Marker associations for fusiform rust resistance in a clonal population of loblolly pine ( Pinus taeda , L.)
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ORIGINAL ARTICLE
Marker associations for fusiform rust resistance in a clonal population of loblolly pine (Pinus taeda, L.) W. Patrick Cumbie 1 & Dudley A. Huber 2 & Victor C. Steel 1 & William Rottmann 1 & Christina Cannistra 1 & Les Pearson 1 & Michael Cunningham 1 Received: 5 June 2020 / Revised: 16 October 2020 / Accepted: 5 November 2020 / Published online: 18 November 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
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. Keywords Pinus taeda . Marker-assisted selection . Disease resistance . Genomics
Introduction Fusiform rust, caused by Cronartium quercuum (Berk.) Miyabe ex Shirai f.sp. fusiforme (Cqf), is an indigenous disease of loblolly pine (Pinus taeda, L.) in the Southeastern United States that causes more than $20 million of damage to plantations each year (Cubbage et al. 2000). Cqf is macrocyclic and heteroecious, alternating between red oaks (Quercus sp. Lobatae) and southern yellow pine (Pinus sp.) (Powers 1975). Management of the disease in forest plantations has generally relied on planting genetically resistant seedlings (Zobel and Talbert 1984). Over the last 60 years, the robust breeding and testing programs of loblolly pine in Communicated by F. Isik * W. Patrick Cumbie [email protected] 1
ArborGen Inc., Ridgeville, SC, USA
2
Quantitative Genetic Services, LLC, Toccoa, GA, USA
the Southeastern United States have identified rust-resistant families, and recent advances in forest genomics now offer the opportunity to select resistant trees based on their DNA sequence. Building upon extensive previous research, the potential for developing genomic tools to enhance Cqf resistance is both feasible and worthw
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