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Pitro50K: A multispecies genotyping array for tropical pines https://npn.rngr.net/publications/tree-improvement-proceedings/southern/2021/pitro50k-a-multispecies-genotyping-array-for-tropical-pines Using a combination of reduced representation sequencing methods, we performed targeted SNP discovery towards the development of a genome wide, multi-species genotyping array for tropical and subtropical pine species. Pooled RNA-seq data for five species of tropical pines, originating from pathogen challenge experiments, were used to identify transcript based SNP markers. Additionally, target capture sequencing was performed for six species, utilizing pooled DNA from 81 provenances that represented the natural range of the species across Mexico and Central America. Variant calling yielded a total of 1.8 million candidate SNP probesets, 1.3 million and 563K from RNA-seq and target capture respectively. In total, 300K RNA-seq and 120K target capture derived probesets were evaluated on a 420K screening array through the genotyping of 576 trees from eight species, representing the original 81 provenances and commercial breeding material. Evaluation of the screening array probesets resulted in the selection of 50K SNPs for inclusion on the commercial array. These markers included 20K polymorphic SNPs for P. tecunumanii, P. patula, P. caribaea, and P. oocarpa, 15K for P. maximinoi and P. greggii, 13K for P. elliottii, and 8K for P. pseudostrobus. Of the 50K markers, 75% are polymorphic in two or more species. The Pitro50K genotyping array represents the first high throughput and affordable genomic tool for these species of pines and their hybrids which represent the majority of tropical and subtropical pine plantations globally. Potential applications for the array include population genomics, genetic mapping, molecular breeding, species and hybrid identification, and genetic resource management.No publisherddrummond2024-02-21T17:51:33ZPublicationEmily Senegal-Thyroff https://npn.rngr.net/about/personnel/emily-senegal-thyroff No publisherddrummond2023-12-19T19:16:12ZPagePlanificación de un Vivero Tropical https://npn.rngr.net/publications/manual-de-viveros-tropicales/planificacion-de-un-vivero-tropical No publisherddrummond2022-08-31T19:21:21ZPublication¿Por qué Empezar un Vivero Tropical para Plantas Nativas y Tradicionales? https://npn.rngr.net/publications/manual-de-viveros-tropicales/bfpor-que-empezar-un-vivero-tropical-para-plantas-nativas-y-tradicionales No publisherddrummond2022-08-31T19:20:30ZPublicationPropagation of Tropical Lilythorn (Catesbaea melanocarpa Krug &Urb.): A Federally Endangered Tree on St. Croix https://npn.rngr.net/publications/tpn/65-1/propagation-of-tropical-lilythorn-catesbaea-melanocarpa-krug-urb.-a-federally-endangered-tree-on-st.-croix Tropical lilythorn (Catesbaea melanocarpa Krug and Urb.) is a small, thorny tree with white flowers that is found on only one site on St Croix, two sites in Puerto Rico, and in a few other islands. It is a federally endangered plant species. At the University of the Virgin Islands, we are studying this species’ ecology and developing propagation protocols. The goal is to plant tropical lilythorn seedlings in protected areas on the island of St. Croix because the one site where the species currently grows is not protected from development. This article summarizes nursery and field observations during propagation efforts over the previous 8 years.No publisherddrummond2022-06-10T14:07:17ZPublicationNew Advanced Generation Seedling Seed Orchards Use Methodology Developed for Eucalyptus grandis in Florida https://npn.rngr.net/publications/tree-improvement-proceedings/southern/2017/new-advanced-generation-seedling-seed-orchards-use-methodology-developed-for-eucalyptus-grandis-in-florida Two advanced generation seedling seed orchards (SSO) recently established in Florida followed a novel cost-efficient, effective methodology developed through four generations of E. grandis genetic improvement. Combining short generation time and rapid growth with provenance and progeny testing in one place at one time, early selection, large infusions of new, primarily single-tree accessions, and use of pedigrees to minimize inbreeding resulted in steady and often great genetic gains. Advancing from a 1st-generation genetic base population of 4,352 trees from only 13 accessions to a 4th-generation genetic base population (GPop77) of over 31,000 trees from 529 worldwide E. grandis accessions resulted in productivity gains of as much as 195%. While the 1,500 trees in the 4th-generation SSO GO77 also captured individual tree responses to severe freezes, thus further illustrating the benefit of continued selection and orchard establishment, additional progeny tests contributed to the calculation of breeding values for stand basal area, bluegum chalcid resistance, and/or freeze resilience. Applying similar methodology to the tropical species Corymbia torelliana, a 1st-generation genetic base population (TPop08) included 960 seedlings from 29 local trees of unknown sources. The 72 selected trees in SSO TO08 combine surprising freeze tolerance (as low as −5°C) with good growth and tree form.
