As pecan harvest approaches, growers across Louisiana begin evaluating kernel quality—and sometimes, the results are disappointing. One of the most frustrating issues is the appearance of blackened or shriveled kernels, often hidden inside shells that look perfectly normal. While several factors can contribute to poor kernel fill, boron deficiency is emerging as a key player in this complex problem.

One of the most detailed examinations of this issue comes from the report Black Kernel Rot Malady of Pecan by Wood et al., which proposes that boron deficiency may be a central factor in many cases of black kernel rot. Their findings suggest that boron not only affects kernel development directly, but also interacts with other stressors—such as insect damage, water-stage fruit split, and delayed shell lignification—to amplify internal kernel breakdown.

The Role of Boron in Pecan Trees

Boron is a micronutrient that pecan trees need in small amounts—but it plays a big role in nut development. Here’s what it does:

• Builds strong cell walls
  Boron helps keep plant tissues flexible and healthy, especially in fast-growing parts like developing nuts.
• Supports pollination and nut set
  Without enough boron, pollen tubes may burst before reaching the ovule, leading to poor nut formation.
• Moves sugars and nutrients
  Boron helps transport sugars through the tree. In pecans, this is especially important because they move sugars as sucrose—a form that doesn’t carry boron well.

Here’s the tricky part: boron doesn’t move around once it’s placed in the tree.
Even if leaf tests show good boron levels, the nuts might still be deficient—especially during rapid growth or dry weather. That’s because the seed coat only receives nutrients through the phloem, and boron is only partially mobile in that system.

So, if boron uptake is interrupted while the nut is sizing, the seed coat may not get what it needs. This can lead to tearing, poor kernel fill, and blackened tissue—even when the leaves look fine.

Recognizing the Symptoms

Black kernel symptoms typically show up late in the season, just before or during harvest. Affected nuts may have:

• Darkened, shriveled kernels
• Poor fill or hollow interiors
• Whole, plump kernels that are blackened and inedible
• Normal shell appearance, making the issue hard to detect until cracking

These symptoms are often confused with stink bug damage, drought stress, or scab-related issues. However, when shell quality is unaffected and kernel damage appears widespread, boron deficiency becomes a likely suspect — especially if seed coat tearing or internal darkening is visible when the nuts are cracked.

What Is Seed Coat Tearing?

Seed coat tearing happens when the outer layer of the pecan kernel splits or cracks—usually near the stem end. These tears are hidden inside the shell and often go unnoticed until the nut is cracked open. When tearing occurs, the seed coat may look brittle or stiff, and the kernel inside may be dark, shriveled, or poorly filled.

This kind of damage is closely tied to boron. Boron is a micronutrient that helps keep plant cell walls flexible. In pecans, it also helps move potassium into the kernel, which controls internal pressure as the nut fills. If boron is low—especially during fast growth or dry weather—the seed coat may not stretch properly. Instead, it tears, and the kernel suffers.

Torn seed coats can also lead to darker brown or amber coloring inside the nut. That’s because damaged tissue may build up polyphenols, which are natural compounds that darken the kernel. Even if the shell looks fine, the nut inside may be ruined.

This tearing can also make other problems worse. If stink bugs or other insects damage the nut early on, a healthy tree with good boron levels might be able to seal off the injury. But if boron is low, the damage can spread, leading to blackened or rotting kernels.

In short, seed coat tearing is a warning sign. It often means the tree didn’t have enough boron when the nut was growing—and that can lead to poor kernel quality at harvest.

The Connection to Stink Bug Damage

Sometimes black kernels aren’t caused by just one problem. In many cases, insect damage and boron deficiency work together to make things worse.

Stink bugs and other piercing-sucking insects can damage the seed coat early in the season. If the tree has enough boron, it may be able to seal off the injury and limit the damage. But if boron is low, the kernel may not heal properly. Instead, the injury spreads, and the nut ends up blackened or shriveled.

This is especially common in:

• Low-input orchards, where boron isn’t regularly applied
• Dry seasons, when boron uptake from the soil is limited
• Years with high insect pressure, when more nuts are injured

Even mild stink bug damage can lead to serious kernel problems if boron levels are low at the time of injury.

What to Watch For:

• If you see black kernels but the shell looks normal
• If seed coat tearing or poor kernel fill is present
• If drought isn’t the issue, and insects were active

Then boron deficiency may be part of the problem.

Evidence Linking Boron Deficiency to Black Kernels

Black kernel symptoms can come from several stressors—but boron deficiency stands out as a consistent cause, especially in low-input orchards and southeastern soils.

