Monday, October 1, 2018

Grape clones and varieties are not always what they seem

The twin ideas of "varieties" and "clones" are basic to grape-growing, whether they are used for wine-making, table grapes, raisins, juice, jelly, canning, or rootstocks. However, these concepts don't quite match the usage of these words in general biology. In practice in grape-growing, a variety is a variety when it is officially declared to be such, and the same for a clone, not when they match the biological definitions.

Illustration By Keith Ward

Jamie Goode (What is a grape variety? What is a clone?) notes that, in biology, a new variety is produced by sexual reproduction, where there is cross pollination between a mother and a father flower from different varieties, resulting in a seed, which is then grown as a new plant. That new plant could then be a new variety. Clones, on the other hand, come from vegetative propagation — a genetic mutation occurs in a plant's growing tip, which then forms a new shoot, and then a cutting of that shoot is taken and propagated, to form a new plant. That new plant could be a new clone.

Obviously, new varieties and new clones are normally recognized in the grape-growing industry only if they have desirable characteristics that are not present among the current collection of varieties and clones. If not, then the new plant will be discarded. So, not all mother x father crosses will produce new varieties, nor will all cloned plant material be recognized as a new clone.

The point here is that varieties will have considerably different genetic makeup from their parents, since they have genomes that are a mixture of those from both parents. Clones will, instead, be almost identical to their parents, likely differing only in a single mutation in their genome. This is what creates the difference between the word "variety" as used in grape-growing and its more general usage in biology — grape varieties are sometimes almost identical!

The Pinot group of "varieties"

You see, by these formal definitions of variety and clone, grapes like Pinot noir, Pinot gris and Pinot blanc would not be separate varieties, but would instead be separate clones — they were originally produced by the process of vegetative propagation, and are genetically almost identical. Pinot noir is a very ancient variety within which many mutations have occurred naturally over the centuries, some of which we have recognized as worthwhile, by viticulturists taking cuttings and producing new plants — hence, the "family" of Pinots.

The table shown later in this post shows you what I mean. However, most people don't know how modern viticulture uses genetics to recognize different grape clones and varieties, so I will first explain the genetics here.

Each individual organism has its own unique genome, even identical twins (after their first cell division). However, there is an awful lot of each genome that is identical across groups of organisms, whether those groups are entire kingdoms, such as animals or plants, or much smaller groups, such as grape varieties. This allows us to use the genome to identify which group each individual belongs to. All we need to do is find some bits the genome that vary between the groups but not within those groups.

Microsatellites are bits of the genome that are useful for identifying closely related organisms, such as varieties. Each microsatellite is a location in the genome that is known to be very variable, because part of the genome sequence at each location is repeated many times. This is illustrated above, which shows three genomes (horizontally) — the first genome has 5 repeats (represented by the blue arrows), while the second one has 7, and the third one has 3 repeats.

Just as importantly, each microsatellite needs to have an immediately adjacent region of the genome (marked in red in the figure) that does not vary within or between groups. We use these flanking regions to find the microsatellite within the genome, and to count the number of repeats between the paired flanks.

Note that there are two copies of the genome for each individual in the figure, just as we ourselves have — one from our mother and one from our father. The blue arrows point in opposite directions for the two copies, because the copies actually function in opposite directions.

There are oodles of microsatellites in the genomes of all complex organisms, but for grapes we have chosen just nine of them, which we have given the fancy code names listed at the head of each column in the table below. To identify any given grapevine genetically, we simply count the number of repeats it has at each of the microsatellite locations, and we then compare this to what we already know about different grape varieties. When we find a match — bingo, we have identified its variety, which is why this procedure is sometimes called DNA-fingerprinting.

Microsatellite counts for different Pinot grape varieties

For the Pinot example in the table, I provide the relevant genetic information for six different grape varieties (taken from Liste des clones agréés en France). The columns of the table refer to the nine microsatellites, and the data within the columns tell you how many repeats there are for each microsatellite (typically several hundred repeats).

The rows refer to the six grape varieties. Different varieties usually have uniquely different numbers of repeats for these nine microsatellites. There are two "alleles" for each variety, because the grapes have two copies of their genome — the allele pairs do not have to have the same number of microsatellite repeats.

Looking through the table above, you can see that Pinot noir, Pinot gris and Pinot blanc have 18 identical numbers, meaning that they are genetically identical for both alleles at all nine locations in their genomes. This is what you can expect to see most of the time when comparing clones — clones are expected to be identical. As also shown in the table, Pinot meunier, another Pinot clone, differs in only 2/18 numbers.

For comparison, Gamay noir differs from Pinot noir at 10/18 microsatellites, while Chardonnay differs at 7/18, indicating that in both cases they were originally produced by cross-pollination, not cloning — they vary too much to be clones. This information also suggests that Chardonnay is more closely related to the Pinots than is Gamay (the microsatellites are not involved in determining skin color, and so the color mutations are not involved in the identification process). Both Chardonnay and Gamay are currently estimated to be the result of crosses of Pinot noir with the Gouais blanc variety, which is no longer even listed for viticulture in France. The Gamay cross is likely to have occurred much earlier in history (and there are lots of other varieties that are also the offspring of Pinot x Gouais crosses).


Grape varieties are whatever the grape industry decides to recognize. Mostly, they match the definition generally used in biology — new varieties result from sexual reproduction, while new clones come from vegetative propagation. However, modern genetics has allowed us to recognize that this is not always so — some clones are too important to the industry not to have their own varietal name.

Finally, it is perhaps worth noting that not all new varieties are universally revered. Sometimes, they are more "interesting", rather than simply an improvement (eg. An ancient, rare wine that can be beautiful, or smell like old lady's perfume: Lacrima di Morro d'Alba ).

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