Hickory genotyping results

General Fruit Growing
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Hi y’all, I thought I’d share with you here some preliminary results of Dr. Warren Chatwin’s hickory genotyping project. He works with the USDA, filling the shoes of his predecessor LJ Grauke. While his data is not yet published, we caught up at the NNGA conference in Michigan and he and Alex Tanke and I sat down with his computer and poured through and discussed the data for awhile.

This data is the result of leaf tissue samples sent in to Dr. Chatwin. If you want to be involved, he is still collecting samples – send me a message for more information.

From what I recall, several pecan cultivars received a full genome sequencing. Then, 1 cultivar or specimen of each species received a full genome sequencing to establish a reference genome for each type.

For example, Grainger shagbark got a full sequencing as a type specimen for shagbark hickory. There are some problems here, such as how Grainger is considered a southern shagbark Carya carolinae-septentrionalis, rather than a regular Carya ovata, but overall these issues will be solved by more data.

Reference genomes were also established for bitternut, nutmeg hickory, red hickory, and the tetraploids mockernut, pignut, etc, although it is clear we need more data for the tetraploids and the red hickory (which may be tetraploid? Unclear.).

Using the full sequences, Dr. Chatwin was able to identify regions of difference among the various Carya species, and then did genotyping on the samples using those 3,000+ markers. Those genotypes are then scatter plotted to show their spatial relationships to all other samples. For example, there is a cluster for shagbark, and for shellbark, and these are right next to each other in the same direction as the two species diverged from one another only some 4 mil years ago. Whereas, bitternut and pecan will be charted in the other direction, separated from the shag and shell clusters by some space. F1 shag x bitternut samples will cluster in between shagbark and bitternut clusters, as an illustration.

Here are some of the results in relation to shagbark, shellbark, hican, and Carya x laneyi. While his data includes numerous pecan entries, including the entire USDA repository, i just wrote down the stuff from hickory as that’s the data we looked at. When he publishes (probably near the end of this year / early 2026), I assume that data will be included then. Any percentages, such as 82.5%, or 90%, are visual estimates and not actual calculations (those calculations will be part of publication).

