The Science Behind Late Season Purple Soybean Stems

The Science Behind Late Season Purple Soybean Stems

CPN 1028. Published September 13, 2021. DOI:


Dark purple discoloration of soybean stems can sometimes be observed when scouting soybean fields close to full maturity (~R7 growth stage). The purpling can occur in patches or across the entire stem, and both the main stem and branches may be discolored (Figure 1). On lodged plants, the purpling is observed on portions of the plant that received direct sun while the underside of the stem remains green (Figure 2).

Figure 1. Soybean stem showing purple discoloration.

Image: Daren Mueller

Figure 2. Purple discoloration is present on parts of the stem receiving direct sunlight (A); while the part of the stem not in direct sunlight shows no purple discoloration (B).

Image: Adam Sisson

Demonstration of Purple Discoloration on One Side of the Soybean Stem

What causes soybean stem purpling and what does it do to the soybean plant?

The most likely explanation of soybean stem purpling is the buildup of anthocyanins in the stem tissue. Anthocyanins are non-photosynthetic pigments in plants that protect plant cells from oxidative damage caused by too much light. Anthocyanins act as visible light screens, or natural “shade cloths,” which reduces light exposure. The purpling is sometimes localized to areas receiving direct sunlight, which show a clear delineation between the purple and green stem tissue (Figure 3). This is because individual cells control anthocyanin production, providing protection only where needed.

Figure 3. A soybean stem showing clear delineation between tissue with and without purple discoloration.

Image: Xavier Phillips

Why are anthocyanins produced?

Anthocyanin production is linked to carbohydrate production and may be triggered when there is an abundance of sugars produced in the plant that cannot be used. This can be caused by a “source-sink” disruption, where the plant continues to produce carbohydrates that cannot be used. The light absorbing properties of anthocyanins help the plant re-establish source-sink balance by normalizing light capture, carbohydrate use, and CO2 assimilation while limiting photo-oxidative damage.

What causes source-sink imbalances?

When stem purpling is observed, 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 can also be observed after abnormal cold spells or seasonal reductions in temperature, which can induce anthocyanin synthesis. Cold temperatures slow down enzymatic activity and less light is needed for photosynthesis.

Although stem purpling can indicate a source-sink disturbance, it is a natural protective response by the soybean plant to mitigate damage under suboptimal conditions. Purple stems may be more difficult to cut during harvest, requiring harvest speed and combine setting adjustments. The purple stems may be a clue to an underlying issue resulting in a source-sink disturbance. If possible, farmers should try to identify the cause of pod reduction, limit future occurrences, and maintain yield.


Conley, S. 2006. Purple soybean stems. Soybean Production Systems. Purdue University Cooperative Extension. (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




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


Travis Faske, University of Arkansas and Kiersten Wise, University of Kentucky.


The authors thank the United States Department of Agriculture - National Institute of Food and Agriculture for their support.


This publication was developed by the Crop Protection Network, a multi-state and international collaboration of university/provincial extension specialists and public/private professionals that provides unbiased, research-based information to farmers and agricultural personnel.

This information in this publication is only a guide, and the authors assume no liability for practices implemented based on this information. Reference to products in this publication is not intended to be an endorsement to the exclusion of others that may be similar. Individuals using such products assume responsibility for their use in accordance with current directions of the manufacturer.

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The Science Behind Late Season Purple Soybean Stems

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