Gene editing improves the digestibility of beans

A team of researchers from Embrapa has, for the first time, performed gene editing in beans to develop a new variety with fewer antinutritional factors linked to a group of substances called raffinose, a type of compound known to cause digestive discomfort and flatulence in humans. The scientists were able to eliminate genes related to the production of oligosaccharides (carbohydrates) from the raffinose family, based on their knowledge of the bean genome and their mastery of genetic engineering tools such as CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats).

Two genes in the plant's genome were deactivated, according to researchers in Molecular Biology at Embrapa Arroz e Feijão (GO), Josias Correa and Rosana Vianello, coordinators of the unprecedented study. Vianello says that the research analyzed the levels of oligosaccharides from the raffinose group in different tissues and development stages of the bean plant. This information was evaluated in relation to the knowledge already produced by the study of the bean genome, sequenced almost ten years ago.

The goal was to understand the expression pattern of potential target genes that would be behind the biosynthesis of raffinose. In this process, the researchers investigated the expression pattern of genes, and two of them, raffinose and stachyose – another difficult-to-digest oligosaccharide – were identified and inactivated. These genes had their expression blocked by adapting gene editing tools from CRISPR systems.  

Vianello believes that the CRISPR technique is revolutionary for gene editing. “In the case of characteristics related to the technological and nutritional quality of grains, the technique emerges as an important tool for editing specific genes and, with this, achieving precision improvement, opening new perspectives for the development of varieties that are more attractive to producers and consumers,” he says.

Edited plant generations

According to the researcher, the next stage of this study, which is already underway, is to advance generations of edited plants with the raffinose pathway genes deactivated. This involves planting seeds, growing plants, harvesting and replanting seeds in a controlled greenhouse environment. The intention, as in every genetic improvement process, is to make the heritability of the new characteristic stable.

“The edited generation T0 is producing T1 seeds. We will plant T1 and hope that the edit will be transmitted to the next generation. Only with the advancement of generations, from T1 to T2 and from T2 to T3, will we have the edits in homozygosity (which makes the edited characteristic with stable heritability) and we will be able to evaluate the phenotype of the plants (set of characteristics resulting from the interaction with the environment), in addition to testing lines in different locations that could become a new variety”, highlights Vianello.

The phenotyping tests will also help determine how significant the reduction in raffinose levels in the bean grain was. All this work could lead to the launch of a genetically edited variety within a period of five to eight years.

This research is part of a project entitled: “Development and application of new biotechnological solutions in the genetic improvement of common beans”, funded by the National Council for Scientific and Technological Development (CNPq), under the leadership of Embrapa Genetic Resources and Biotechnology researcher Francisco Aragão.

Human digestive system does not digest molecules of the raffinose family

Beans are a source of amino acids, fiber and minerals that are important for health. However, beans, like other foods, contain antinutritional factors, such as phytic acid, tannins and carbohydrates of the oligosaccharide type, of which the raffinose family is a part. The human digestive system does not produce the enzymes necessary to digest molecules of the raffinose family.

Despite this, there are microorganisms in the intestinal tract capable of digesting it, but in this process, fermentation can result in the production of carbon dioxide, hydrogen and methane, which are components that cause flatulence. In addition to beans, other foods that also contain raffinose are lentils, cabbage, broccoli, asparagus, Brussels sprouts and whole grains.

One of the most common alternatives to improve digestion, in the case of beans, is what you can do at home: soak the beans overnight and change the soaking water. The research carried out reduces antinutritional factors such as raffinoses, since genes in the plant that trigger the production pathway of these compounds were eliminated.  

“Molecular scissors” for cutting DNA

Genetic engineering has gained a new perspective thanks to CRISPR-based systems. The process of editing genetic material has become more agile and precise, opening up possibilities for the generation of new products, not only in food, but also in cultivars and bioinputs that can help combat pests and diseases in the field or make plants more tolerant to dry spells, for example.

The knowledge that makes it possible to use CRISPR systems, a kind of guide for current research, is the result of a work published in 2012 by two scientists: Emmanuelle Charpentier, from the Max Planck Institute for Infection Biology, and Jennifer A. Doudna, a biochemist at the University of California.

They released a kind of step-by-step guide on how to apply CRISPR-based techniques that work like “scissors,” making it possible to cut a specific part of the DNA, causing the cell to produce certain molecules or not. Because of this, Charpentier and Doudna won the 2020 Nobel Prize in Chemistry.