OILSEEDS

from OFI July/August 2023

Solex Thermal Science acquires Econotherm

RNA involved in silencing a gene. After three generations, the effect’s strength declined. The researchers observed more enduring epigenetic memory associated with pathogen or UV light-induced stress. Such abiotic stressors may even induce heritable changes leading to more environmentally-robust phenotypes.

Taking epigenetic knowledge from the laboratory to the field is the next step in realising the potential of this breeding strategy. The epigenomes of critical staple crops like rice, corn, wheat and barley have been picked over in recent years to identify epigenetic memory markers on stress-responsive genes that could be useful. Oilseed crops that have been investigated include rapeseed and, to a lesser extent, soyabeans.

Since rapeseed is a recently domesticated hybrid crop, it has yet to develop extensive genetic diversity. Less diversity in rapeseed DNA provides an opportunity for greater influence from epigenetic changes. Studies on DNA methylation of rapeseed genes indicate a sensitivity to heat and salinity. Overall, it seems that rapeseed genotypes with less methylation also have higher stress tolerance. Hence, crop varieties with this epigenetic profile could be agriculturally more resilient.

Researchers identified the epigenetic component that determines how efficiently a rapeseed plant uses energy. The way the plant uses energy predicts its vigour and yield. Artificial selection of the plants with this desired epigenetic trait became heritable upon self-fertilisation. Furthermore, hybrids from parental lines selected for high energy use efficiencies had a 5% yield increase.

“According to data available so far, recurrent selection seems to be the best tool for introducing epigenetic traits in crops,” says Miladinović. She cautions that, aside from rapeseed, most of this research has been carried out on model plants and not yet applied to crops. “As the genome becomes more complex, it is more difficult to control some things,” she says. This challenge has not deterred a few entrepreneurs.

Commercialisation

According to Forbes, the overall epigenetics market will grow to US$35bn by 2028. Most of that value will likely come from diagnostic and treatment products for human health, but crop enhancement firms are also gaining traction.

Last year, a start-up company called Sound Agriculture, established in California in 2013, announced it had secured US$45M in funding to support two new platforms for creating climate-resilient crops. The first focuses on adjusting a soil’s microbiome to increase a crop’s nutrient uptake efficiency. The second is aimed at developing specific heritable traits through altered plant epigenetics.

On-demand breeding, as it is called, accelerates plant trait development 10 times faster than gene editing, according to the company’s website. The firm hopes to identify and optimise traits that make plants more resilient in relation to climate change, diseases and reduced chemical use. They are also considering traits that optimise nutrition, appearance, and flavour.

Sound Agriculture claims that breeders can progress from concept to a plantlet with a new trait in 15 days, compared to the 150 days needed for gene editing.

A similar company was founded by plant biologist Sally Mackenzie, currently at Pennsylvania State University, USA. Mackenzie discovered that a plant protein, known as MSH1, encodes for processes that determine DNA binding and recombination suppression.

She says evidence indicates MSH1 is environmentally adaptive, so breeders can direct how a plant adjusts to its environment by targeting methylation on the gene that encodes MSH1.

In Nebraska, where Mackenzie was previously a professor at the University of Nebraska-Lincoln, Epicrop Technologies was set up in 2013. After receiving funding from TechAccel, the company launched platforms to use epigenetics to improve two crops – strawberries and canola. It hopes to improve the strawberry’s disease resistance and environmental range, while its research efforts for canola focus on yield.

The future of epigenomic breeding has many exciting prospects, according to Miladinović. The involvement of a variety of scientists using a range of tools means a quicker pace of discovery. A combination of epigenetics, genomics, and other omics tools with high-throughput analytics tools and artificial intelligence allows more data to be gathered and evaluated faster.

Miladinović says that since the concept for epigenetic breeding is still unproven in some crops, there is no way to know if desired traits will be heritable over many generations of a plant. “We still need to go case by case, crop by crop, and trait by trait,” she says. Even with classical breeding, there are some traits that are easier to maintain than others. She says researchers will have to be careful to first identify traits with potential for heritable change.

One limitation of epigenetics is made obvious by the earlier example of Bt corn. Scientists cannot add or remove any information from a plant’s genetic code. This means that incorporating the gene from a natural pesticide into a crop plant is off-limits in the epigenetic breeding playbook. If a gene responsible for some self-protective measure to ward off pests is not already present in the genome, there is no epigenetic course of action to address such a threat.

Another issue is that a plant epigenetically bred to resist heat may be left vulnerable if exposed to flooding. Miladinović says epigenetics is not going to produce crop varieties that can be planted everywhere. More likely, the discipline will assist with the new trend of agroecology, where crops are specialised for specific regions. “Farmers will not grow the same variety for different countries around the world, like they do now with seeds from a big corporation,” she says. Instead, farmers will select crops with one or two traits best suited for their agroecological area.

“We have discovered something beyond the classical genetics alphabet,” says Miladinović. “We have the potential to create a plant genotype that is really adaptive to a certain climate or a certain soil. This new breeding tool opens new ways to explore genetic diversity so we can assure stability of crops production as it faces environmental change.”