Scientists at University of California, Davis have identified the cellular and genetic mechanisms behind pistachio hull split, a long-standing problem that damages nuts, increases contamination risk and costs growers millions each year.

Hull split occurs when the outer hull of the pistachio fruit cracks before harvest, allowing insects and fungi to enter. Around 4% of California’s pistachio crop is affected annually, though some cultivars can experience rates as high as 40% under certain conditions.

The findings could help breeders develop varieties with more resilient hulls, supporting California’s $2 billion-a-year pistachio industry.

The research shows that changes in pectin – a key component of plant cell walls – play a central role. As pistachio hulls ripen, the composition of pectin shifts, weakening the bonds between cells. This causes cells to separate, leading to cracks and tears in the hull.

Published in the Journal of Experimental Botany, the study was led by recent PhD graduate Shuxiao “Susan” Zhang in the laboratory of plant sciences professor Georgia Drakakaki. Zhang identified specific genes that regulate how cell walls change during ripening, triggering hull breakdown.

“This is the first time anyone has studied the pistachio hull at the anatomical and cellular level while also looking at gene expression and physiological data,” Drakakaki said. “Susan really got into the details of how the hull is built with different layers and how the cells in those layers are of different sizes. The layers respond differently to changes in pectin, and that causes the hull to split in different ways.”

Linking anatomy, genetics and ripening

Over a three-year period, researchers collected pistachio hull samples from commercial orchards near Fresno and from the Wolfskill Experimental Orchard near Winters. The team studied the state’s most widely grown varieties, including Kerman, Golden Hills and Lost Hills, sampling fruit at multiple stages late in hull development.

Using advanced imaging techniques, the researchers measured hull thickness, cell size and the degree of cell adhesion, categorising hulls as intact, cracked or tattered. RNA analysis then revealed which genes were active at each developmental stage.

The team found that while all hulls were intact 91 days after flowering, hull split increased as ripening progressed. Cells in the inner hull layer expanded during ripening, while outer-layer cells remained largely the same size.

Combined with pectin modification in the cell walls, these differences generated internal stresses that caused the hull to split in distinct ways. Humidity and physical forces within the hull layers were also found to influence degradation.

“This is one of the major novelty factors for our paper,” Zhang said. “Loads of people have looked at pectin in all kinds of fruits, but not many people have observed that, depending on which cell layer you’re in, the pectin, cell size and so on will change differently during ripening.”

The work builds on earlier research by UC Davis scientists Grey Monroe and Barbara Blanco-Ulate, who assembled a reference genome for Pistacia vera ‘Kerman’ and defined key growth stages of the nut. Together, the studies provide a framework for linking fruit anatomy, ripening and genetic control.

As the pistachio hull is botanically a fruit, despite the edible portion being the seed, the findings may also have relevance for other non-berry fruit crops that are susceptible to pre-harvest splitting.