A 5th-generation E. grandis genetic base population (GPop15) established at the UF/IFAS Indian River Research and Education Center near Ft Pierce, FL, from July to October 2015 consisted of 4,157 propagules from 42 up to 4th-generation, open-pollinated progenies with superior growth, freeze resilience, and/or chalcid breeding values and four UF commercial cultivars. Sixty trees of 10 progenies were replanted in April 2016, resulting in 20 60x90’ replications (10x3’ spacing) with 36 progenies/cultivars systematically assigned to six rows of six 5-tree row plots and four incomplete replications. Based on periodic growth, freeze, form, chalcid, and windfirmness measurements, GPop15 was rogued to the best tree in each plot in April 2017 to create SSO GO15. Using performance through 2018, each replication will be further rogued to approximately the best six trees, resulting in GO15 having ~150 trees when abundant flowering begins in Fall 2019. GO15 should produce large quantities of seed by Spring 2020 and provide fast growing, freeze resilient, windfirm, and chalcid resistant E. grandis seedlings for central and southern Florida and similar areas.
TPop12, the 2,027 tree 2nd-generation C. torelliana genetic base population planted October 2012 on former citrus beds near Ft Pierce, included 66 progenies: 10 TO08 progenies, 25 Australian single-tree seedlots, and 31 Florida “wild” progenies. Tree size, form, fecundity, windfirmness, and survival were measured periodically. Seedlings coming from the diverse 115 trees selected for retention in SSO TO12 representing 54 progenies (25 from 10 TO08 trees, 52 from 22 Australian trees, and 38 from 22 “wild” trees) may be deployed in central and southern Florida.No publisherddrummond2022-04-20T12:56:59ZPublicationSNP Discovery in Tropical and Subtropical Pines Using Reduced Representation Sequencing Methods https://npn.rngr.net/publications/tree-improvement-proceedings/southern/2019/snp-discovery-in-tropical-and-subtropical-pines-using-reduced-representation-sequencing-methods This study performs SNP discovery and characterization using RNA-seq and targeted sequencing for use in developing a high throughput genotyping assay for tropical and subtropical pine species. Targeted sequencing was performed on six species of pine: Pinus patula, Pinus tecunumanii, Pinus oocarpa, Pinus greggii, Pinus caribaea and Pinus maximinoi. Sequence data was generated from a custom set of 40K capture probes (RAPiD Genomics Gainesville, FL) of which 30K were designed from single copy locations in v2.01 of the Pinus taeda genome assembly and 10K were designed from the P. tecunumannii and P. patula transcriptome assemblies. A total of 81 pooled samples were sequenced among the six species. The 81 pools represented between 4-8 trees from a single provenance and covered the natural ranges of the species in Mexico and Central America. Target sequencing generated between 3.1 and 7.7 million reads per pool with coverage of 20-30X across capture regions. Approximately1.1 million SNPs were detected in at least two of the 81 provenances, of which 403K are shared among most species. RNA-seq data was generated for the species mentioned above minus P. caribaea. Pooled RNA was isolated from shoot tissue of between 8-16 seedlings from two or more families per species. Paired end sequencing generated between 29.4 and 67.7 million raw reads per pool. Reads were trimmed and mapped to each species’ respective transcriptome assemblies. SNP detection yielded between 426K and 1.3M SNPs per species. SNP probe design resulted in 1.8 million candidate probes designed between species and across platforms. The probes generated from each dataset were further assessed for unique vs. repetitive mapping against the v2.01 P. taeda genome assembly and similarity across species. Assessment of RNA-seq derived probes showed a large proportion of probes being unique to a given species with few being shared between. Approximately 53% of probes mapped to a unique location in the reference assembly. Target capture derived probes showed a larger proportion of probes being shared across species with greater than 80% of probes mapping to a unique location. From these 1.8 million probes, 323K RNA-seq and 121K target capture derived probes were selected for assessment on a screening array. Currently, 480 samples have been submitted for genotyping.No publisherddrummond2022-04-14T16:04:13ZPublicationForest Seedling Root Development and Function for Reforestation and Restoration - Day 1 https://npn.rngr.net/resources/webinars/2021-root-development-symposium/forest-seedling-root-development-and-function-for-reforestation-and-restoration-day-1 No publisherddrummond2021-11-29T16:25:59ZWebinarForest Restoration on Degraded Soils in Yap, Federated States of Micronesia https://npn.rngr.net/publications/tpn/64-1/forest-restoration-on-degraded-soils-in-yap-federated-states-of-micronesia Reforestation of sites with acidic, highly leached soils has been a problem in the tropics worldwide, and results of fertilization have been varied. We applied both fertilizer and lime to a new plantation of Acacia auriculiformis A. Cunn. ex Benth. on an Oxisol on the island of Yap in the Federated States of Micronesia. Fertilized trees had 46 percent more height increment than control trees over a 2.4-year period, but there was no effect of lime application. A. auriculiformis is well known for being tolerant of soil acidity. Our results emphasize the value of fertilization during establishment and early growth for trees planted on leached, acidic tropical soils.No publisherddrummond2021-05-20T13:09:37ZPublicationDLH resume.2020.pdf https://npn.rngr.net/about/personnel/DLH%20resume.2020.pdf No publisherddrummond2020-11-25T14:33:13ZFile2020 Native Plant Production in Puerto Rico and U.S. Virgin Islands https://npn.rngr.net/resources/webinars/2020-native-plant-production-in-puerto-rico-and-u.s.