The study, published in Plant Cell Reports, began with a careful comparison of two quinoa lines that behave very differently in the field. The researchers observed that the variety R157 showed significantly greater resistance to pre-harvest sprouting than the line S222. This natural contrast provided a powerful experimental system: by dissecting what distinguishes a seed that stays dormant from one that germinates prematurely, the team could trace the physiological and molecular differences that underpin resistance. Their measurements revealed that resistance to pre-harvest sprouting in quinoa is closely tied to the balance of two key plant hormones, gibberellin and abscisic acid, as well as to amylase activity and the rate of starch metabolism within the seed.

The hormonal tug-of-war at the heart of seed behavior is well documented in plant biology. Gibberellin promotes germination by stimulating the production of enzymes that break down stored starch into sugars that fuel the emerging seedling. Abscisic acid, by contrast, enforces dormancy and counteracts germination. When rain soaks a mature crop, the balance between these hormones can tip, amylase enzymes surge, starch reserves are dismantled and the seed commits to germination whether or not the farmer is ready. Understanding which genes control this switch in quinoa has been a persistent challenge, because the crop’s large, complex genome has only recently become accessible to detailed genetic analysis.

To find the regulators responsible, the team turned to weighted gene co-expression network analysis, a computational method that scans thousands of genes measured across different conditions and clusters those that rise and fall together. Genes that move in concert often participate in the same biological process, and the technique frequently pinpoints master regulators hidden within large transcriptomic datasets. In this case, the analysis converged on a striking candidate: a transcription factor called CqRVE5, a member of the REVEILLE family of genes, together with its predicted target gene, CqHAI3. Both genes emerged as central hubs associated with pre-harvest sprouting resistance in quinoa.

Follow-up characterization showed that CqRVE5 and CqHAI3 share remarkably similar expression patterns, with both preferentially active in seeds rather than in leaves, stems or roots. When the researchers tagged the corresponding proteins with fluorescent markers, both were found to localize to the nucleus, the expected destination for proteins that regulate gene expression. These features are consistent with a role in which CqRVE5, acting as a DNA-binding transcription factor, directly controls the activity of CqHAI3 within seed tissue, where the decision to germinate or remain dormant is ultimately made.

To test whether these genes actually influence germination, the team overexpressed each of them in Arabidopsis thaliana, the standard laboratory workhorse of plant genetics. The results were unambiguous. In transgenic seeds carrying either CqRVE5 or CqHAI3, the levels of gibberellin relative to abscisic acid shifted, amylase activity declined and the rate of starch degradation slowed. The consequence was a measurable reduction in germination capacity. In other words, both genes act as negative regulators of seed germination, holding the seed back from sprouting. This finding directly links the gene pair to the physiological traits, hormone balance, starch breakdown and germination vigor, that determine whether a quinoa seed sprouts on the plant.

The researchers then probed the relationship between the two genes at the molecular level. Using promoter-binding assays, they demonstrated that the CqRVE5 protein can bind to specific sequences in the promoter region of the CqHAI3 gene and activate its expression. This establishes CqHAI3 as a direct downstream target of CqRVE5, forming a coherent regulatory module rather than two genes acting in parallel. The architecture is notable because CqHAI3 belongs to a family of protein phosphatases associated with abscisic acid signaling, suggesting a mechanism in which a circadian-linked transcription factor reinforces the dormancy-promoting arm of hormone signaling precisely when the seed reaches harvest maturity.

The implications for agriculture could be substantial. Pre-harvest sprouting is a major problem not only in quinoa but also in wheat, barley and rice, where it degrades grain quality and costs growers billions of dollars worldwide. In wheat, breeders have long sought genes that maintain dormancy through wet harvests, and several regulatory modules have been characterized in cereals. The identification of the CqRVE5-CqHAI3 module adds a new piece to this puzzle and proposes a previously unappreciated mechanism for sprouting control in a crop whose genome is unusually complex. Because the module suppresses germination by influencing starch metabolism through hormone pathways, it offers a clear entry point for marker-assisted selection or genome editing aimed at enhancing dormancy without compromising other agronomic traits.

There are, of course, important caveats. The functional evidence for the module comes primarily from overexpression studies in Arabidopsis, a distantly related species, and from correlation-based network analysis in quinoa itself. Confirming that the same module operates in quinoa seeds under field conditions will require additional experiments, such as knockout or knockdown of the genes in quinoa and testing across diverse germplasm and environments. The authors also note that resistance to pre-harvest sprouting is a quantitative trait shaped by multiple genes, seed coat structures and environmental factors, so the CqRVE5-CqHAI3 module is best viewed as one key component of a broader regulatory network rather than a single master switch.

Even with those qualifications, the study represents a meaningful advance for a crop whose global importance is rising rapidly. As demand for plant protein grows and climate variability makes harvest-season weather increasingly unpredictable, protecting quinoa from pre-harvest sprouting becomes both an economic and a food-security priority. By tracing the trait from a resistant variety through hormone physiology, starch biochemistry and a defined transcriptional cascade, the Gansu team has delivered a mechanistic framework that breeders and molecular biologists can now build upon. If subsequent work validates the module in elite quinoa lines, the humble grain’s tendency to wake up too soon could finally be switched off, at the level of its own DNA.

Subject of Research: The CqRVE5-CqHAI3 gene module regulating pre-harvest sprouting resistance in quinoa seeds.

Article Title: CqRVE5-CqHAI3 is the potential key gene module regulating pre-harvest sprouting in quinoa

Article References: Wang, X., Wang, B., Liu, W., Zhao, Y., Zhu, X., Wang, Y., Chai, J., Liu, H., & Wei, X. (2026). CqRVE5-CqHAI3 is the potential key gene module regulating pre-harvest sprouting in quinoa. Plant Cell Reports, 45(10), Article 287. https://doi.org/10.1007/s00299-026-03971-x

Image Credits: AI Generated

DOI: 10.1007/s00299-026-03971-x

Keywords: quinoa, pre-harvest sprouting, seed germination, CqRVE5, CqHAI3, abscisic acid, gibberellin, starch metabolism, transcription factor, seed dormancy, WGCNA, Plant Cell Reports