Blog: Why the Same Strain Performs Differently - Understanding Genotype by Environment Interactions.

Published 9AM EST, Mon Nov 10, 2025

You've heard amazing things about a particular strain. Instagram is full of gorgeous photos showing dense, frosty buds with incredible color. Reviews rave about the potency and unique terpene profile. You buy premium seeds from a reputable breeder, follow best practices for cultivation, and wait eagerly for harvest.

Then reality hits. Your plants look nothing like the photos. The structure is different. The buds are less dense. The terpene profile is there but muted. The yields are acceptable but not impressive. What went wrong?

Most likely, nothing went wrong. You just encountered a phenomenon that frustrates cultivators and complicates breeding: genotype by environment interaction, or G×E for short. The same genetics (genotype) produce different results (phenotypes) depending on environmental conditions. What looks incredible under one grower's specific conditions might look mediocre under yours, even with identical genetics.

Understanding G×E interactions is crucial for both breeders developing new cultivars and cultivators trying to maximize performance from the genetics they grow.

What Is Genotype by Environment Interaction?

In the simplest terms, G×E interaction means that genetic performance depends on environmental context. A cultivar that yields exceptionally well indoors under LED lighting might yield poorly outdoors. A strain with stunning purple coloration in cool climates might stay completely green in warm environments. Terpene profiles that are loud and complex under certain conditions might become muted under others.

This isn't about genetics being "good" or "bad" in absolute terms. It's about genetics being more or less suited to specific environmental conditions. Some cultivars are environmental specialists, performing brilliantly under narrow conditions but struggling when conditions change. Others are environmental generalists, maintaining decent performance across varied environments without excelling in any particular one.

From a breeding perspective, this creates challenges. You can't evaluate a genetic's true potential without testing it across multiple environments. What looks like the best selection in your indoor facility might actually be an environmental specialist that only performs well under your specific conditions.

The Major Environmental Variables That Matter

Numerous environmental factors influence plant performance, but several stand out as particularly impactful for cannabis cultivation.

Light Spectrum and Intensity

Cannabis responds dramatically to changes in light quality and quantity. LED lighting with specific spectral profiles produces different plant responses than HPS lighting or natural sunlight. Blue-heavy spectrums tend to promote compact, vegetative growth. Red-heavy spectrums drive flowering and stretch. UV exposure influences trichome production and secondary metabolite synthesis.

Some genetics show strong responses to light spectrum, essentially being different plants under different lighting. Others maintain relatively consistent morphology and chemistry regardless of light source. For breeders, this spectrum sensitivity needs characterization to provide cultivators with meaningful recommendations.

Temperature and Climate

Temperature influences everything from growth rate to terpene volatilization to anthocyanin production (color). Cool temperatures slow growth but often enhance terpene retention and can trigger purple coloration in genetics carrying anthocyanin genes. Warm temperatures accelerate growth but may reduce terpene concentrations through volatilization and can prevent color expression even in purple-capable genetics.

Genotype by temperature interactions are substantial. Some cultivars maintain performance across wide temperature ranges (18-28°C) while others perform optimally only within narrow windows. For outdoor cultivation where temperature control is impossible, selecting temperature-tolerant genetics is critical.

Nutrient Management

Cannabis genetics vary substantially in nutrient requirements and tolerance. Heavy feeders demand high nutrient concentrations and show deficiency symptoms on moderate feeding schedules. Light feeders perform well on minimal nutrients but show toxicity symptoms when overfed.

These differences reflect G×E interactions between genetics and nutrient environment. A cultivar that wins cannabis cups when grown by nutrient-dialed experts might perform poorly for average cultivators using standard feeding programs. Conversely, a cultivar that performs decently under various nutrient regimes might never reach the peaks achievable by finicky but responsive genetics in expert hands.

Water Management and Humidity

Drought tolerance varies dramatically between cannabis genetics. Some lines wilt quickly when substrate moisture drops, while others tolerate dry conditions remarkably well. Similarly, humidity tolerance ranges from genetics that thrive in humid tropical conditions to those that develop mold issues above 60% relative humidity.

For cultivators in humid climates or using water-conserving practices, selecting genetics tested under relevant environmental conditions dramatically improves success rates.

Measuring G×E: How Breeders Quantify Environmental Interactions

Understanding that G×E exists is one thing. Quantifying which genetics show strong versus weak environmental interactions requires systematic multi-environment testing.

Multi-Location Trials

The gold standard approach is growing identical genetics across multiple distinct locations simultaneously. Indoor facility, outdoor plot, greenhouse, different geographic regions—the more diverse the test environments, the better you characterize G×E patterns.

For each genetic entry, key traits are measured across all environments: yield, cannabinoid content, terpene profile, flowering time, plant height, disease incidence. Statistical analysis then reveals which genetics perform consistently across environments (stable, broadly adapted) versus those whose performance varies dramatically with environment (unstable, environmentally sensitive).