SF1. (shag x bit) x shag
Fairbanks. 50:50 shagbark:bitternut
Abundance. 50:50 shagbark:bitternut
Trexler. 50:50 shagbark:bitternut
SF1 seedling 2. closer to 50:50 than SF1
Lundale. 50:50 shagbark:bitternut
Siers. 50:50 shagbark:bitternut
SF2. 50:50 shagbark:bitternut
NJBG N1. 50:50 shagbark:bitternut
NJBG S4. 50:50 shagbark:bitternut
SF1_1. 50:50 shagbark:bitternut
SF3. 50:50 shagbark:bitternut
SF5 d2. 50:50 shagbark:bitternut
SF6. 50:50 shagbark:bitternut
NJBG_NE2. (shag x bit) x pecan
NJBG seedling. 75:25 bit:shag
Pequea Manor (aka Paradise). 50:50 bit:shag
Paradise seedling 2. 75:25 bit:shag
Abby (Abbott seedling). 50:50 bitternut:pecan
Abbott seedling. 50:50 bitternut:pecan
Pleas. 50:50 bitternut:pecan
S_4292_1_A_14. 50:50 shagbark:pecan
Horton. 50:50 shagbark:pecan (synonymous with Burton)
Burton. 50:50 shagbark:pecan
Gun Club (Mizzou variety). 50:50 shagbark:pecan
Henke. 50:50 shagbark:pecan
Weese. 50:50 shagbark:pecan
Hartman/Heartman. 50:50 shagbark:pecan (possibly syn. w/ Country Club)
Country Club. 50:50 shagbark:pecan (possibly syn. w/ Hartman)
Lenz (Mizzou variety). groups with Hartmans in shag
Vernon. 50:50 shellbark:pecan
Palmer. 50:50 shellbark:pecan
Des Moines. 50:50 shellbark:pecan
T-92. 50:50 shellbark:pecan
Underwood. 50:50 shellbark:pecan (three distinct Underwood samples)
Bixby. 50:50 shellbark:pecan
Wabash. 50:50 shellbark:pecan
McAllister. 50:50 shellbark:pecan
Hershey (from Spurgeon collection). 50:50 shellbark:pecan
Lenz. groups with shell
James. 50:50 shellbark:pecan
Vernon. 50:50 shellbark:pecan
J. Wilson. 50:50 shellbark:pecan (possibly syn. w/ Vernon)
Burlington. 50:50 shellbark:pecan
Newlin. 50:50 shellbark:pecan
Westbrook. 50:50 shellbark:pecan
Marquardt. 50:50 shellbark:pecan
Gelhaus. hybrid
Gerardi. hybrid
New Baden. hybrid
Deerstand. shag x pecan (one groups as shag, the other as pecan)
Dooley Burton. 75:25 shag:pecan
79-3-4. 75:25 shell:pecan
24_OVT_KY_15_Pittman. 82.5% shag x bitternut
Neilson. 80:20 shag:pecan
Seas. 80:20 shag:pecan
Porter. 90:10 shag:pecan
Davis. 90:10 shag:pecan
Stohlers Thinshell. 90:10 shag:pecan
Wilmoth. 90:10 shag:pecan
Harold. 90:10 shell:pecan
CES-24. 90:10 shell:pecan
Simpson #1. 90:10 shell:pecan
Curt Price. 90:10 shell:pecan
Lindauer. 90:10 shell:pecan
Weiker. 50:50 shag:shell
Conowingo. 50:50 shag:shell
Bradley. 50:50 shag:shell
Doghouse. 50:50 shag:shell
Cody Cox. 50:50 shag:shell
S026. 50:50 shag:shell
Seven Leaf Shag. 50:50 shag:shell
Keystone. 75:25 shell:shag
Hoagland. 75:25 shell:shag
Elmer Kneuss. 75:25 shell:shag
Florrin-Smith. 80:20 shell:shag
Holterman. 90:10 shell:shag
Van Winkle. 90:10 shell:shag
Yoder #1. 85:15 shag:pecan
Lorane. 90:10 shag:bitternut
Walters. 90:10 shag:bitternut
Etter #2
synonymous with Walters
Etter hican #1. shagbark
Grainger. type specimen of shagbark
Mick Terry. 90:10 shag:bit
Hirshi. 90:10 shag:bit
C324. 90:10 shag:bit
Weschcke River Shell. 75:25 shag:shell
Sankanac. 90:10 shag:bit
Weaver Barn. 90:10 shag:bit
Weaver Pasture. pulled in outlier direction
Mitch Russell. 75:25 shag:shell
Conococheague #1. shagbark
Conococheague #2. shellbark
JJ47. shagbark
Weschcke. shagbark

Understanding the results. 50:50 hybrids are f1s. There are several results with a 75:25 relationship, which indicate a bc1 backcross. Anything in the 80-90% range in regards to hybrids probably represents a level of introgression, rather than a straightforward backcross bc2.

There were a few surprising results. Keystone shellbark appears to be only 75% shellbark and 25% shagbark. Pennsylvania shagbarks like Yoder #1 and Porter both show introgression with pecan. Kentucky shagbark Wilmoth also shows pecan introgression. There appears to be no parent:child relationship between Grainger and Lorane. Some shellbarks such as Simpson #1 from Kentucky and Lindauer reveal pecan introgression. There are a fair number of shagbarks with bitternut introgression (as expected).

There are probably limitations to the data. For example, Etter hican #1 clustered with shagbark, even though very clear Apocarya influences can be seen morphologically. It may be the case that 3,000 markers isn’t enough and masking is occuring. To use an analogy, humans and chimps share 99.9% of their DNA… inadequate markers will put us in the same cluster, but the little bit of difference makes all the world.

Weschcke, commonly to thought to have bitternut introgression, which accounts for it’s pollen-sterility, was found to just cluster with shagbark.

A similar effect occurs with Tanke’s bitshag samples, which I did not include here. These were trees planted allegedly from bitternut x shagbark nuts, either f1s or backcrosses (all OP). Yet the genotyping clusters all these trees as shagbark. Many of those samples have kernel ratios near or above 50%, with very thin shells and other subtle features of Apocarya, but they cluster as shagbark. So this raises questions about whether enough markers were used, and/or how genetics works in hickories.

