A magic toolbox to build better crops

Source: Univ. of Maryland College of Agriculture and Natural Resources

by Kimbra Cutlip

Imagine if farmers had access to a magical toolbox that helps them tweak their crops to grow faster, resist pests, or bloom early—no need for years of trial-and-error breeding. Well, that’s sort of what University of Maryland’s Yiping Qi and his colleagues have built: a toolkit full of powerful genetic tools that plant scientists can use to develop improved crop varieties for farmers around the world.

Plant scientists often tweak the DNA of a plant to study how certain genes work or what characteristics they convey. But this usually requires a unique experiment for every gene or piece of genetic code, and a multitude of genetic tools, which can be slow, complex, and hard to scale up.

The toolkit acts like a Swiss Army knife for editing plant DNA or enhancing gene expression. Image credit - University of Maryland

Qi and his team have adapted the gene editing technology CRISPR to develop a comprehensive, all-in-one toolkit that makes editing plant genes much easier and quicker, and allows for multiple edits at a time. They described their work in a research paper published in Plant Cell.

“This work demonstrates the development of a comprehensive CRISPR genome engineering toolbox that aids large-scale screening,” Qi said. “This kind of genomic work is still in its infancy in plants, and it is very important to have such tools.”

The toolkit acts like a Swiss Army knife for editing plant DNA or enhancing gene expression. With this single system, scientists can:

• Edit a collection of genes up to a genome scale, using CRISPR-Cas9 and Cas12a, which are like precision scissors that can cut DNA at specific locations, allowing for targeted modifications.​

• Fine-tune single DNA letters within a gene (called base editing) without cutting both DNA strands, which enables precise corrections.​

• Turn genes on using CRISPR-Act3.0, which lets them study the function of genes and change a plant’s traits.

These tools work in many different kinds of plants, and what is most exciting to the researchers is that they can scale their experiments to explore hundreds or thousands of different gene edits at once, and in combination. That’s a huge leap forward.

To demonstrate that their toolkit works, Qi and his colleagues ran experiments in two kinds of plants.

In rice, they used the toolkit to change specific letters in a gene, and then exposed the rice plants to a common herbicide. They then confirmed that among the surviving plants, the genes they had changed helped block the chemical.

In a small plant called Arabidopsis, they turned on a gene that makes plants flower early, using their tool to find the best "switches" for triggering early flowering, which could be very helpful for speeding up crop growth.

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Additional researchers from AGNR who co-authored this study are: Post-Doctoral Associates Yanhao Cheng and Rushil Ramesh Mandlik, Assistant Research Professor Gen Li, and former Post-doctoral researcher Changtian Pan.

The following interns from Montgomery Blair High School contributed to this research: Aileen Qi, Doris Wang, Sophia Ge.