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Massive Genome of Economically Important Loblolly Pine Sequenced; Candidate Resistance Gene Identified for Fusiform Rust Disease

U.S. Forest Service Southern Research Station (SRS) scientists co-authored an article published on March 4, 2014 in an open-access article in the journal Genome Biology that reports the sequencing, assembly, and annotation of the loblolly pine (Pinus taeda) genome. As the primary source of pulpwood and saw timber for the U.S. forest industry, loblolly pine is of great economic importance to the South and to the nation. Dr. David Neale, professor of plant sciences at the University of California, Davis, led the loblolly pine genome project. “The project was a huge undertaking because at 22 gigabases, the loblolly pine genome is about eight times larger than the human genome,” said Dr. C. Dana Nelson, SRS Southern Institute for Forest Genetics (SIFG) project leader and research geneticist. “The group chose loblolly pine both because of its economic importance, and the knowledge gained from 60 years of breeding the species and managing millions of trees in genetic trials.” As part of the project, researchers identified a candidate for a gene involved in resistance to fusiform rust, a disease that infects southern pines. SIFG biological science technician Katherine Smith worked with Dr. John M. Davis, professor and associate director of the School of Forest Resources and Conservation at the University of Florida (UF), to compare mapped sections of the genome with sections found in loblolly specimens previously inoculated with the pathogen that causes fusiform rust. “Fusiform rust is the most damaging disease of southern pines—and one of the most complex, due to genetic interactions between the pathogen and its host,” said Dr. Davis, who also serves as faculty and Executive Committee member at the UF Genetics Institute. “Genetic resistance is the only realistic way to manage the disease, which infects young trees within their first five years of growth and weakens or girdles the stem. Chemical control is expensive, impractical, and not very good for the environment.” Researchers and breeders can use the resistance genes as markers to track resistance in pine breeding populations and to guide tree planting at the stand level. “The fusiform rust pathogen has evolved to defeat some rust resistance genes in loblolly,” said Dr. Nelson. “The increased molecular understanding from the loblolly genome sequencing effort provides managers with a new effective tool to determine how well seedlings will grow on a particular site.” SIFG involvement in sequencing the loblolly genome actually goes back at least two decades, when SIFG helped develop an array of resources to help speed up mapping and sequencing the loblolly pine genome and provide the ability to identify genes that influence factors such as tree growth, wood quality, stress tolerance, and resistance to disease. SIFG also conserved and supplied the plant tissue used in the genome sequencing project and provided quality control on the DNA samples that were sequenced. The loblolly genome project was led by a team at the University of California, Davis, and the assembly stages were led by researchers at the Johns Hopkins University and the University of Maryland. Other collaborating institutions included Indiana University, Bloomington; Texas A&M University; Children’s Hospital Oakland Research Institute; and Washington State University. The image shows genetically improved loblolly pine stand in North Carolina at 30 years. (Photo by Steve McKeand). [Press release] [Genome Biology article]