Abstract
Fusiform rust resistance in loblolly pine, Pinus taeda L., is comprised of both polygenic and major gene effects. In this study, we applied a Bayesian approach to test for single nucleotide polymorphisms (SNPs) associated with resistance to fusiform rust, which is caused by Cronartium quercuum (Berk.) Miyabe ex Shirai f.sp. fusiforme. A population of 3810 clonal varieties from 100 full-sib families was produced through somatic embryogenesis and planted in replicated field experiments in the Southeastern United States. Rust phenotypes were measured after 6 growing seasons, and each of 863 clones from 35 full-sib families was genotyped with 3340 SNPs. We identified five associated SNPs with posterior probabilities of inclusion above 0.4 in the clonal population using a BayesCπ model. A second experiment was conducted with one of the identified SNPs (SNP2374) using seedlings from 2 full-sib families that were included in the first experiment. Resistant genotypes exhibited an overall infection rate of 11% compared to the susceptible genotype which had 57% infection. Using one of the full-sib families, we were able to map SNP2374 (CL1208Contig1-03-75) to linkage group 7. Confirmation of the SNP2374 association with rust resistance demonstrates the potential for selecting and screening genotypes to further reduce disease incidence in forest plantations of loblolly pine.
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Data availability
SNP names/sequences, rust phenotypes, and genotypes are available for the population used in this experiment.
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Acknowledgments
We wish to thank Alice Perry and Jay Coke for their contributions towards the propagation of plants utilized in this experiment. We also wish to thank David Brown, Chris Judy, Robert Moore, Jimmy Seckinger, and Hugo Palm-Leis for their assistance in field trial data collection. The authors also wish to thank Sunny Lucas and the staff of the USDA Forest Service Resistance Screening Center for assistance with the greenhouse screenings.
Funding
This research was funded by ArborGen Inc.
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Data archiving statement
The SNP sequences are currently available for download from the TreeGenes website in the Pita CTGN data section (https://treegenesdb.org/). Pedigree information, genotypes, and phenotypes used for genomic analysis are available in the electronic supplemental materials.
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Cumbie, W.P., Huber, D.A., Steel, V.C. et al. Marker associations for fusiform rust resistance in a clonal population of loblolly pine (Pinus taeda, L.). Tree Genetics & Genomes 16, 86 (2020). https://doi.org/10.1007/s11295-020-01478-4
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DOI: https://doi.org/10.1007/s11295-020-01478-4