Overall, the data confirms morphological identification as on par with what the genetics shows. For example, the various hicans have been described as f1 hybrids between shag or shellbark and pecan, and the genotyping data agrees. But the genotyping is able to reveal deeper relationships not seen morphologically (like pecan introgression in shagbark).

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My daughter has a bitternut x pecan in her front yard.

The tree looks like pecan.

The nuts and hulls… also look very similar to pecan except they are a little shorter than pecans.

The taste … unfortunately… exactly like a bitternut hickory. Quite astringent.

TNHunter

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I’m waiting patiently for publication of the genome data. Meantime, I’m grafting and planting more pecan trees. I currently have T92 as my only hybrid here at home. I have a few other hybrids at another location.

One of the disparities highlighted by results given so far is the sheer number of hybrids where shagbark is the repetitive parent. I’m not sure if this is selection bias or if there is a genetic reason. It could be that there are crossing barriers in F1’s such that shagbark is the most viable parent. This could be as simple as the timeframe when hybrids bloom which might overlap with shagbark but not with the other parent species.

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Interesting that ‘Etter hican #1’, which has historically been claimed to be a cross of ‘Weschke’ (which had been claimed to be a shagXbitternut) and ‘McAllister’ (a large shellbarkXpecan) typed out as shagbark.

I submitted leaf samples from about 2 dozen selections for Dr. Warren Chatwin to evaluate in this first wave of analyses. Most were named cultivars in my collection, but with concentration on those that originated in KY, as well as a few random ‘wild’ KY natives… mostly bitternut & shellbark.
I’ve lost my notes from my submission, so don’t know which tree is ‘24-OVT-KY-15-Pittman’, in that table, which appears to be 82.5% shagbark/17.5% bitternut.

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Yes Etter hican is the most baffling one. Although the tree has general shagbark characteristics in its bark and form, its clear from the buds and the leaflet count that some hybridization is going on. That’s not mentioning the nuts, which have thin leathery husks with wings on them like pecan or bitternut, have a smooth hull like pecan or bitternut, and practically no lobes inside the shell like pecan. With fuzz typical of Apocarya, and a large kernel like shellbark. Doesn’t have the maple flavor of shagbark. The nut looks like a perfect intermediate between Weschcke and McAllister.

Perhaps materal influence in hickories is dominant, and introgression gets siloed to a narrow range of expressions, such as seen within the nut. In other words, 3,000 markers isnt enough, when it ought to be, suggesting inheritance in hickory is more complicated than we would have thought.

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3000 markers in a full genome with 187.22 gigabases is kind of like dipping a toothpick in a 55 gallon drum of water.

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I am curious as to whether you feel Etter Hican is capable of filling nuts in more northern zones.

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What do you mean by northern? Zones 5, 6? Or 3 and 4? I don’t see why Etter hican would have trouble in zones 5 and 6, as long as you have enough hickory pollen around for good cross-pollination. Filling of the nuts seems to be decided mostly by pollen compatibility and rainfall.

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I’m in zone 4b/5a. I was thinking that maybe my area wouldn’t get enough heat for the nuts to mature properly over the course of the season. Our first frost is around October 10th. That’s good to know though in regards to pollen compatibility. I would likely plant it alongside other hickories.

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I just went through the first post of varieties with identities and saw something that I can’t quite put my finger on. It looks like shagbark may be splitting into another species. Instead of northern and southern shagbark, there may be northern, western, and southern shagbark. It is in the early stages of splitting if this is the case.

Other considerations aside, the sheer number of shagbark and shellbark hybrids with pecan is intriguing. One note of possible importance, there are no indications of C. myristiciformis in the listed data. I wonder what would show up if some of the nutmeg trees near Selma Alabama were sampled? Reason for asking is because native pecans have grown in the Selma area for at least 3000 years, maybe longer. Nutmeg hickory is native there. Would we find nutmeg x pecan hybrids? Also, there is a hican growing in the side yard of the school in Castleberry Alabama that may be a complex cross of nutmeg, water hickory, and pecan. There are lots of trees out there that can be tested and will shed light on the hickory genome.

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