The Science Behind Late Season Purple Soybean Stems

Updated in 2025, this version replaces the previous 2021 The Science Behind Late Season Purple Soybean Stems publication.

Dark purple discoloration of soybean stems is sometimes observed near full maturity (~R7 growth stage). The purpling may appear in patches or cover the entire stem, and both the main stem and branches can be discolored (Figure 1). On lodged plants, the purpling typically occurs on surfaces exposed to direct sunlight, while the shaded underside of stems remains green (Figures 2 and 3).

What causes purple soybean stems?

The most likely cause of soybean stem purpling is the buildup of anthocyanins in the stem tissue. Anthocyanins are non-photosynthetic pigments that help protect plant cells from oxidative damage caused by too much light. Acting as visible light screens, anthocyanins function like natural “shade cloth,” reducing light exposure where needed. Because individual cells regulate anthocyanin production, the purpling often appears only on sun-exposed portions of the stem, creating a clear delineation between the purple and green stem tissues (Figures 2 and 3).

Although Cercospora leaf blight can produce purplish lesions on petioles and stems, it also causes bronzed, leathery upper leaves, whereas late-season purple stems lack foliar symptoms and show anthocyanin pigmentation confined to sun-exposed surfaces.

Why are anthocyanins produced?

Anthocyanin production and accumulation is linked to carbohydrate production and can be triggered when there is an abundance of sugars produced in plant tissues. This typically occurs when the plant continues producing carbohydrates that it cannot use, a situation known as a “source-sink” imbalance. By absorbing light, anthocyanins help the plant re-establish source-sink balance by moderating light capture, regulating carbohydrate use, and reducing photo-oxidative damage.

What causes source-sink imbalances?

When stem purpling is present, it is important to determine what disrupted the source-sink balance. These imbalances usually occur when there are fewer pods than normal on a soybean plant. Pod reduction can be caused by a combination of abiotic and biotic stresses, such as diseases, insect pests, and environmental stress or nutrient deficiencies. Purple stems may also appear after cold spells or seasonal dips in temperature, which can trigger anthocyanin synthesis. Cold temperatures slow enzymatic activity, lowering the plant’s need for light and increasing the risk of photo-oxidative damage.

What does stem purpling mean for yield and harvest?

Although stem purpling can indicate a source-sink disturbance, it is a natural protective response by the soybean plant under suboptimal conditions. However, purple stems can be tougher to harvest, potentially necessitating slower harvest speed or combine adjustments. Purple stems are a useful visual indicator that an underlying issue reduced pod set or limited yield. When possible, farmers should try to identify the cause of pod reduction to limit future losses and maintain productivity.

References

Conley, S. 2006. Purple soybean stems. Soybean Production Systems. Purdue University Cooperative Extension. https://ag.purdue.edu/department/agry/faculty-pages/soybean-station/_docs/purplestems.pdf. (Accessed September 13, 2021)

Steyn, W. J., Wand, S. J. E., Holcroft, D. M., and Jacobs, G. 2002, Anthocyanins in vegetative tissues: a proposed unified function in photoprotection. New Phytologist. 155:349–361. doi:10.1046/j.1469-8137.2002.00482.x Article / Google Scholar

Acknowledgements

Authors

Xavier A. Phillips, formerly with Iowa State University; Daren Mueller, Iowa State University; Shawn Conley, University of Wisconsin-Madison; and Adam Sisson, Iowa State University.

Reviewers

Martin Chilvers, Michigan State University; Travis Faske, University of Arkansas

How to cite: Phillips, Xavier A.; Mueller, Daren; Conley, Shawn; Sisson, Adam. The Science Behind Late Season Purple Soybean Stems. 2025. Crop Protection Network. CPN-1028. doi.org/10.31274/cpn-20210920-0.