Epigenetics and old vines

By Jamie Goode | 19th February 2021

Have you ever got close and personal with a holly bush? The European holly, Ilex aquifolium, exhibits a phenomenon wonderfully named as heterophylly. This means that although all its leaves are genetically different, they can vary quite widely in terms of how prickly they are. Rummage around a holly bush and you’ll find mature leaves that have no spikes, as well as leaves that are very spiky indeed. Now we might expect leaves on the same plant to differ in shape and even colour a bit (depending on where they are and the environmental conditions, particularly light intensity). This is because they have grown at different rates, or have adapted a bit to low or high light. But to have leaves that have developed completely different morphology – smooth or spiky – is a bit more unusual. In 2013, a research group from Spain studied this, and they found out that whether or not the leaf was spiky was because of a mechanism called epigenetics. The plant uses epigenetic changes, which aren’t changing the DNA code, yet which can still be hertitable, to adapt to its environment. In this case the plant dials spikes up or down depending on herbivory – whether it is being grazed on by animals or insects.

Epigenetics and old vines

Epigenetics is a relatively new research area in molecular biology, and of late this term has become a bit of a buzz word. It’s a field that looks to be highly relevant to agriculture, including grape production. It is thought that epigentic modifications are particularly important in plants because it allows them to change how they grow in response to the environment, which can be quite changeable.  Epigenetics could be a way that vines 'remember' environmental stresses, and that by applying insights from epigenetics, it might be possible for viticulturists to adapt vines to the difficult conditions they might later be exposed to, effectively pre-priming for a stress event. From a South African perspective, it’s of great interest because of the great old vine vineyards that the country has. While everyone recognizes the quality potential of these old vineyards, no one can really explain why they get better with age. It’s likely to be a number of reasons, of which epigenetics could be an important one.

Epigentics is complex, and hard to explain in a straightforward way. It's probably best to begin with a quick review of genetics. In each of our cells we have a full set of genes – some 19 000 of them – in two interlocking strands of DNA. There are equal contributions from our mother and our father. This is the DNA library that makes us 'us', and the key factor is how these genes are then read by each cell. The pattern of gene expression determines the identity and also the ongoing functioning of a cell.

These strands of DNA are extremely large molecules, and are packed in a very specific way in the nucleus of each of our cells. The way this packing is organized is critical for understanding the subject of epigenetics. Genes aren’t just DNA: this DNA is also coated with proteins, such as histones. Everything is packed up in chromosomes, and the way they are packed affects how they are read.

Most of us are familiar with the notion of evolution: that mutations occur in our cells whereby there are changes in the DNA sequence, and that when these changes occur in sex cells (producing sperm and eggs), they can be passed on. Most of these mutations are bad, but very occasionally they can be good. Over many generations, there is selection for organisms who have the most reproductive success, and genes that contribute to this success will be selected for, and thus increase in frequency. But it turns out that there are some heritable changes that can be passed on without any changes to the genetic code itself. This is termed epigenetics, where ‘epi’ means ‘on top of’. So this is something heritable, not altering the DNA sequence, but altering the way that it is read. In most cases we are talking about changes that are heritable when a cell divides by mitosis. But there is some evidence that they can also persist when sex is involved – when the division is by meiosis. It is important to note that epigenetic modifications are both heritable and reversible with no changes to the underlying genome.

Epigenetics transmits information separately from DNA changes by mechanisms such as DNA methylation (the most well studied), histone modifications, chromatin remodelling and non-coding RNA changes. These chemical alterations change the way that the DNA is packed, or act as barriers to stop certain bits being read. Think of them as molecular dimmer switches: they are mechanisms for turning genes on or off, or turning them up or down. The exciting thing is that these changes can be passed on to daughter cells when cells divide, and can even be passed transgenerationally, from one organism to another. This is what makes epigenetics so interesting, because it is dealing with heritable changes without changing the DNA sequence itself. And epigentic changes such as methylation can be triggered by environmental stimuli. It is important in us humans, especially with disease. Epigenetic changes can be affected by development (environmental conditions in the womb), chemicals in the environment, drugs and medicines, ageing and also diet.

Epigenetics is particularly exciting for agriculture. Plant scientists have been looking at whether exposing plants to various stresses could result in epigenetic changes that caused the plant to adapt to these stresses, and then remember this adaptation when the clone was propagated for planting in the field. This is interesting for viticulture, because vines are often exposed to hostile environments, and stay put for 20 or more years. Could vines be adapting to their environment? Could this be one reason that old vines often produce more interesting wines, and show a degree of environmental resilience?

In Australia, a research group led by Cassandra Collins has looked at this, and the work formed PhD studies for Dylan Grigg, who wanted to see whether old vines were better than young. He chose five vineyards in the Barossa Valley (South Australia) to study over three consecutive seasons. Each had a mix of old and young vines, with the younger vines vegetatively propagated from the old vines on the same site. The old vines gave greater yields, which is a slightly surprising result, but it might be because, with their greater trunk size, they have increased reproductive capacity. Looking at the wines from these vines, there were consistent flavour differences in sensory studies, with the old vines preferred (more red fruit and floral characters), and the younger vines tasting more alcoholic. Grigg also looked at the epigenetic status of the old vines in each of the vineyards. What he found was that despite no discernible differences in DNA profile between the sites (they were all Shiraz) differences in methylation were found mainly driven by the distance between the vineyards (they were site specific), but they were also associated by the differences in vine age.

Epigenetics has also been studied in vineyards in Argentina. In a study published in 2020 by Varela and colleagues, they looked at three clones of Malbec in two vineyards with very different environmental conditions. The found that there was epigenetic variability in the two sites, and that it was clone dependent. Overall, they found 29 differently methylated sites that were related with genes and promoters, and concluded that this was important in terms of phenotypic plasticity. In particular, they speculated that the epigenetic changes might be affecting plant hormone sensing or homeostasis.

It would be fascinating to do some research like this in South Africa’s old vineyards. Maybe this is a job for the Old Vine Project?