How Polygenes and Epigenetics Connect to Create a "Phenotype"

When growing plants, even if they have the same cross and are supposed to be the same clone, the expression of the leaves differs.
Light, temperature, water, fertilizer, stress... depending on the differences in conditions, they may become glossier, the velvet texture may deepen, or conversely, the color may fade.

These are the times when the terms "genes" and "epigenetics" come up.

However, if we organize things just a little bit here, some things become clear.
This time, I will break down the relationship between "polygenes" and "epigenetics" from the perspective of breeding and cultivation.

First of all, what are "polygenes"?

In short, polygenic traits are traits that:
• Are not determined by a single gene
• Are influenced by many genes little by little
• Produce a "gradient of intensity" as their sum

Height, yield, leaf size, color, disease resistance, etc.—most things in the natural world that "change continuously" are like this.

What is important here is that polygenic traits are strongly susceptible to environmental influences.

This is because, since they are the "addition of small effects," fluctuations caused by the environment are easily reflected directly in the results.

Epigenetics does not "change the genes" but "changes how they are read"

Epigenetics is often misunderstood, but the basics are as follows:
• The DNA sequence (A/T/G/C) does not change
• But the "readability" of the genes changes

If you imagine genes as a "blueprint," epigenetics is like:
• Sticky notes attached to the pages
• The order of reading
• Emphasis on text
• How easy or difficult it is to open a page

Representative mechanisms include:
• DNA methylation
• Histone modification
• Non-coding RNA
and so on (details are omitted here).

Main topic: The relationship between polygenes and epigenetics works like this

To conclude,

Epigenetics is a higher-level control that collectively moves the "way many genes act" involved in polygenic traits.

Polygenic traits are like a "mixer with a huge number of knobs."
Epigenetics is the "higher-layer control" that changes:
• The effectiveness of the knobs
• The range of movement
• The conditions for reaction

What actually happens? (4 patterns that take effect in breeding and cultivation)

1) Even with the same genetic background, the "whole thing shifts up or down"

When the epigenetic state changes due to light intensity, temperature, nutrition, moisture, or stress, the expression of the involved gene groups can appear to move simultaneously.

As a result,
• Gloss increases
• Velvet texture deepens
• Leaves become thicker
• Conversely, color fades or the plant becomes leggy
can occur.

It is closer to view it as the "way of outputting" genetics having moved, rather than "genetics having changed."

2) "Only this line jumps in this environment" (G×E) occurs

This is a common phenomenon.
Even when placed in the same environment, there are "individuals that react" and "individuals with a weak reaction."

In addition to differences in the genotype itself, this involves factors such as:
• That locus being susceptible to epigenetic control
• The switch being easily turned on in that environment

※ Supplementary note
In short, G×E (Genotype × Environment) is a phenomenon where "the way of growth (how it reacts) when the environment is changed differs for each line."

3) "Unevenness" increases/decreases (phenotypic variance changes)

If epigenetics is unstable, the phenotype tends to scatter even with the same genotype.

Conversely, if management conditions are adjusted and the epigenetic state stabilizes,
they may "become uniform."

When there are "uniform shelves" and "scattered shelves" on a growing rack, this is suspicious.

4) The parent's environment may "remain" in the next generation (especially in plants)

In plants, there are known examples where the epigenetic state is not completely reset and partially remains in the next generation (however, the extent to which it remains stably depends on the trait, species, and conditions).

Part of the phenomenon where "the offspring's appearance differs depending on how the parent was grown" can potentially be explained here.

However, as a rule of breeding, until reproducibility can be confirmed, treat it as "potentially remaining" and handle it separately from genetics (fixation).

Practical talk as a breeder: Do not be deceived by apparent "hits"

When epigenetics is involved in polygenic traits, this is what often happens in selection:
• Conditions happened to match, and a "miracle phenotype" appeared
• But it does not reproduce when the environment changes

Therefore, in practice,
• Observe the same individual under multiple conditions and multiple times
• Standardize the evaluation environment
• Select after deciding "in which environment that trait has value"
• Separate "genetics (design)" and "condition (output)"
These points are effective.