CRISPR Genome Editing Strategy Could Improve Rice, Other Crops

By Amy Quinton

Scientists at UC Davis and collaborators at the Joint BioEnergy Institute (JBEI) have used CRISPR technology to genetically engineer rice with high levels of beta-carotene, the precursor of vitamin A. The technique they used provides a promising strategy for genetically improving rice and other crops. The study in Nature Communications was published by a research team led by Pam Ronald, a professor in the Genome Center and the Department of Plant Pathology at UC Davis and Scientific Lead of Plant Pathology at JBEI.

Rice grains

UC Davis plant scientists used CRISPR technology to introduce beta-carotene, the precursor to vitamin A, into rice. The biofortified rice is shown on the right. Genetically modified “golden rice” enriched with carotene is already grown in the Philippines as a way to fight vitamin A deficiency. CRISPR could be a new route to such crop improvements. (Photo by Oliver Dong, UC Davis)

Rice is a staple food crop for more than half the world’s population. Golden Rice, a genetically engineered rice with high levels of beta-carotene, has been approved for consumption in more than five countries, including the Philippines, where vitamin A deficiency in children is widespread. Because of the social impact of the Golden Rice, the researchers chose the high beta-carotene trait as an example.

Conventional plant genetic engineering uses a bacterium or a particle gun to transfer genes encoding desired traits into the plant genome. In this case, researchers would use a bacterium to take beta-carotene producing genes and transfer them into the rice genome. But those transgenes can integrate into random positions in the genome, which can result in reduced yields.

“Instead, we used CRISPR to precisely target those genes onto genomic safe harbors, or chromosomal regions that we know won’t cause any adverse effects on the host organism,” said first author Oliver Dong, a postdoctoral scholar in the UC Davis Department of Plant Pathology and Genome Center.

Targeted insertion of genes

In addition, the researchers were able to precisely insert a very large fragment of DNA that does not contain marker genes. By contrast, conventional genetic engineering relies on the inclusion of marker genes in the inserted DNA fragment. These marker genes are retained when the plant is bred over generations, which can often trigger public concern and stringent regulations of the transgenic products before their entrance to the marketplace.

“Scientists have done targeted insertions before and without marker genes, but we haven’t been able to do it with such big fragments of DNA,” said Dong. “The larger the fragment of DNA, the more biological function or complex traits we can provide the plants.”

Dong said this opens up the possibility that genes controlling multiple desirable traits, such as having high levels of beta-carotene as well as being disease-resistant or drought-tolerant, can be clustered at a single position within the genome. This can greatly reduce subsequent breeding efforts.

Other authors include Shu Yu, Rashmi Jain, Nan Zhang, Phat Duong, Corrine Butler, Yan Li, and Li Tian from UC Davis; Anna Lipzen, Joel Martin, Kerrie Barry and Jeremy Schmutz at the the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab).

The work was funded by the U.S. Department of Energy, the Winkler Family Foundation and the Innovative Genomic Institute.

Pam Ronald Elected to National Academy of Sciences

Pam Ronald, scientific lead of plant pathology at the Joint BioEnergy Institute (JBEI), was elected to the National Academy of Sciences in recognition of her distinguished and continuing achievements in original research. She joins 100 scientists and engineers from the U.S. and 25 from across the world as new lifelong members and foreign associates.

All new NAS members and foreign associates are nominated by existing NAS members for outstanding contributions to their field. Only 100 or fewer researchers make it through the selection process each year. The four new members bring the number of Berkeley Lab scientists elected as NAS members to 84.

On top of being one of the highest honors a scientist or engineer can receive, membership to NAS also provides a platform for advocacy and leadership. Since its creation in 1863, NAS has served as a nonpartisan, nonprofit institution that offers science, engineering, and health policy advice to the federal government and other organizations.

Pam Ronald is also a distinguished professor in the College of Agricultural and Environmental Sciences at UC Davis. Ronald’s research focuses on plant genes that control resistance to disease and tolerance to environmental stressors, with the goal of using genetic engineering to improve food security for the world’s poorest farmers. Read more.

Sloan Fellowship Will Help Patrick Shih Investigate Ancient Origins of Photosynthesis

Patrick Shih, JBEI’s Director of Plant Biosystems Design who also serves as an Assistant Professor at the Department of Plant Biology at UC Davis, was recently selected as a 2019 Alfred P. Sloan Research Fellow in Computational and Evolutionary Molecular Biology.

Shih, will use this fellowship to help fund his research to reconstruct the evolution of photosynthesis, a process that originated billions of years ago.

