Crops and climate change: How studying epigenetic changes during droughts may help build hardier crops
Nancy Brill| Epigenetics Literacy Project | June 20, 2017

What would it look like if the rate of an environmental change such as drought outpaced a plant’s ability to adapt to that change?  What if those plants were important agricultural crops and we could no longer grow them?

The scientists in the Lemaux laboratory in the Department of Plant and Microbial Biology at the University of California-Berkeley, led by Peggy Lemaux, are looking for ways to prevent exactly that from happening.

Many scientists now believe that epigenetics may play a role in the evolution of plants. “And quite frankly,” said Lemaux, “we’re dealing with that now,” i.e. the need for plants to adjust to environmental changes rapidly. “We are working on a cereal that is natural drought- and flood-tolerant, Sorghum bicolor. I want to understand that process, how sorghum, a staple crop in Africa, is able to do that and how microbes attach to roots.” Some of those mechanisms involve epigenetics and some will involve the microbiome, which lives in the soil near the roots.

Lemaux’s study is a five-year project entitled “Epigenetic Control of Drought Response in Sorghum” (EPICON), which follows a four-year historic drought in California that, despite recent flooding, created economic, agricultural, and natural resource impacts.

Because California produces 70 percent of the nation’s fruit and tree nut farm value, 55 percent of vegetable farm value, and 20 percent of the nation’s milk, environmental stressors on crop and dairy production have rippling effects on the U.S. food economy.

The effects of drought are not always seen right away. According to the US Department of Agriculture, there is a lag in retail price increases for produce because of the time it takes for the weather to alter crop production.

When asked how her research methods are novel compared to other research in epigenetics, Lemaux got right to the point: “People have done a lot of things in the greenhouse and chambers to study drought tolerance, but it doesn’t always work when it gets taken to the field.”

Lemaux said she won’t do anything unless she takes it to the field – in her experience this is the only way to find out if the research is useful.

However, measuring those traits in field conditions is also the greatest challenge in her research. When working in the field she is limited to the growing season, which is the beginning of June through early October for sorghum. They have 21 individual plots, and because sorghum can be drought-tolerant before or after the plant flowers, the team collects pre- and post-flowering drought samples from the field from all plots. They are trying to control a lot of conditions – temperature, water, etc. — but it is not always possible to control so much in the field as compared to the greenhouse. “Other groups have tried to do similar drought studies as us, but it rains on them,” she said.

Plants release metabolites that also attract microbes. What’s novel about Lemaux’s research is that she’s also studying the microbiome, the bacteria that live in the soil of the sorghum plants. “Within one week or 10 days of imposing drought you can already see the microbial populations changing,” she said. They are examining this microbiome under replicated treatments of water or no water for a three-year trial to correlate changes within this microbial community to sorghum’s drought tolerance.

What makes the field research even more difficult is that Lemaux and her team are collecting leaf, soil and root tissue in the middle of the field in 105 degree heat. The materials then have to be brought into the lab, crushed, and put into liquid nitrogen within two minutes. “The signals we receive from plants both between and within the cell are short-lived, so if we waited the signals are gone,” she said.

Those samples are then taken to two labs that process the samples and are collaborative partners in Lemaux’s project – the Pacific Northwest National Lab (PNNL) and the Joint Genome Institute (JGI). PNNL looks at metabolomics, the metabolites released by the plants, and proteomics to see if the proteins they find matches up at the DNA level. The JGI looks at the plant samples’ epigenetics to associate the characteristics of sorghum under drought conditions with certain genes that make more or less of those expressions.  Both the PNNL and JGI receive the same plant samples to bring those two data sets together.

Lemaux’s lab also does genome editing and genetic engineering, so “for example, if we see that during pre-flowering drought a particular protein might be a regulator or structural protein, we can ask if that means anything. What we can do is engineer it – edit it to turn it off, or engineer it to turn it on – to see if we get a phenotype that is drought tolerance.”

This process will help them understand how other crop plants can be made more resilient to environmental effects. If this knowledge can be transferred to other plants it could have a tremendous impact in managing plant stress related to environmental changes. “If we do figure this out, then we can use some of these technologies to improve capabilities of other crop plants to survive drought and flood. We’re creating something that’s happening rapidly, so we are helping plants to evolve faster,” Lemaux said.

Epigenetic modifications can occur quickly –if we can understand how epigenetics helps plants deal with environmental changes than Lemaux’s research can help armor plants with changes that will happen rapidly. “California does not have an average year with weather and it is much more severe here than it has ever been which will affect food, fuel and feed production,” she said. “So, I feel there’s an important need for plant biologists to address this. Given global climate change and also the fact that water tables have gone way down this is something we can’t ignore. Plants have had centuries to evolve. We don’t even have decades now.”

Nancy Brill is a freelance writer from PA. She has a Ph.D in Entomology and an M.S. in Horticultural Science, both from NC State University. Her website is  Follow her on Twitter @DrNancyLBrill

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