CRISPR and Crop Improvement at AgriLife Research

We talk to seed grant winners and facility leaders in the Texas A&M AgriLife Research genome-editing pipeline.

Judging by the vast number of review articles on the topic, agricultural and life sciences researchers are becoming increasingly aware that new gene editing technologies can save so much time and money as to create entirely new avenues of crop improvement. Yet for many labs, these technologies remain out of reach because they require such high investments in infrastructure and expertise.

To provide researchers with gene-editing capabilities, in November 2017 Texas A&M AgriLife Research coordinated the efforts of three core facilities: the internationally recognized Genomics and Bioinformatics Service (TxGen), founded in 2010, as well as the brand-new Crop Genome Editing and Multi-Crop Transformation facilities. AgriLife Research also awarded a significant amount of money to 15 teams of investigators for the integrated services of this “genome-editing pipeline.” These seed grants roughly cover the creation of three to five transformed plants for each team.

In April 2018, we spoke with three investigators whose teams won a seed grant and with leaders of facilities within the genome-editing pipeline to check on their progress.

Background

The new gene-editing technologies have become widespread because they offer drastically faster, cheaper, and more precise results than previous methods. And unlike with previous methods, gene-edited plants need not contain DNA from a foreign organism. The new technologies employ features found in bacterial immune systems — Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) — that help seek out and destroy the genetic material of invading viruses. This targeting system is now being utilized by scientists to seek out genes for editing.

Because plants edited with CRISPR need not contain foreign DNA, CRISPR can be thought of as a shortcut in traditional breeding methods, says Dr. Michael Thomson, director of the Crop Genome Editing Lab. The USDA corroborated that viewpoint in March, declaring that it does not consider CRISPR-edited plants to fall under the same regulatory oversight as genetically modified organisms.

Plant Scientists’ Perspective

Leading one of the seed grant projects is Dr. Libo Shan, professor of plant pathology and microbiology and interim director of the Institute for Plant Genomics and Biotechnology. Her team’s project in the genome-editing pipeline concerns the interaction between cotton and a fungal pest, and she talks enthusiastically about the promise she sees for CRISPR-based technologies.

“With the technologies developed in the past few years, increased application of genome editing is almost everywhere, including the medical and agricultural sectors,” Shan says. “The AgriLife Research genome-editing seed grant program is really a good idea in terms of fostering an active research environment that encourages faculty to implement the technology into their research.”

For two other seed grants, principal investigators Drs. Amir Ibrahim and Jackie Rudd co-direct the AgriLife Research Small Grains Improvement Program. Ibrahim is stationed at College Station and Rudd at Amarillo.

The wheat varieties they want to improve must continue to meet high standards in yield, forage production, and bread-making quality, as well as tolerance to drought and heat and resistance to pests and diseases. The researchers were not able to talk about their specific projects due to the guidelines for protecting intellectual property. However, they did point out that their teams usually take 10–15 years to release a new wheat variety. With CRISPR, Rudd and Ibrahim expect the process to take only 5–7 years.

Cutting development time in half enables Ibrahim and Rudd to pursue experiments they would not have even attempted otherwise. And gene editing itself is not something they would have attempted if the pipeline did not exist, Ibrahim says. “The infrastructure is huge, and it takes a team effort to create edited plants.”

Ibrahim adds that gene editing does not replace traditional breeding methods but rather adds another tool to the wheat improvement arsenal.

Rudd is optimistic about the effect of CRISPR and the pipeline on his team’s projects. “I’m always a little skeptical around new technology, but I really think this is going to work,” he says. “Wheat is the most widely grown grain crop in the world and I’m thrilled that we have this opportunity to accelerate our wheat improvement program.”

Step 1: Crop Genome Editing Lab

The 15 seed grant projects entered the genome-editing pipeline in February 2018. Michael Thomson, who holds the H.M. Beachell Rice Chair in the Department of Soil and Crop Sciences in addition to directing the Crop Genome Editing Lab, acts as the first point of contact.

“A lot of coordination is involved before we can get started,” Thomson says.

He’s been discussing with investigators on each seed grant what genes and plant varieties they would like to target. He has also been arranging for each of the research teams to begin growing plants that the Multi-Crop facility will eventually use for the project — at least 1,000 immature embryos will be needed as initial explant.

