Building a corn cob—cell by cell, gene by gene

image of baby corn

Thousands of genes are needed in order for baby corn to develop properly. CSHL Professor David Jackson mapped gene expression (genes turning on and off) in a tiny developing ear of corn. On the right, a 5 mm-long ear of corn is developing kernel buds (blue). The gene ZmYAB14 (red) is turned on in the older buds toward the bottom of the picture. The left image shows a slice of a 5 mm-long ear of corn. The ZmSHR1-like gene (red) lights up cells that transport water and nutrients. Image: Xiaosa Xu/Jackson lab.

Corn hasn’t always been the sweet, juicy delight that we know today. And, without adapting to a rapidly changing climate, it is at risk of losing its place as a food staple. Putting together a plant is a genetic puzzle, with hundreds of genes working together as it grows. Cold Spring Harbor Laboratory (CSHL) Professor David Jackson worked with Associate Professor Jesse Gillis to study genes involved in corn development. Their teams analyzed thousands of individual cells that make up the developing corn ear. They created the first anatomical map that shows where and when important genes turn on and off during key steps in development. This map is an important tool for growing better crops.

Humans have been breeding corn to make it more useful for thousands of years. Jackson says:

“Ten thousand years ago, corn did not exist, right? There was a wild plant called teosinte. Teosinte itself only makes about 10 seeds. It makes these really tiny ears that don’t give much nutrition. In fact, the seeds they make are so tough that they would break your teeth if you try to eat them anyway.”

The secret to more and bigger kernels is found by looking at baby ears of corn 1–10 mm long. The scientists used a technique that allowed them to track every cell. They gave each cell a genetic ID tag, called a barcode. Xiaosa Xu, the lead author of the study, compares it to building a building. Xu says:

“We are able to use this single-cell RNA-seq technology to identify which block is what kind of identity: if this block is from our kitchen room or that block is from our bedroom.”

The scientists took corn plants at early stages of development, broke them into individual cells, barcoded them, and then saw what genes were turned on in each one.

Jackson notes, “in the past we haven’t been able to separate the cells and figure out the genetic information that’s specific to each cell. So that’s really, what’s new and exciting.”

They could then reconstruct an anatomical map to pinpoint where genes important for corn development were used.

Crops are still evolving. Jackson looks forward to developing different kinds of corn plants to fill new ecological niches. He also hopes this new technique will help other plant geneticists in their efforts to sustainably improve crop yields.

Source – Cold Spring Harbor Laboratory

Xu X, Crow M, Rice BR, Li F, Harris B, Liu L, Demesa-Arevalo E, Lu Z, Wang L, Fox N, Wang X, Drenkow J, Luo A, Char SN, Yang B, Sylvester AW, Gingeras TR, Schmitz RJ, Ware D, Lipka AE, Gillis J, Jackson D. (2021) Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery. Dev Cell [Epub ahead of print]. [abstract]

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