Alphatype's breeding evaluation includes multi-environment testing as a mandatory step before commercial release. We don't release cultivars based solely on performance in our controlled breeding facilities. Elite selections are tested across partner facilities in different regions, under different cultivation systems, to verify performance stability.

Stability Statistics

Several statistical measures quantify environmental stability. The most intuitive is simply looking at variance in performance across environments. A cultivar yielding 180-200 grams per plant across five different environments is more stable than one yielding 120-240 grams across the same environments, even if their averages are similar.

More sophisticated approaches use regression analysis to separate main effects (average genetic performance) from interaction effects (how much performance changes across environments). Cultivars with low G×E interaction maintain consistent performance relative to other cultivars across environments. Those with high G×E interaction perform well in some environments but poorly in others.

Phenotypic Plasticity: When Flexibility is a Feature

Not all environmental responsiveness is problematic. Phenotypic plasticity—the ability to adjust growth patterns based on environmental cues—can be advantageous when it allows plants to optimize performance across conditions.

For example, a cultivar that stretches more under low light but stays compact under high light is exhibiting adaptive plasticity. It's adjusting architecture to capture available light efficiently. This flexibility could be valuable for cultivators using various light intensities or training techniques.

Similarly, genetics that produce more trichomes under UV stress or increase terpene concentrations in response to nutrient availability are showing potentially beneficial plasticity. The plant is responding to environment in ways that enhance desirable traits.

The key distinction is between adaptive plasticity that improves performance versus maladaptive plasticity that causes instability. Adaptive plasticity is a feature worth preserving. Maladaptive plasticity is a problem requiring stabilization through breeding.

Breeding Strategies for Environmental Stability

Breeders can select for broad adaptation and environmental stability through strategic approaches.

Selection Under Target Environments

The most straightforward strategy is selecting under conditions matching target commercial cultivation. If most customers will grow indoors under LED lighting, conduct selection trials under LED lighting. Genetics that perform well under these conditions are likely to succeed for customers using similar setups.

This approach works but limits flexibility. Cultivars selected exclusively under indoor LED might not translate well to outdoor cultivation or greenhouse production. It develops environmental specialists rather than generalists.

Selection Across Diverse Environments

A more powerful approach is conducting selection across multiple environments simultaneously. Rather than selecting the best performer in Environment A or the best in Environment B, select individuals that perform well across both environments.

This multi-environment selection develops broadly adapted cultivars that maintain acceptable performance across varied conditions. They might not be the absolute best in any single environment, but they're reliably good across many environments.

Alphatype's evaluation pipeline includes this multi-environment selection phase. Advanced breeding lines are tested across indoor, greenhouse, and outdoor environments. Only genetics showing stable, strong performance across all three environments advance to potential commercial release.

Using Stability Itself as a Selection Criterion

The most sophisticated approach treats stability as a trait to be selected like yield or potency. Rather than just measuring average performance, explicitly measure performance variance across environments and select for low variance.

This requires substantial testing infrastructure because you need to grow enough plants in enough environments to accurately estimate stability for individual genetics. But for breeding programs with adequate resources, selecting explicitly for stability produces cultivars with the broad adaptation that commercial cultivators value.

Real-World Examples: When G×E Makes or Breaks Success

Abstract discussion of G×E is useful, but concrete examples illustrate why this matters practically.

The Instagram Strain That Disappoints

A cultivar becomes social media famous based on stunning photos from a particular grower. That grower has a highly dialed indoor setup with specific lighting, temperature control, and nutrient program optimized over years. The genetics respond beautifully to those specific conditions.

Hundreds of other cultivators buy those genetics expecting similar results. Most are disappointed because their environments differ from the original grower's. The strain isn't bad—it's environmentally sensitive, requiring specific conditions to express its full potential. For cultivators who can replicate those conditions, it's amazing. For everyone else, it's mediocre.

The Reliable Workhorse Nobody Photographs

Conversely, some cultivars never trend on social media but are workhorses for commercial production. They don't produce jaw-dropping photos under ideal conditions, but they maintain solid performance across diverse conditions. Indoor, outdoor, greenhouse, various nutrients, different climates—they consistently deliver acceptable yields and quality.

These broadly adapted cultivars might not win cannabis cups, but they pay bills for commercial cultivators who need reliability more than Instagram appeal. From a breeding perspective, these are incredibly valuable genetics even if market perception doesn't always reflect that value.

The Outdoor Specialist That Fails Indoors

Some genetics evolved or were selected under outdoor conditions and carry adaptations specific to natural sunlight, temperature fluctuations, and outdoor growing requirements. These outdoor specialists often perform poorly when moved indoors, showing unexpected growth patterns, nutrient sensitivities, or lackluster production under artificial lighting.