Here’s what the evidence shows:

• Damaged seed coats
  Kernels with black or brown rot often have splits or tears in the seed coat, especially near the stem end. These tears allow polyphenols (natural compounds that darken tissue and may signal stress or damage) to build up inside the nut.
• Boron’s limited mobility
  The seed coat gets nutrients only through the phloem, and boron doesn’t move easily in that system. So even if leaf levels are fine, the nut can still be deficient—especially during rapid growth or dry weather.
• Field observations match the pattern
  The Wood et al. report found that black kernel symptoms often appear:
  • In orchards with water-stage fruit split
  • When shell lignification is delayed
  • During heavy crop loads, when boron demand is high
• Soil type matters
  The problem shows up more often in trees growing on southeastern soils, which tend to have lower boron availability.

Even though other factors—like insect damage or transition metal deficiencies—can contribute, boron deficiency is the most consistent thread across affected orchards.

Diagnosing Boron Deficiency

Boron deficiency in pecans can be tricky to spot. The symptoms often show up late in the season and can look like other problems—such as drought, insect damage, or poor pollination. Here’s how to tell if boron might be the issue:

Leaf Sampling: Your First Step

• The most reliable way to check boron levels is by testing leaf tissue.
• Sample leaves in late July to early August, when the tree is actively growing.
• Aim for 75–100 ppm boron (dry weight). Levels below this may signal a deficiency.

Important: Even if leaf levels look good, nuts can still be deficient. That’s because boron doesn’t move easily from leaves to nuts once it’s in the tissue.

Visual Clues in the Nuts

Look for these signs when cracking pecans:

• Kernels that are shriveled, dark, or poorly filled
• Seed coats that tear or split, especially near the stem end
• Dark amber seed coats (may indicate polyphenol buildup from stress)

Orchard History Matters

Think back to past seasons. Boron may be a problem if you’ve seen:

• Fruit drop during sizing
• Poor kernel fill or hollow nuts
• Water-stage fruit split (nuts cracking during rapid growth)

Soil Testing: Use with Caution

• Soil tests for boron aren’t always reliable—levels are low and can change quickly.
• They may still help identify long-term issues, especially if your soil has high calcium or aluminum, which can block boron uptake.

Correcting and Preventing Boron Deficiency

Managing boron well can make a big difference in kernel quality. But because boron doesn’t move easily inside pecan trees, timing and method matter. Here’s how to do it safely and effectively.

Foliar Sprays: Fast but Risky

Spraying boron directly on the leaves is the quickest way to help the tree—especially during nut sizing in mid to late August.

Benefits:

• Helps the seed coat stretch instead of tear
• Supports kernel fill and shell hardening
• Improves potassium movement inside the nut

Risks:

• Too much boron can burn leaves or stunt growth
• Toxicity can happen quickly if rates are too high

Safe Use Tips:

• Use low rates: 1/16 to 1/8 lb of actual boron per 100 gallons of spray
• Limit to 2–3 sprays in August, unless a deficiency is confirmed
• Don’t mix boron with other nutrients unless you’re sure they’re compatible

Soil Applications: Slower but Safer

Applying boron to the soil builds long-term availability, but it works slowly and depends on soil conditions.

Best Timing:

• Apply in fall to prepare for spring growth

Things to Watch:

• Dry soil or high calcium/aluminum can block boron uptake
• Avoid repeated high doses—boron toxicity in soil is harder to detect but still harmful

Best Practices for Growers

• Aim for 75–100 ppm boron in leaf tissue during late summer
• Keep soil consistently moist in August to support uptake
• Watch kernel quality at harvest to guide next year’s boron plan

Takeaways for Growers

If you’re seeing black kernels in your orchard, here’s what to keep in mind:

• Don’t overlook boron. Even if leaf tests look good, nuts can still be deficient—especially during dry spells or rapid growth.
• Check boron levels with foliar sampling. Aim for 75–100 ppm in late July to early August.
• Watch for seed coat tearing. It’s a key sign of boron-related damage, especially when paired with poor kernel fill or darkened tissue.
• Consider insect pressure. Stink bug damage can worsen kernel symptoms if boron levels are low.
• Use boron carefully. Foliar sprays work fast but carry a risk of toxicity. Soil applications are safer but slower.
• Keep soil moisture steady in August. Dry soil can block boron uptake, even if enough is present.
• Plan ahead. If you saw symptoms this season, include boron in your postharvest fertility strategy.
• Share what you see. Grower observations help us learn more. Report issues to your local extension agent or university contacts.

References:

Wood, B., Bock, C., Wells, L., Cottrell, T., & Hotchkiss, M. (n.d.). Black Kernel Rot Malady of Pecan. Southeastern Pecan Growers Association.