Genetics of Shortleaf and Longleaf Pine in Seed Orchards

Orderly rows of shortleaf pine trees under a blue sky
A second generation shortleaf pine seed orchard in Arkansas. Photo by Barb Crane, USFS.

Shortleaf pine (Pinus echinata) and longleaf pine (Pinus palustris) ecosystems have been dwindling for decades. Restoration is a huge priority for the USDA Forest Service, the Longleaf Pine Alliance, the Shortleaf Pine Initiative, and many others.

Restoration requires seed, and on National Forest System lands the seed comes from USDA Forest Service seed orchards. The Forest Service owns and manages 70 percent of all longleaf and 90 percent of all shortleaf orchards across the South.

In 2015, managers at a southern nursery began seeing weird-looking longleaf pine seedlings and became concerned about their genetic identity. Some of the seedlings had irregular or elongated stems, others had shorter needles – which are more typical of loblolly pine (Pinus taeda).

Both shortleaf and longleaf pine can hybridize with loblolly pine, which is grown in plantations throughout the South for timber production.

Researchers were already investigating hybridization. Fire suppression can favor the survival of shortleaf-loblolly hybrids on the landscape, as SRS research has shown. And scientists suspect that climate variability could increase hybridization, as temperature affects the timing of flowering and pollen production.

In 2016, a team of scientists from Oklahoma State University and the Forest Service analyzed nuclear DNA to tell the degree of hybridization in shortleaf seed orchards. They found that up to 30 percent of the shortleaf pine trees in seed orchards had at least some loblolly pine genes in their genomes.

map of the southeastern U.S. that shows where longleaf pine and shortleaf pine grow. The two species have different ranges, with shortleaf pine growing further north of longleaf
Current geographic range map of longleaf and shortleaf pine. Created by Chelsea Leitz, USFS.

“In that study, we classified a hybrid as any tree with more than six percent of its genome from loblolly pine,” says Dana Nelson, an SRS geneticist and project leader who contributed to the study. A low percentage of loblolly pine genes in a shortleaf pine tree suggests that the hybridization occurred several generations ago.

If the hybridization had been recent – if for example, a seedling’s dad was loblolly pine and its mom was shortleaf, that seedling would have 50 percent of its genes from each parent species. That seedling would be considered a first generation or F1 hybrid. “We found those at a low percentage,” says Nelson. “Depending on the orchard, one to three percent of the trees were F1 hybrids.”

A follow-up study led by Barb Crane used DNA markers in chloroplasts to identify any potential  F1 hybrids in the seed orchards. Unlike nuclear DNA, the DNA in a pine tree’s chloroplasts is only inherited from the dad. This makes chloroplast DNA a good way to identify the male parent’s species.

The results had good news for seed orchard managers, tree planters, and silviculturists as only 17 of the 619 shortleaf pine clones (less than three percent) in the seed orchards were F1 shortleaf-loblolly hybrids. The study was published in Tree Planter’s Notes.

“They were all located in the same seed orchard, and have been introduced to the chainsaw,” says Crane, regional geneticist for the Forest Service Southern Region. She also contributed to the 2016 study.

The team also tested 250 longleaf pine clones. None of these trees had a hybrid DNA fingerprint. In addition, they tested the DNA fingerprints of shortleaf and longleaf pine seeds in the Forest Service seed bank. This seed is critical in support of reforestation. Less than three percent of those seeds had a hybrid DNA fingerprint.

It took several years to identify the DNA markers that could be used to fingerprint pure shortleaf and longleaf pine.

SRS geneticist Craig Echt and biological laboratory technician Sedley Josserand have both retired. But they developed the genetic markers for longleaf pine. That research was published in 2018. The shortleaf pine markers were developed in collaboration with SRS and Oklahoma State University and published in 2012.

Rows of longleaf pine trees grow in a seed orchard
Longleaf pine seed orchard in Mississippi. Photo by Barb Crane, USFS.

“The Southern Research Station is the only forest genetics institute around that could develop those markers in a cost effective and efficient way,” says Crane. Echt and his colleagues screened needle and seed samples for more than 2,000 longleaf pines, more than 1,000 shortleaf pines, and almost 300 loblolly pines. Their work eventually identified the genetic markers in the chloroplasts that differentiate the three species.

Echt and Josserand sent 2,500 samples to the National Forest System Genetics Laboratory, where Forest Service geneticists used the markers to identify the DNA fingerprints of each species.

Valerie Hipkins was the lead geneticist on the project at the NFSGL. Her contributions were instrumental to the DNA fingerprinting study. She is currently serving as the acting station director at the Pacific Southwest Research Station.

Forest Service researchers have made major contributions to what’s known about the genetics and silviculture of shortleaf and longleaf pine.

Crane and other forest geneticists are part of a small cadre of approximately 20 remaining geneticists within the Forest Service. They work across deputy areas with researchers, seed orchard managers, and silviculturists. For example, after a timber sale, geneticists help managers pick the species and seed sources best suited for replanting.

Trees are adapting to climate change, but very slowly. Trees’ genetics must be adapted to where they’re growing. USFS photo, courtesy of Bugwood.

“When you plant seedlings, you want them to survive until rotation, which is often up to a hundred years,” says Crane. “That means their genetics must be adapted to that area. People from Alabama might not want to move to Alaska, and similarly, you wouldn’t want to plant an Alabama tree source in Alaska and expect it to grow. Plant the wrong species on the wrong site, and the whole stand could fall apart.”

Longleaf pine trees have somewhere around 50,000 genes. The full genome has not been sequenced – it would take years of research to do so. But scientists know that within that immense genome, not all of the genes are active at all times. Trees can activate various genes in response to environmental signals – including climate change and climate variability.

“The climate is changing much faster than trees can change in order to survive. Trees are adapting but very slowly, hence some species may face extinction. Seed orchards are an important conservation strategy,” says Crane, who is retiring soon. “An additional paramount management strategy is succession planning and training new people in forest genetics.”

Read the full text of the study.

For more information contact Valerie Hipkins at or Dana Nelson at

Access the latest publications by SRS scientists.

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