Atlas shows gene activity in seed development

Researchers in Mary Gehring's lab at the Whitehead Institute, affiliated with the Massachusetts Institute of Technology, have created a transcriptional atlas of the early development of seeds of Arabidopsis thaliana. The study mapped gene activity in different cell and nuclear types at 3, 5, and 7 days after pollination. The study points to mechanisms associated with the coordination between the embryo, endosperm, and maternal integument.

The atlas contains 54.210 seed nucleus profiles. Of this total, 24.024 correspond to seeds 3 days after pollination, 16.039 to seeds 5 days after pollination, and 14.147 to seeds 7 days after pollination. The base includes approximately 10,5% embryo, 23,4% endosperm, 64,3% seed coat, in addition to unfertilized ovule and funiculus.

Seed development

The team used single-nucleus RNA sequencing to track a dynamic phase of seed development. At 3 days, the embryo appears in the globular stage and the endosperm still maintains coenocytic organization. At 5 days, the endosperm begins cellularization in the micropylar region. At 7 days, cellularization is complete and the embryo undergoes rapid expansion.

The study expands the resolution of previous atlases of Arabidopsis. According to the press release, previous databases did not distinguish many cell types due to technological limitations. The new set allows for the localization of genes active in tissues linked to seed growth, nutrient storage, and communication between compartments.

Scientists have identified the main cell or nuclear types of the seed. The work also refined transcriptional states in the endosperm and mapped selection signals in specific genes for cell types. Among the results, the analysis showed compartmentalization of genes associated with the activation of transcription factors responsive to brassinosteroids.

Brassinosteroids regulate growth processes in plants. In the study, genes linked to the biosynthesis of these hormones showed concentrated expression in the micropylar region of the seed coat. The data also showed nearby cells in the endosperm with genes associated with the hormonal response. This location suggests local coordination between hormonal production and response during seed development.

Previous studies

The work relates this information to previous studies on seed size. The dissemination material reports that the interruption of brassinosteroid production had already reduced seed size, but the location of production within the developing seed remained undefined.

The atlas also detailed the chalazal region of the seed coat, a point linked to the entry of maternal resources into the seed. Researchers identified subtypes in the placentochalazal region with complementary functions. One group showed markers associated with callose synthesis. Another showed genes linked to phosphate transport and phosphatase activity.

In the endosperm, the team described greater tissue specialization. The study found abundant expression of genes encoding secreted short peptides, especially in the chalazal and micropylar endosperms. These regions are located at important seed interfaces: the chalazal region is involved in the entry of maternal resources, while the micropylar region is close to the embryo.

Founding population

The analysis also proposed the existence of a founder population in the chalazal endosperm. This population may contribute to establishing a region at the interface between maternal tissues and tissues derived from fertilization. According to the publication, the quantity and timing of resource supply by the mother plant influence oil, starch, and protein reserves in the seed.

Further information at doi.org/10.1038/s41477-026-02295-8