How rice plants tell head from toe during early growth

Tokyo, Japan – Scientists from Tokyo Metropolitan University have uncovered how fertilized rice seeds begin to divide and establish their “body axis.” Using a new imaging method, they discovered that while the first cell divides in an asymmetric way initially, this is followed by random growth and the apparently “collective” determination of a body axis. This is a significant break with known pathways, a rare glimpse into the birth and growth of plant embryos.

A key puzzle in plant science is how plants develop their “body axis,” the reference direction by which they grow different parts of their anatomy. Scientists are only beginning to come to terms with the complex series of events which lead to axis formation, starting from a single fertilized cell or zygote. Studies on Arabidopsis, or thale cress, have shown that the axis is already decided when the zygote splits into two distinct daughter cells. They each contain different proteins and undergo different growth; one begins to elongate, while the other doesn’t. This means that they have decided their “apical-basal” (tip to base) axis from the first time they divide. However, while Arabidopsis is an important model organism for plant science, it is not clear whether this mechanism is carried over identically to other plants.

Now, a team of scientists led by Assistant Professor Atsuko Kinoshita from Tokyo Metropolitan University have studied the rice plant. They used three-dimensional confocal microscopy to image the three-dimensional structure of the early embryo, starting from a single zygote up to a few hundred cells. Plant cells are notoriously difficult to study like this due to poor imaging once the cells become crowded. Their unique success came from using new techniques to make the cells clear, letting them peek inside clusters.

The team discovered that rice develops through radically different steps to Arabidopsis. Firstly, the rice zygote splits by a plane which is diagonal to its long axis, leaving two asymmetric daughter cells, an apical and basal cell. Curiously, both cells set about dividing in an apparently random way, producing a roughly spherical blob with no apparent directionality. To get a better idea of what was happening inside, they traced the appearance of auxin, a key hormone in plant growth. Only on the second day, after a few tens of cells were produced, was auxin discovered at the center of the blob. The auxin then spread towards the basal cell side. This suggests that there is some way in which the cells act “collectively” to allow axis development over the whole spherical blob. This is clearly different from the localized, single-cell level “polarization” found in Arabidopsis and shows that maintenance of the apical-basal axis is robust against the apparent randomness of the cells in the embryo.

The team’s findings not only present a rare glimpse into the embryogenesis of an important plant for agriculture but also highlight a new framework by which embryo development may be traced in a wide variety of other plants.

This work was supported by Japan Society for the Promotion of Science (JSPS) KAKENHI Grant Numbers JP20K06689, JP24H00857, JP25K01990, JP24H00856, JP25H00933, and JP22H04978, JST PRESTO Grant Number JPMJPR22D6, and JST-Mirai Program Grant Numbers JPMJMI23C1 and JPMJMI20C8.

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