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Mortimer Participates at AAAS Forum on Science & Technology Policy

Jenny Mortimer, JBEI’s Deputy VP of the Feedstocks Division and Director of Plant Biosystems Design, participated at a 2018 AAAS Forum on Science & Technology Policy panel entitled “Science Competitiveness in Relation to Public Support for Science”. Panelists discussed how the scientific community must work to maintain societal relevance and build trust. Mortimer presented a code of ethics for scientists recently developed by the World Economic Forum’s Young Scientists community. The code serves as a tool to nurture a positive change of culture in the research world by not only guiding and shaping the behavior of individuals but also the processes of the scientific institutions that are to facilitate this cultural shift.

Plants Really Do Feed Their Friends

– By Christina Procopiou

Researchers at Berkeley Lab and UC Berkeley have discovered that as plants develop, they craft their root microbiome, favoring microbes that consume very specific metabolites. Their study could help scientists identify ways to enhance the soil microbiome for improved carbon storage and plant productivity.

Just one gram of soil contains tens of thousands of microbial species. Scientists have long known that plants impact the composition of the soil microbiome in the area surrounding their roots by sending out chemicals (metabolites). Yet, little research had gone into the relationship between specific metabolites that plants release and the microbes consuming them. Now, a new study delving into this relationship has just been published in the journal Nature Microbiology.

The work was led by first author Kateryna Zhalnina, postdoctoral researcher in the Berkeley Lab’s Environmental Genomics and Systems Biology (EGSB) Division and Earth and Environmental Sciences Area (EESA), and corresponding authors Trent Northen, senior scientist in EGSB, and Eoin Brodie, senior scientist in EESA. With expertise in soil science, microbial and plant genomics, and metabolomics, their team explored these potential metabolic connections in the rhizosphere of an annual grass (Avena barbata) common in California and other Mediterranean ecosystems.

Other current or former Berkeley Lab scientists contributing to this studying were: former JBEI scientists Nasim Mansoori and Dominique Loqué, Katherine Louie and Benjamin Bowen of EGSB; Zhao Hao, Ulisses Nunes da Rocha, and Ulas Karaoz of EESA. Shengjing Shi and Heejung Cho of UC Berkeley were also co-authors. The DOE Office of Science supported the research. The authors used a hydroponic setup at the Joint BioEnergy Institute, a DOE Bioenergy Research Center. This work was done in part through the DOE Joint Genome Institute Community Science Program. Read more in the Berkeley Lab News Center press release.

Study speeds transformation of biofuel waste into useful chemicals, Phys.org

JBEI’s Feedstocks Division collaborated with Sandia National Laboratories in a study that looked into efficient ways to turn discarded plant matter into chemicals.

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Mortimer participates at WEF’s Annual Meeting of the New Champions

Jenny Mortimer, JBEI’s Deputy Vice President of the Feedstocks Division and Director of Plant Systems Biology participated at the World Economic Forum’s (WEF) 2017 Annual Meeting of the New Champions alongside business and political leaders. The annual meeting whose overall theme this year was inclusive growth in the fourth industrial revolution took place from June 27-29 in Dalian, China. At the meeting Mortimer participated at a press conference entitled “Young, talented and fighting for science” which can be viewed here.

Mortimer was selected in 2016 to be part of WEF’s Young Scientists community which brings together the most forward-thinking and advanced young scientific minds in the world under the age of 40. The selected individuals have demonstrated their commitment to public service and actively play a transformational role in integrating scientific knowledge into society for the public good. To learn more about her experience joining this community read this article.

A Whole-Genome Sequenced Rice Mutant Resource for the Study of Biofuel Feedstocks

Researchers at the DOE Joint BioEnergy Institute (JBEI) in collaboration with the Joint Genome Institute (JGI) are reporting the first whole-genome sequence of a mutant population of Kitaake, a model variety of rice. Their high-density, high-resolution catalog of mutations facilitates the discovery of novel genes and functional elements that control diverse biological pathways. Read more

JBEI’s Vy Ngo Awarded Grace Fimognari Memorial Prize

Vy Ngo, student assistant with JBEI’s Feedstocks Division was awarded the Grace Fimognari Memorial Prize during UC Berkeley’s Molecular & Cell Biology (MCB) 2017 Commencement. The Prize established in 1969 is awarded to outstanding graduating senior in the Biochemistry and Molecular Biology (BMB) emphasis of the MCB major. Ngo was mentored by Jenny Mortimer, JBEI’s Director of Plant Systems Biology, initially through Berkeley Lab’s Community College Internship (CCI) program in 2015 and then completed the Science Undergraduate Laboratory Internship (SULI) program in 2016. She continued to intern at JBEI as she transitioned to UC Berkeley.