When attempting to produce new traits and properties in plants, it’s commonplace to try and expose them to stressful conditions alongside mutagenic agents in the hopes that this will help induce the formation of resistance genes. This process sometimes is successful, but it involves a large amount of trial and error, as most experiments involving random mutations tends to. There’s also the likelihood of plants dying during the stress exposure, setting the researchers back even further. But what if you could create such resistance without ever having to create or add new genes? And what if you could do so without even needing to actually have plants be put under real stresses?
Methylating A Miracle
Sounds like a bit of a pipe dream, doesn’t it? Yet, it is precisely this that epigenetics allows us to do. As the prefix “epi” implies, it involves the parts that act upon our genetics. The most frequent control system that this is used to refer to is DNA methylation, where genes are turned on or off based on whether they have a methyl group tagged onto them. The methylation of a gene silences it and prevents its RNA and possible protein from being transcribed. By crossing different lines of plants, including producing inbred lines, you can alter the general pattern of gene regions that are methylated. This, in turn, can also reveal unique variations in stress response and other characteristics.
A team of researchers at the University of Nebraska Lincoln and Penn State decided to focus on a specific, important gene sequence in plants known as MutS HOMOLOG1 (MSH1), which acts as a DNA repair gene for the cellular mitochondria and plastids (chloroplasts are an example of a plastid, though there are many others). The phenotypic effects of this gene include major growth and development periods for plants, such as flowering and leaf formation. Interestingly, when a mutant lacking this protein production was created, it had obvious negative effects on growth at all stages, but it also presented with higher levels of tolerance to heat, light, and drought stresses. The plants acted as if they were under attack from these stressful conditions even when they were not.
When searching for the reason for this, it was discovered in past studies that these responses happen when MSH1 proteins are depleted from the plastids, which causes them to enact genome wide methylation changes. This gene inactivation and activation includes turning on defense responses, stress resistances, phytohormone production, and more. RNA interference (RNAi) suppression of MSH1 RNAs has shown a similar result and a intriguing effect was shown in sorghum and tomato experiments in 2014 and 2015. The phenotypic benefits of stress tolerance appear to be inheritable as a kind of “memory”, per se, into future generations. If a mutant with the gene turned down is crossed with a normal wild type line, their offspring are normal and have the gene functioning properly, but also exhibit the enhanced tolerances. Though this doesn’t happen in all offspring, so multiple lines are often needed.
The Memory of Soybeans
The researchers decided to take this effect and see if it could be applied to soybeans, one of the most important crops in the world today. Over the past several decades, yields for this crop have been improved to a high level, but stresses resulting from things like climate change threaten this part of the food supply. To create the needed active resistance traits, the scientists made several lines of soybeans with the common varietal known as Thorne. The RNAi muted lines for msh1 were set up as the “memory” lines that would retain the developed traits and they were grouped based on how extreme the negative phenotypes from msh1 loss were for the line.
A transcriptome analysis showed the up and down regulation of transcribed genes in the genomes for each line and presented similar impacts as what had previously been reported in Arabidopsis model test lines. While specific genes didn’t overlap, the general gene regions that were altered did and were again defensive-related traits. Two areas found to be activated in soybeans that had not been seen in the model plant or in tomatoes were those related to the metabolism of vitamins and senescence (aging) of cells. This appears to be a species-specific phenotype response to loss of the gene.
The epigenetically-altered lines were then crossed with wild type soybeans, creating three offspring groups based on whether the parent epigenetic lines were normal, intermediate, or extreme for negative msh1 loss traits. 30 child lines were made from each group, including a control wild type set. What was immediately apparent is that the amount of variation among the epigenetic cross descendents was far higher than the control wild type group, in both positive and negative trait outcomes. Selected lines in the former groups showed increased yield across multiple years of testing, with the only penalty being slightly lower oil concentration.
Additionally, these phenotypes in the epigenetically altered offspring lines were remarkably stable no matter the location or growth conditions. The same could not be said for the wild type lines. This is a good sign showing that the vigor of these improved resistance and yield traits is resilient to growing region changes.
Sources of Stable Crops
Overall, this study showed that not only are msh1 gene perturbation effects applicable to further plant species, but that these traits are inheritable within offspring generations and are highly stable and resilient no matter where they are grown. This knowledge offers opportunities for developing stress resistance traits in key crop species without altering their genes directly and instead creating a favorable set of activated gene resistances. For the purposes of food security and the future, having stable yields are of major importance.
Photo CCs: Soja por doquier – panoramio from Wikimedia Commons
