A second-generation cloned population of Pinus taeda was developed to validate genomic selection in Pinus taeda (Photo by Austin Heine).

Genomic Selection in Forest Trees:  Beyond Proof of Concept

(2019–2024, USDA-NIFA Award No. 2019-67013-29169)
Selecting superior tree varieties requires costly field trials that can take more than five years in loblolly pine (Pinus taeda). The NC State University Cooperative Tree Improvement Program developed a genomic selection strategy and began implementing it in 2026. With USDA-NIFA support, we also genotyped approximately 2,000 full-sib seedlings from two families to investigate the genetic basis of fusiform rust resistance. This work produced high-density linkage maps and identified three major-effect QTL for broad-spectrum resistance. See our Heredity article for details.. 

Population Genomics of Race Non-specific Disease Resistance in the Endemic Pinus-Cronartium Pathosystem

(2022-2026, NSF/USDA-NIFA Award #: (2022-04779). 

Characterizing the population genetics of the fusiform rust fungus Cronartium quercuum f. sp. fusiforme (Cqf) and identifying candidate effector loci will improve our understanding of gene-for-gene interactions in this genetically variable pine–rust pathosystem. Using long-read PacBio sequencing of four haploid isolates, we will generate and publish a highly contiguous Cqf reference pangenome. This resource will support genome-wide scans for selective sweeps and comparisons with other Cronartium rusts to identify regions affected by gene loss or diversification during host adaptation. Because the Cqf genome (<100 Mbp) is much smaller than the *Pinus taeda* genome (>20 Gbp), pathogen avirulence genes may be easier to identify than the corresponding host resistance genes. Cloned avirulence genes could ultimately facilitate the identification and cloning of genes underlying non-race-specific resistance in P. taeda.

Conifer SNP Consortium (CSC)

I established the Tree Consortium in January 2018 at the Plant and Animal Genome Conference to bring together the forest genetics and tree breeding community and facilitate the development of genotyping platforms. The consortium subsequently signed a memorandum of understanding with Thermo Fisher Scientific to develop SNP arrays using Axiom technology. Since then, 16 arrays have been designed for different organizations and tree species. A few examples are provided below.

CSC-Pita50K (Pinus taeda)  – Lead PI: Fikret Isik, USA
CSC-Pira50K (Pinus radiata)  – Lead PI: Natalie Graham, New Zealand
CSC-Piab50K (Picea abies)  – Lead PI: Harry Wu, Sweden
CSC-Pitro50K (tropical pines)  – Lead PI: Zander Myburg, S. Africa /Juan Acosta, USA
CSC-4TREE (EU-B4EST, Pinus pinea, Pinus pinaster, Fraxinus (excelsior and angustifolia) and Populus (nigra and deltoides) – Lead PIs: Leopoldo Sanchez-Rodriguez and Patricia Faivre-Rampant (INRAe, France)
CSC-Psme50K (Pseudotsuga menziesii) – Lead PI: Glen Howe, USA

Optimal Mating Design of Monoecious Species

Khushi Goda, a Ph.D. student in the Cooperative Tree Improvement Program, developed software for optimizing mating designs in conifers. Many conifers are monoecious, producing both male and female strobili on the same tree, but are highly susceptible to inbreeding depression because of their genetic load of deleterious alleles. Her software allocates crosses to maximize genetic gain while controlling inbreeding. Watch this short video to learn more about her research.

Click here to run the software (shiny app by Khushi Goda).