Environmental Memory in Heredity: How Rice Learns Cold Tolerance through Epigenetics

Since Charles Darwin proposed the concept of natural selection, biological change has generally been understood as a process driven by genetic mutation and inheritance. Yet more than half a century before Darwin, the French biologist Jean-Baptiste Lamarck proposed a different possibility: environmental changes might directly influence an organism's traits and even allow those traits to be passed to the next generation. For a long time this idea, often summarized as the inheritance of acquired characteristics, was widely dismissed as scientifically implausible.

In recent decades, however, the rise of epigenetics has revived interest in how the environment might shape heredity. Epigenetics describes regulatory systems that modify gene activity without altering the underlying DNA sequence. One of the most important mechanisms is DNA methylation, a chemical modification in which methyl groups attach to cytosine bases in DNA. These marks can influence whether a gene is active or silent. Even though the DNA sequence remains unchanged, methylation patterns can alter how genes are expressed and can sometimes be transmitted across generations.

DNA methylation, yellow circles represent methyl groups（Image source：Ana Valente,Luís Vieira,Maria João Silva and Célia Ventura， CC BY 4.0 ）

A recent study on rice offers striking evidence that environmentally induced epigenetic changes can generate adaptive traits that persist through heredity. In this case, the trait involves the ability of rice to tolerate cold temperatures. The findings illustrate how environmental experience can reshape gene regulation in a way that becomes biologically meaningful for future generations.

Rice (Oryza sativa) originally evolved in tropical Asia, where warm climates dominate. Yet today the crop grows successfully in regions far north of its ancestral range, including the colder environments of northeastern China. This geographic expansion suggests that rice populations have gradually developed mechanisms to cope with lower temperatures during their evolutionary history.

To investigate how this adaptation might occur, researchers focused on a rice line known as KenDao8 (KD8), which is particularly sensitive to cold. The scientists subjected plants to low-temperature stress during the reproductive stage when meiosis occurs in developing panicles. Male reproductive development in rice is especially vulnerable to cold, so chilling at this stage can severely reduce fertility and grain production.

The experiment was repeated across multiple generations. In each generation, plants whose panicles retained higher seed-setting rates under cold conditions were selected, and their seeds were used to grow the next generation. After only three generations of cold treatment, the resulting line—referred to as KD8-3C—showed a striking improvement in cold tolerance. Even under low temperatures, these plants maintained a much higher proportion of filled grains than the original cold-sensitive line.

The most remarkable observation appeared in later generations. After the fourth generation of cold exposure, researchers grew the plants for five additional generations without subjecting them to further cold stress. Despite the absence of the original environmental trigger, the enhanced cold tolerance remained stable. The plants continued to maintain high fertility under cold conditions, indicating that the newly acquired trait had become heritable.

Successive generations of cold treatment（Image source：Song X et al. (2025)， CC BY 4.0 ）

This raised an obvious question: had the rice genome mutated during the experiment? Whole-genome sequencing provided the answer. When the researchers compared the DNA sequences of the original KD8 line and the cold-tolerant descendants, they found that the genomes were essentially identical. Only a small number of minor sequence differences appeared, and none could explain the large shift in cold tolerance.

Instead, the critical difference lay in DNA methylation. Genome-wide methylation analysis revealed that one gene region had undergone a significant change in methylation patterns. This gene was named ACT1 (acquired cold tolerance 1). In the cold-tolerant plants, a short region in the promoter upstream of ACT1 displayed markedly reduced methylation compared with the original line.

Promoters function as regulatory switches that control when genes are turned on. When methylation levels are high in promoter regions, gene expression is often suppressed. Conversely, reduced methylation can allow the gene to remain active. In the cold-tolerant rice lines, hypomethylation of the ACT1 promoter prevented the gene from being silenced under cold conditions. As a result, ACT1 continued to be expressed even during chilling stress.

The ACT1 gene encodes a protein called AGP1, an arabinogalactan protein. Proteins of this class are located in the plant cell wall and extracellular matrix, where they participate in cell signaling, growth regulation, and environmental sensing. When ACT1 expression remains high, the plant appears better able to detect and respond to the cellular stress caused by low temperatures.

To confirm that methylation changes were truly responsible for the new trait, researchers performed targeted epigenetic editing experiments. When they artificially removed methylation marks from the ACT1 promoter in a cold-sensitive rice line, the plants rapidly gained cold tolerance. Conversely, when methylation was restored in the tolerant line, the plants once again became sensitive to cold. These manipulations demonstrated that the methylation state of the ACT1 promoter directly controlled the phenotype.

Further molecular analysis revealed the mechanism linking methylation to gene activation. The promoter region of ACT1 contains a binding site for the transcription factor Dof1. Under cold conditions, the amount of Dof1 increases, and the protein normally binds to the ACT1 promoter to activate transcription. However, when the DNA in that region is methylated, Dof1 cannot attach efficiently. Hypomethylation removes this barrier, allowing Dof1 to bind and activate the gene even in cold environments.

Hypomethylation upstream of the rice ACT1 gene allows Dof1 binding（Image source：Song X et al. (2025)， CC BY 4.0 ）

The researchers then investigated how this epigenetic variation appears in natural rice populations. They examined 131 rice landraces from different regions of China. The results revealed a clear geographic pattern. In warm southern regions, most rice varieties carried a highly methylated ACT1 promoter and were relatively sensitive to cold. In contrast, rice varieties from northern regions—where growing seasons are cooler—frequently possessed the hypomethylated version of the gene.

More than seventy percent of the northern landraces carried the hypomethylated ACT1 epiallele, suggesting that this epigenetic state had been favored by natural selection as rice cultivation spread toward colder climates.

Finally, the researchers explored how cold exposure initially produces this epigenetic shift. They focused on enzymes responsible for maintaining DNA methylation, particularly two methyltransferases known as MET1b and CMT3. During cold stress, the expression of both enzymes decreases. Without sufficient activity from these methyltransferases, methylation marks in certain genomic regions—including the ACT1 promoter—cannot be maintained. Over successive generations exposed to similar conditions, the loss of methylation becomes stabilized.

Another factor contributes to the persistence of this state. In many parts of plant genomes, small interfering RNAs guide enzymes to reestablish methylation marks. However, the region surrounding the ACT1 promoter lacks such small RNAs. Once methylation is lost there, the genome has little capacity to restore the previous pattern. This allows the hypomethylated state to remain stable over generations, forming what researchers call an epiallele—a heritable variant defined by epigenetic marks rather than DNA sequence changes.

The discovery has important implications for evolutionary biology. It demonstrates that environmental conditions can trigger epigenetic changes that generate adaptive traits and that these traits can persist even after the original environmental stimulus disappears. In this case, repeated exposure to cold produced a heritable regulatory change that helped rice survive in colder climates.

Such findings blur the traditional boundary between environmental influence and genetic inheritance. While the DNA sequence remains unchanged, epigenetic regulation allows organisms to incorporate environmental experiences into heritable biological variation.

At the same time, many questions remain. Researchers still need to determine how common environmentally induced epialleles are across plant genomes and whether similar mechanisms operate in other species. It also remains unclear how long such epigenetic states can persist in natural populations and how reliably they can be manipulated in agricultural settings.

Even so, the study reveals a fascinating aspect of biological adaptability. Environmental signals can leave molecular traces within the genome's regulatory landscape, traces that may guide how future generations respond to the world around them.

Author: Shui-Ye You

Reference:

Song X et al. Inheritance of acquired adaptive cold tolerance in rice through DNA methylation. Cell.

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