And, Thomson has been checking whether each grant recipient knows the exact genetic sequence of target genes. His lab will need this information to create the guide RNAs that will direct the editing machinery to the location of the planned edit in the specimen’s genome. So, much of the pipeline’s work right now involves genetic sequence analysis and bioinformatics, and the Gene Editing Lab consults often with TxGen.

Thomson’s lab plans to complete the guide RNA design and transformation construct development for each seed grant project by the end of August. After that, the next step in the pipeline is the Multi-Crop Transformation Facility.

Multi-Crop Transformation Facility

Co-directing the Multi-Crop Transformation Facility is a married couple with over a decade’s experience in working together on plant tissue culture and plant transformation. Marco and Mayra Molina gained expertise at corporations that include Monsanto, Bayer CropScience, and DuPont Pioneer before joining Texas A&M University in 2016.

Plant transformation is a notoriously tricky process even with simple model plants, says Marco Molina. The protocol becomes even trickier with sophisticated commercial crops renowned for their high yields, hardiness, or high quality. Temperatures, light levels, and incubation periods for each step in the process must be tightly controlled for months. In addition, crop transformation protocols usually differ widely even between closely related cultivars. A new protocol must be developed or adapted for every species or plant variety.

The Multi-Crop Transformation Facility shepherds research teams through this treacherous process. The lab aims to save researchers time in multi-year experiments, but also to train graduate students to perform plant tissue culture and transformation techniques, says Mayra Molina.

The Molinas are already leading other transformation projects and optimizing their protocols while they wait for August, when they will receive genetic constructs from the genome editing lab and plant embryos from grant recipients. The full transformation process depends on the crop and could take 3 to 12 months. The next step in the pipeline will be for TxGen to confirm that the transformed plants contain the proposed edits.

Genomics and Bioinformatics Service

Already a busy facility, TxGen is about to become much busier. While participating in the genome-editing pipeline, TxGen recently expanded its capabilities by becoming a Perkin-Elmer Center of Agricultural Excellence. An infusion of new technology will allow the facility to process at least 50,000 samples per year at a fraction of its previous price — or, simply put, to “genotype a really large number of samples at a price point that’s unheard of,” says Dr. Charles Johnson, director of TxGen. “We can reach these new benchmarks because besides PerkinElmer we are now the only lab in the world with access to PerkinElmer’s custom AgriGenomic DNA preparation chemistry.”

“Our role in the exciting seed grant program is to provide sequencing and bioinformatics support,” Johnson says. Sequencing and bioinformatics are needed for developing the crop-specific DNA reference. That reference is used first during the CRISPR design phase, then to validate the specific gene modification, and finally to validate its effect on RNA expression.

And Beyond, Toward a Second Green Revolution

Genome editing aims to change something in a plant’s form or function, or, in other words, its phenotype, says Dr. Bill McCutchen, executive associate director of AgriLife Research. Yet the relationship between phenotypic traits and genetic sequences is far from well-understood, he says, adding that although genome editing shows tremendous promise, several challenges must be overcome before it can truly become a routine part of crop improvement. Overcoming these challenges is an overarching goal for the three labs in the genome-editing pipeline. As the labs work on their clients’ projects, they are also perfecting their methods to make them more precise and efficient.

“The Multi-Crop Transformation Facility is optimizing tissue culture regeneration, which is genotype-specific and species-specific,” McCutchen says. “And the Crop Genome Editing Lab is optimizing the CRISPR delivery system.”

The seed grant program should bear fruit in the latter half of 2018. Once TxGen confirms that edits were made correctly, the transformed plants will return to their research teams and be tested for functional changes. If new traits appear, some teams may approach AgriLife Research Corporate Relations and Texas A&M Technology Commercialization to inquire about protecting their intellectual property.

“Genome science technologies make a worthwhile investment for us at an agency level,” McCutchen says. “Our genome-editing pipeline aligns several related technologies to address well-defined basic and applied problems and, in unexpected and holistic ways, help our researchers transform information into knowledge.”

We look forward to speaking with the seed grant recipients again when they can tell us more about their edited crop plants.