are not just the domain of a handful of huge companies making feed crops, but can be done by one guy in a university lab with a great idea.

This article was originally published in the November/December 2016 <http://www.popsci.com/tags/nov-dec-2016> issue of Popular Science, under the title “Do Not Fear Gene-Edited Food.”

-Written by Jen Schwartz in Popular Science.  See article link here.

China lays groundwork to be major producer of GMO crops

China has a fifth of the world’s population, but only about 7 percent of its arable land. Farming plus safe and healthy foods are national obsessions. So it came as no surprise that government-owned ChemChina is poised to snap up Swiss-based Syngenta, one the world’s largest seed and pesticide companies. It’s a bet on the future by the country’s ruling elite.

The biggest challenge is overcoming widespread public skepticism. Resistance from groups like Greenpeace and the ultra-Maoist group Utopia that regularly vilify biotechnology research has had a great impact. In one recent survey, 84 percent of respondents opposed GMOs.

Despite this public wariness, agriculture and biotechnology topped the Communist Party’s wish list in its Central Document for the 14th straight year. The government has signaled it will actively encourage their development in order to boost food production.

The agriculture blueprint published in August recommended “pushing forward the commercialization of new pest resistant cotton, pest resistant corn and herbicide resistant soy beans.” The government has also designated biotechnology as a “strategic emerging industry” and has funded a large research program for GE crops.

The government also appears to be putting money where its directives are. According to to Wired, Caixia Gao, a plant geneticist at the Institute of Genetics and Developmental Biology, has used money from the Chinese Ministry of Science to engineer rice for herbicide resistance and corn for drought resistance. “We want to put our product on the market as soon as possible,” she says.

At present only two GE crops have been approved for cultivation: a virus resistant papaya authorized in 2006 and insecticide resistant cotton, which is engineered to include a natural bacterium, Bacillus thuringiensis (Bt) that naturally repels insects, approved in 1996. The use of the Bt bacterium dramatically reducing the need for pesticide use. Two GM rice crops have received Ministry of Agriculture safety certificates but the government has not approved them for commercialization. China also plants millions of Bt GM poplar trees that have been shown to have no harmful impact on the environment.

Bt cotton is the major GE crop grown. As of 2015 it accounted for 96 percent of the country’s total cotton acreage. China is the second largest producer of cotton in the world behind India, which is also a major grower of Bt cotton. According to the International Service for the Acquisition of Agri-biotech Applications (ISAAA), incomes of cotton farmers have increased “by approximately $220 per hectare due, on average, to a 10 percent increase in yield and a 60 percent reduction in insecticides” as a result of the use of Bt cotton.

In an attempt to stir public opposition to GE crops, Greenpeace alleged last January that farmers in northeast China were growing GM corn. It claimed 93 percent of samples taken in 2015 from corn fields in five counties in Liaoning province, which is one of the major grain growing regions of the country, tested positive for GMOs. If the allegations proved true, the crops were not sanctioned by the government and were instead the result of GMO plants tested in field trials being sold illegally to farmers. There have also been allegations of the illegal growing of GM rice in Hubei province.

A series of food scandals have contributed to the erosion of public trust in the food supply system. In 2008 milk and infant formula products were found adulterated with melamine. As a result, 54,000 babies were hospitalized and six died after developing kidney stones.

Other food scandals include: watermelons exploding after excessive use of growth hormones, borax in beef, bleach found in mushrooms, the sale of cooking oil recovered from drains and soy sauce made from arsenic.

These scandals have made the public leery of government food safety, increasing public suspicion about government-backed GMOs. A 2014 poll indicated that less than 1 percent of those surveyed accepted that GE foods were safe. Worries about the safety of GM crops have been exacerbated by unfounded rumors, often spread by Greenpeace and other NGOs, that they might cause infertility, cancer and other health problems.

“Many people in China still have limited knowledge about biotechnology, and rumors and misinformation is widespread,” noted a report on the food security challenges in China by the U.S. Department of Agriculture. “A common and persistent misperception is that consumers in biotechnology producing countries, such as the United States, do not themselves consume genetically modified food. The emerging media, such as the MicroBlog, WeChat, and on-line forums, are often used by opponents of agricultural biotechnology.”

Although the government has been hesitant about sanctioning the growing of GM crops, it has approved their large scale importation. China is the world’s largest importer of GMO soybeans, which along with imported GE corn is used as animal feed. In addition, it also imports soybeans to produce soybean oil, rapeseed oil made from GE rapeseed and sugar derived from GE sugar beets.

In 2013, President Xi Jinping signaled to the public a more accepting stance towards GMOs when he said China must “occupy the commanding heights of transgenic technology” and not yield that ground to “big foreign firms.”

In an attempt to cut down on its reliance on foreign biotechnology, the government has actively funded a major GM research program, disbursing at least $3 billion to research institutes and domestic companies to develop home-grown disease and drought resistant wheat, disease resistant rice, drought resistant corn and soybeans that produce more oil. In addition, there have been field trials and research conducted on GM peanuts.

“Agricultural biotechnology is one of the few technologies in which China is on an equal footing with the world’s best,” said Yan Jianbing, a corn genomics researcher at Huazhong Agricultural University in Wuhan. Yan works at the University’s laboratory of crop genetic improvement, which is a government designated GMO research facility.

A senior agriculture ministry official, Liao Xijuan, recently said the government plans to focus on new types of insect-resistant cotton and corn. There is a particular focus on developing China-engineered products and not depending on imported patented technology.

“We cannot lag behind others in GMO research,” said Han Jun, the deputy of the Central Office for Agricultural Work. “Our GMO market should not be saturated by foreign brands.”

To hasten that reality, the government backed the $43 billion ChemChina takeover of Syngenta.

In addition to investing in GM crops, China is also spending heavily on gene editing as a means of modifying plants and animals. Chinese scientists claim they are among the first to use CRISPR technology to make wheat resistant to a common fungal disease, disease resistant tomatoes and to make pigs that have leaner meat. Paul Knoepfler, an associate professor of cell biology and human anatomy at UC Davis School of Medicine, said he “would rank the U.S. and China first and second” in CRISPR-Cas9 technology.

Given the Chinese public’s distrust of GMOs, cultivation will likely proceed at a gradual and cautious pace. The government is likely to embark upon a major education campaign to reassure the public that GE foods are safe to consume before any major commercialization begins.

As part of its reassurance campaign for GM crops, the Agriculture Ministry indicated this summer that it will support new food labeling laws “based on a certain threshold” of GE content “at a suitable time.”

The government clearly recognizes the need to increase farm productivity at a time when arable land is increasingly disappearing as a result of spreading urbanization, curb the damage done to crops by pests and deal with the threat of climate change—all factors which will necessitate the application of GE technology to grow drought and flood resistant crops.

If China does utilize transgenic and gene editing technology to produce food on a large scale it could encourage other Asian nations to also grow GE crops given that China is the region’s largest trading partner and a major source of foreign assistance and investment.

Steven E. Cerier is a freelance international economist.

-Written by Steven E. Cerier in Genetic Literacy Project.  See article link here.