This doesn't mean the genetics are inferior. It means they're adapted to a different environmental context than indoor cultivation provides. For outdoor cultivators, these same genetics might be ideal selections.

Practical Implications for Cultivators

Understanding G×E helps cultivators make better genetic selection decisions and adjust expectations realistically.

Match Genetics to Your Environment

Rather than chasing the hottest trending strain, prioritize genetics that were bred and tested under conditions similar to yours. If you're growing outdoors in a Mediterranean climate, seek genetics from breeders conducting outdoor trials in similar climates. If you're growing indoors under specific lighting, look for genetics selected under that lighting type.

Many breeders now provide information about the environments where their genetics were developed and tested. This information is more valuable than yield claims or THC percentages because it indicates whether genetics are likely to perform well in your specific situation.

Start with Small Test Runs

When trying new genetics, start with small populations rather than committing entire facilities to unproven cultivars. Grow 5-10 plants to see how they respond to your specific environment before scaling up. Genetics that performed amazingly for someone else might underperform in your setup due to G×E interactions.

Document Your Conditions

Track environmental parameters in your growing space and document how different genetics respond. Over time, you'll identify which environmental factors most influence performance in your specific setup and can select genetics accordingly.

Temperature-sensitive? Prioritize heat-tolerant genetics. Struggle with humidity control? Focus on mold-resistant selections. Your unique environmental context should guide genetic selection rather than following generic hype.

Adjust Expectations Based on Environment Differences

If you're growing genetics that were developed under substantially different conditions than yours, adjust expectations accordingly. A cultivar bred indoors under LEDs might require a few cycles to adapt to your outdoor or greenhouse environment. Performance might improve as you dial in cultivation practices specific to that genetic under your conditions.

Alphatype's Multi-Environment Testing Protocol

Our commitment to developing broadly adapted cultivars requires substantial investment in multi-environment evaluation.

Phase 1: Controlled Indoor Selection

Initial breeding generations occur in controlled indoor facilities where environmental variables are standardized and genetic differences can express clearly. This allows accurate parent selection without environmental noise obscuring genetic potential.

Phase 2: Multi-Environment Validation

Advanced breeding lines that show promise indoors enter multi-environment validation trials. Identical genetics are grown simultaneously:

• Indoor LED facility (controlled environment)

• Outdoor plots (full sun, natural conditions)

• Greenhouse production (hybrid controlled/natural environment)

  
  

Performance is measured identically across all three environments for direct comparison.

Phase 3: Geographic Distribution Testing

Final candidates are distributed to partner facilities in different geographic regions for local trial evaluation. This tests performance under diverse climates, altitudes, and day lengths to ensure broad geographic adaptation.

Phase 4: Commercial Verification

Before official release, small-scale commercial production runs at partner cultivation facilities verify that genetics maintain quality when grown at scale under commercial conditions rather than small research plots.

Only genetics that successfully complete all four phases enter Alphatype's commercial catalog. This rigorous multi-environment testing ensures customers receive genetics that will perform reliably across diverse cultivation situations.

The Future: Genomic Prediction of Environmental Response

Current G×E characterization requires physically growing plants across multiple environments, which is time-consuming and resource-intensive. Emerging genomic approaches may enable predicting environmental response patterns from DNA analysis without extensive field testing.

By identifying genetic markers associated with environmental sensitivity or broad adaptation, breeders could screen thousands of candidate selections at the seedling stage, predicting which will show stable performance across environments before investing months growing them to maturity.

This marker-assisted environmental screening remains developmental for cannabis but has proven effective in major crop species. Alphatype monitors these technological developments and maintains the genomic infrastructure to adopt them when they become practical for breeding applications.

Conclusion: Context Matters as Much as Genetics

The cannabis industry tends to discuss genetics as if they exist in a vacuum, with inherent quality independent of growing conditions. Reality is messier. The same genetics produce radically different results depending on environmental context.

For breeders, this means multi-environment testing isn't optional—it's essential for developing cultivars that perform reliably for diverse customers. Single-environment selection produces genetic specialists that excel under specific conditions but disappoint when conditions change.

For cultivators, understanding G×E explains why highly-hyped genetics sometimes underperform. It's not necessarily about genetic quality—it's about genetic-environment match. The genetics that work brilliantly for one grower might be mediocre for another purely due to environmental differences.

Alphatype's breeding philosophy embraces this complexity rather than ignoring it. Our multi-environment testing ensures that cultivars reaching the market aren't just good genetics—they're broadly adapted genetics that maintain quality across the diverse conditions where commercial cultivation occurs.

When evaluating new cultivars, don't just ask "are these good genetics?" Ask "are these genetics suited to my specific environmental conditions?" That's the question that determines real-world success.

Great genetics in the wrong environment produce mediocre results. Good genetics in the right environment produce excellence. Understanding this distinction separates sophisticated cultivation from trial-and-error frustration.