Epigenetically Informed Farming, or a New Era That Began with the Seed’s “Upbringing”

A seed’s “upbringing” matters

Agricultural performance is not always determined by expensive machinery, chemical inputs, or whether a new variety is available. Sometimes it begins with a single well-prepared, “well-raised” seed placed in a farmer’s hand, ready to grow. If strong genetics are the “hardware,” then proper storage and agronomy are the “software” that help that potential perform as intended. What has happened in Uzbekistan’s wheat sector in recent years has reminded us, and more broadly world agriculture, of this simple truth. For decades we have studied varieties, fertilizers, water, planting dates, diseases, and pests. But we paid far less attention to the seed's physiological condition before it ever reached the field. We knew that proper storage before planting could influence the entire growing season, yet in practice we often underestimated that opportunity. Does it really matter?

That question helped shape what we call epigenetically informed farming. The term may sound unfamiliar to a farmer, but the logic is straightforward. If DNA is the seed’s alphabet, physiological and epigenetic regulation influences when and how that alphabet is “read.” A seed’s age, moisture, temperature history, storage conditions, physiological state, and later environment all affect when and how it germinates, develops roots, grows, and matures. In the era of genomics and pangenomics, modern biology increasingly shows that these states emerge through the combined action of genetic, hormonal, metabolic, and epigenetic regulation.

The goal of modern agriculture is no longer to talk about elegant laboratory results or mechanisms. In a world facing major global challenges, one of our central tasks is to turn complex, and sometimes overlooked, knowledge into affordable, practical technologies that can work across large areas.

A seed is more than planting material

When a farmer sows a seed, a complex biological process stands behind it, closely tied to the seed’s own developmental history. How it formed on the mother plant, how fully it matured, the moisture at which it was stored, and the conditions and length of time it spent in dormancy in storage can all shape its later vigor. So even when a seed looks “dry and inactive,” it has its own timing of awakening, its own internal rhythm, and its own state of readiness.

Scientists describe much of this through the concept of seed vigor. A vigorous seed emerges faster and more uniformly, helps establish a healthy early stand, and enters later crop-management stages more synchronously. In wheat, seed dormancy, germination, and temperature responses are linked to genetic, hormonal, metabolic, and epigenetic regulation. Breeding creates the DNA of a variety, but the seed's physiological condition also helps determine how fully that genetic potential is expressed by the time the seed reaches the farmer.

That led us to a new question. What if we did not change the variety or alter a gene, but instead used biological knowledge to manage the seed’s condition before planting? Could we prepare seed so that it starts the season alert, faster, and more uniformly? That became the practical question behind our concept of epigenetically informed farming.

From idea to practice: taking dry seed through dormancy under cold conditions (conditioning)

The practice tested in Uzbekistan involves storing dry seed under controlled cold conditions for up to two months. The approach began as a pilot in 2025. It was then formally regulated through the Ministry of Agriculture Order No. 35 of August 7, 2025, registered by the Ministry of Justice as No. 3675.

The legal document uses the operational term “vernalization”; from here on, I will refer to it simply as the program. But this is not the classic treatment in which moistened seed is held in the cold. The program uses prepared, treated, and packaged dry seed stored in refrigerated facilities under controlled moisture. The package specifies seed moisture of no more than 14%, storage at +1 to +5°C for 45 to 60 days, and documented quality control. Cold here is a controlled condition used to manage the seed’s pre-plant state and dormancy. The program is not temperature alone. It is an integrated package of seed preparation, treatment, moisture control, packaging, refrigerated storage, and quality checks. Our scientific analysis evaluates the field performance of that full package.

From 973 hectares to 685,000

In 2025, the program was tested on just 973 hectares. One year later, for the 2026 harvest, it had expanded to 685,065 hectares. That is 72.3% of Uzbekistan’s irrigated wheat area. Moving in one season from a 0.1% pilot to more than 72% is an unusually rapid agricultural scale-up.

Of course, expanding acreage is not a result by itself. Almost any technology can be rolled out quickly, but for a farmer what matters is its performance. So our new study did not stop at asking how many hectares were covered. Within the same harvest year, we directly compared program seed with traditionally stored seed for the same named variety, variety class, and region.

In 2026, we identified 92 exactly matched variety-by-region pairs across ten regions. Together they represented 65.2% of the national program area. Most importantly, in all 92 comparisons, the positive difference in program fields was clearly visible relative to traditional fields. Let us look at the results more closely.

In plain terms, when the same variety was compared within the same region, program fields produced nearly one additional metric ton of grain per hectare. Program adoption in 2026 ranged from 45.6% to 100% across regions. Andijan, Bukhara, and Khorezm had fully converted recorded wheat area, while other regions still grew traditional and program seed side by side. Those mixed-adoption regions gave us the opportunity for direct comparison.

The fairest comparison: compare a variety with itself

Large national datasets always carry a risk. A strong variety may be planted in one region and another variety somewhere else; water and soils differ, and it then becomes easy to compare the numbers and credit the technology for differences that may have another cause. That is why, in 2026, we separately analyzed cases in which the same wheat variety, variety class, and region included both program seed and traditionally stored seed. We found 92 such exact matches across ten regions. Those pairs represented 446,746 hectares of program wheat, or 65.2% of the national program area.