-virgin-islands The State and Private Forestry Unit at the International Institute of Tropical Forestry organized these six webinars on management of tropical nurseries producing native trees. Topics included species selection, containers, growing media, seed collection, culturing techniques, pest management, seedling quality, and outplantingNo publisherddrummond2022-01-11T14:56:51ZWebinar SeriesA Nursery Guide for the Production of Bareroot Hardwood Seedlings (complete) https://npn.rngr.net/publications/a-nursery-guide-for-the-production-of-bareroot-hardwood-seedlings/complete Temperate hardwoods are cultured across the United States, with most production occurring in the eastern half of the country. Most chapters within this manual cover one topic for the entire area. Other topics exhibit geographic variation such as seedbed preparation and sowing, weed management, and practices related to lifting and packing. These chapters provide a range of content to give a full perspective. Other topics, such as fertilizer and soils, can be applied more generally regardless of location. The seed chapter highlights topics related to hardwood seed, but readers may also want to refer to The Woody Plant Seed Manual, which is available online (Bonner and Karrfalt 2008). Protocols for handling many commercially valuable species are fairly well established because of extensive research and decades of production. Research on the culture of most hardwood species is far from complete, and many questions remain. This paucity of research is not unique to hardwood—other species (tree and plant) favored for restoration plantings are not as well studied and pose unique
Bonner, F.T.; Karrfalt, R.P., eds. 2008. The woody plant seed manual. Agric. Handb.727. Washington, DC: U.S. Department of Agriculture, Forest Service: 274–280.
Duryea, M.L.; Landis, T.D., eds. 1984. Forest nursery manual: production of bareroot seedlings. The Hague/Boston/Lancaster: Martinus Nijhoff / Dr. W. Junk Publishers, for Forest Research Laboratory, Oregon State University, Corvallis. 386 p.
Wilkinson, K.W.; Landis, T.D.; Haase, D.L. [et al.]. eds. 2014. Tropical nursery manual: a guide to starting and operating a nursery for native and traditional plants. Agric. Handb. 732. Washington, DC: U.S. Department of Agriculture, Forest Service. 376 p.challenges to nurseries. Our goal is to provide practical, up-to-date science-based information on hardwood seedling culture. We recognize that each nursery is unique, and these recommendations may need to be adjusted to meet local conditions.
A cadre of professional nursery workers, many with decades of experience working in nurseries across the Eastern United States, wrote this guide. The audience for this guide is nursery managers who grow temperate hardwood trees in a bareroot nursery in the Eastern United States. Beginners who wish to construct a new nursery or have no experience growing hardwoods will find greater detail in other manuals devoted to culture of bareroot stock, such as the Tropical Nursery Manual (Wilkinson et al. 2014), The Woody Plant Seed Manual (Bonner and Karrfalt 2008), and the Forest Nursery Manual (Duryea and Landis 1984). Also, while hardwood trees can be grown successfully in containers, their copious root systems require large containers; the management of these is beyond the scope of this manual.No publisherddrummond2020-06-08T18:37:30ZPublicationEstablishing Silvopastures with Acacia Koa https://npn.rngr.net/tropical/instructional-videos/establishing-silvopastures-with-acacia-koa-1 Dr. James Leary, CTAHR Invasive Weed Scientist, Dr. J. B. Friday, CTAHR Extension Forester, and Dr. Travis Idol, CTAHR Associate Professor of Tropical Forestry, research an innovative approach to restoring koa corridors on pastureland in Hawaii for land management to support both cattle and koa production. Herbicide trials and scarification methods are examined. Funding from USDA NRCS Conservation Innovation Grant (NRCS-CIG), RREA and TSTAR.No publisherddrummond2020-02-19T17:36:39ZSmart LinkEstablishing Silvopastures with Acacia Koa https://npn.rngr.net/tropical/instructional-videos/establishing-silvopastures-with-acacia-koa Dr. James Leary, CTAHR Invasive Weed Scientist, Dr. J. B. Friday, CTAHR Extension Forester, and Dr. Travis Idol, CTAHR Associate Professor of Tropical Forestry, research an innovative approach to restoring koa corridors on pastureland in Hawaii for land management to support both cattle and koa production. Herbicide trials and scarification methods are examined. Funding from USDA NRCS Conservation Innovation Grant (NRCS-CIG), RREA and TSTAR.No publisherddrummond2020-01-17T15:17:20ZLinkNurseries for Forestry and Conservation https://npn.rngr.net/tropical/tropical-plant-photos/nurseries-for-forestry-and-conservation-1 Tropical forest tree nurseries in the Pacific and Southeast Asia.No publisherddrummond2020-01-17T13:47:58ZLink