The result was very clear: in all 92 pairs we observed positive statistical differences on fields where the program was used. The simple average difference was 0.90 metric tons per hectare, and the program-area-weighted difference was 0.94 metric tons per hectare. The positive direction remained when we applied different statistical checks and when we recalculated the estimate after removing regions one at a time.

The difference began at emergence, not at harvest

Even more interesting for us was whether the difference was already appearing as the wheat emerged. To find out, in 2026 we organized separate monitoring across 154 districts, 35,875 farms, and 947,110 hectares. In 106 districts, we used both program and traditional seed, allowing direct paired comparisons.

The positive result became visible from the beginning of the crop’s life. Program fields reached the 75% emergence threshold an average of 2.59 days earlier. Early stand density was 39.1% higher. That large early difference naturally narrowed as wheat partially compensated through tillering. Even so, the number of productive stems remained 9.6% higher at the later stage.

We also observed that crop development moved forward. Tillering occurred an average of 3.68 days earlier, jointing 3.24 days earlier, heading 3.10 days earlier, and full maturity 3.64 days earlier. Of the 106 paired districts, 104 reached full maturity earlier, one matured on the same day, and one matured later.

Some may ask, what difference can three days make? In a region facing rising heat and water scarcity, three or four days can become extremely valuable agronomic time. Earlier emergence can give plants more time to establish roots. Earlier heading and maturity can create an additional window to avoid late-spring and early-summer heat, save water, and better coordinate harvest.

The wider wheat farming ecosystem in Uzbekistan was changing too

One more point should be stated clearly: over the past eleven years, Uzbekistan’s wheat sector has grown alongside changes in variety turnover, crop management, water management, seed systems, financing, market mechanisms, and farmer knowledge.

In 2016, irrigated wheat occupied more than 1.132 million hectares. By 2026, that area had fallen to about 947,000 hectares, a 16.4% decline. Over the same period, the area-weighted average yield rose from 5.64 to 9.78 metric tons per hectare, a 73.4% increase. Despite less land under irrigated wheat, calculated production rose from 6.39 million to 9.26 million metric tons, a 45% increase. In other words, when genetics, agronomy, water, seed systems, markets, and farmer decisions work together, a country can produce more from less acreage.

What does epigenetically informed farming mean?

When people hear the word “epigenetics,” many picture a laboratory, DNA methylation, or complex molecular analysis. That is part of the story, but the farming logic is broader. Seeds with the same genome can still be in different physiological states. Seed moisture, temperature, storage duration, physiological age, and later environment can change germination speed and the course of development. The scientific literature shows that seed dormancy and germination are linked to hormones, metabolism, and epigenetic regulation.

By “epigenetically informed farming,” we mean understanding a plant’s physiological and regulatory state without changing its DNA, then translating that knowledge into agronomic decisions. Cold conditioning of dry seed is one practical example that grew from this way of thinking. For science, the positive results observed in this practice now create the next task: uncovering the biological mechanisms behind them.

Why did the technology scale so quickly in one year?

A good agricultural idea is not enough on its own. If it never reaches the farmer, if logistics fail, if storage is unavailable, or if credit and market incentives are misaligned, a promising technology will remain in the laboratory or on a pilot farm.

The jump from 973 to 685,000 hectares in one year cannot be explained by seed physiology alone. Cold-storage infrastructure, seed preparation and quality control, regional agronomists and extension, farmer participation, market-based wheat sales, preferential credit, agricultural risk insurance, support for water-saving technologies, and digital harvest monitoring all reinforced one another. Biological knowledge becomes useful to farmers only when it is translated into a practical delivery system.

Can this experience be transferred to another country?

Absolutely, and it should be. Across Central Asia, South Asia, the Middle East, and many parts of Africa, farmers work with heat, water scarcity, short agronomic windows, uneven seed quality, and financial constraints. They do not always need the most expensive technology. Sometimes a large gain can come from adapting existing biological knowledge intelligently to local resources.

But it would be a mistake to take Uzbekistan’s exact 45-to-60-day, +1-to-+5°C regime and copy it unchanged elsewhere. Other countries have different varieties, climates, seed moisture, storage infrastructure, planting calendars, and farmer resources. What is transferable is not the number, but the logic. To apply that logic properly, a country first needs to understand the biology of its local varieties and its local problems. It should then develop a simple, affordable technical solution; test it in a small pilot; show farmers the results and earn their trust; define quality standards; and support implementation with infrastructure and finance. Only then should the practice be scaled broadly.

A country with cold-storage capacity may find that a different regimen works. Where cold infrastructure is limited, another way of managing seed physiology may be more practical. The central principle is to adapt epigenetic and physiological knowledge to the local farming ecosystem.

What does this mean for a farmer?

A farmer does not walk into the field carrying statistical formulas and scientific tables. What matters is whether the seed emerges quickly and evenly, whether the field establishes a healthy and uniform stand, whether the crop develops on time, matures before damaging heat or unfavorable weather, and how much grain ultimately reaches the bin.

In the 2026 data, the program showed positive signals at several links in that chain: earlier emergence, a denser early stand, earlier tillering and heading, earlier full maturity, more productive stems, and a program-associated yield difference of nearly 0.9 metric tons per hectare in same-variety, same-region comparisons. Farmers saw the result with their own eyes and gained confidence in it. That was a major achievement. These numbers should not be read as a guarantee for every field, but as results observed in Uzbekistan’s real 2026 farming system. Every farmer has different soil, water, varieties, and management. But that is also the strength of the large dataset we collected and analyzed: the pattern did not come from one research station. We observed it across diverse conditions where tens of thousands of farmers work.

A new way to think about food security

Wheat is not just another crop. It is bread, food security, and national stability. Innovation in wheat therefore cannot be judged only by tons per hectare. We also need to use water, land, seed, time, and farmers’ capital more efficiently.

Uzbekistan’s 2016–2026 trajectory shows that total grain production increased even as irrigated wheat area declined. That matters. It is not agricultural expansion; it is movement toward smarter intensification. Epigenetically informed farming should be understood as one part of that larger system. It does not replace new varieties, water-saving technologies, fertilizer, or sound agronomic discipline. Instead, it helps align those pieces from the start, beginning with the seed.

The next era of agriculture may not be defined only by a new gene or a new variety. A plant cannot walk, but it can “read” its environment: temperature, moisture, light, and storage conditions send signals that shape its development. The new era comes from understanding that internal state, measuring what happens in farmers’ fields, and connecting biological knowledge with management decisions. Our ancestors did not say this without reason: the real secret of farming is to “talk with the crop in the field.” In the age of pangenomics, that deeply human insight takes on even greater meaning.

The 2027 harvest starts this fall: the next layer of agronomic “software”

The practical question for farmers now is simple: after this year’s results, what comes next? The fall wheat planting season for the 2027 harvest is approaching. Depending on the region, planting runs from September into November. The 2026 experience showed how much the condition of the seed before planting can matter. The next step is to carry that knowledge through the whole production system. Well-cold-conditioned (vernalized), high-quality seed needs to go into the field at the right time, at the right density, and then be managed as part of one connected agronomic program throughout the season.

One of the most important new elements in the practical guidance is what I would call plant-density “software.” On open irrigated fields, the guidance recommends 450–500 kg of high-quality certified seed per hectare when modern grain drills are used, while planting between cotton rows calls for about 450–550 kg/ha. But the goal is not simply to increase seed kilograms. The real target is a uniform stand and roughly 8.5–9 million healthy, productive stems per hectare. In our 2026 field observations, some fields that combined higher seeding rates with strong agronomic management reached yields of around 10 metric tons per hectare. That is not guaranteed in every field. It shows the potential of a density-management approach that must be adjusted to variety, germination, soil, planting date, water availability, and field management.

A second layer is more precise nutrition and stress-management “software.” Along with balanced NPK, use additional tools such as boron and other micronutrients, silicon-based inputs, acetylsalicylic acid, and yeast-based biological approaches according to the crop’s actual condition and growth stage. In high-yield, dense fields with a real lodging risk, ethephon may also have a role, but only as a ready-to-use product registered for wheat, applied according to the label and at the correct growth stage. None of these inputs is a “miracle” treatment, and applying the same package to every field would be the wrong approach.

Our message to farmers this fall is therefore straightforward: do not let the seed’s “upbringing” stop when the seed reaches the field. Treat all of the rules in the practical guide as one connected production chain. Measure stand density, manage water and nutrition according to crop condition, test each new practice first on a small comparison strip, and record the result in a field log. If a good variety is the genetic “hardware,” then this disciplined, measurable agronomy is the new “software” that can help unlock the 2027 harvest.

Conclusion: a new era for agriculture in Uzbekistan

In our new preprint on Research Square, we combined eleven years of national wheat data, exactly matched variety-by-region comparisons from 2026, and field monitoring across 154 districts. Our analysis showed the yield difference associated with the vernalization program, while field monitoring showed how that difference developed across the crop’s life cycle.

The most important lesson was seeing a 973-hectare pilot expand to more than 685,000 hectares in a single year and understanding what can happen when science and implementation come together. All 92 same-variety, same-region comparisons were positive, and emergence and crop development moved in nearly the same direction across 106 paired districts. That turns the result into real agronomic knowledge worth studying seriously. It is already encouraging our scientists to investigate these positive agronomic signals more deeply at the DNA level. At the same time, it has already become clear that fundamental biological knowledge can be adapted to farm practice, its results measured at national scale, and that this approach is beginning to deliver practical value.

That is how we see the future of epigenetically informed farming: bringing laboratory knowledge into farmers’ fields, understanding plant life more deeply from the seed onward, and using the right agronomic “software” to unlock more of the potential already present in the genetic “hardware.” One important starting point for the new era is how we properly “raise” and prepare the seed.

Ibrokhim Abdurakhmonov,

Minister of Agriculture of the Republic of Uzbekistan, Academician
Source: https://www.researchsquare.com/article/rs-10823700/v1