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Growing and cultivating the forest genomics database, TreeGenes

Taylor Falk, Nic Herndon, Emily Grau, Sean Buehler, Peter Richter, Sumaira Zaman, Eliza M Baker, Risharde Ramnath, Stephen Ficklin, Margaret Staton, Frank A Feltus, Sook Jung (+2 others)
2018 Database: The Journal of Biological Databases and Curation  
: Hardwood Genomics Web, Genome Database for Rosaceae, and the Citrus Genome Database.  ...  The TreeGenes database is a web-based repository that is home to 1790 tree species and over 1500 registered users.  ...  Acknowledgements We would like to thank the Computational Biology Core within the Institute of Systems Genomics at the University of Connecticut and The High Performance Computing Facility at the UConn  ... 
doi:10.1093/database/bay084 pmid:30239664 pmcid:PMC6146132 fatcat:o5a5wj5ylvdkdncttoebsk3ni4

Progress in physiological and genetic research concerning forest tree response to low temperature

Novokreshchenova Maria, Skowyra Katarzyna, Kempf Marta
2019 Forest Research Papers  
This allows for a more effective implementation of conservation measures and the renewal of forest ecosystems.  ...  Modern biology, such as genomics, transcriptomics, proteomics, etc., significantly facilitates these studies and accelerates the acquisition of new knowledge.  ...  Acknowledgements and source of funding The research was financed from own sources.  ... 
doi:10.2478/frp-2019-0028 doaj:07d9cb66b4db480e82e5c442dd3767e1 fatcat:sjuxfgiez5htlbdvan6s527aaa

USDA Plant Genome Research Program [chapter]

1995 Advances in Agronomy  
The Plant Genome Research Program is one program with two parts: National Research Initiative and Plant Genome Database (PGD).  ...  The goal of the USDA Plant Genome Research Program is to improve plants (agronomic, horticultural, and forest tree species) by locating marker DNA or genes on chromosomes, determining gene structure, and  ...  Search TreeGenes (forest trees) ~ Search ChlanyDB (Chlanydononas) Flgure 3.  ... 
doi:10.1016/s0065-2113(08)60539-8 fatcat:xm33v7lqzje5znmfsk2yhsazke

From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees

Hieu Xuan Cao, Giang Thi Ha Vu, Oliver Gailing
2022 International Journal of Molecular Sciences  
Here, we introduce and discuss the latest progress, opportunities, and challenges of genome sequencing and editing for improving forest sustainability.  ...  Rapidly accumulating genetic and genomic resources for forest trees enabled the identification of numerous genes and biological processes that are associated with important traits such as wood quality,  ...  Acknowledgments: The authors are grateful to the anonymous reviewers for insightful comments and suggestions which greatly helped improve the manuscript.  ... 
doi:10.3390/ijms23020966 pmid:35055150 pmcid:PMC8780650 fatcat:s2nabkpckjgwdbighmym5rukbu

qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)

Nanette Christie, Chanaka Mannapperuma, Raphael Ployet, Karen van der Merwe, Niklas Mähler, Nicolas Delhomme, Sanushka Naidoo, Eshchar Mizrachi, Nathaniel R. Street, Alexander A. Myburg
2021 BMC Bioinformatics  
The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus.  ...  Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking  ...  Acknowledgements The authors acknowledge Sappi Forest Research (Hilton, KZN, South Africa) for the plant materials and growth and wood property data used in the study, S.  ... 
doi:10.1186/s12859-021-04514-9 pmid:34911434 pmcid:PMC8672637 fatcat:risfu4b5njb6ppgikfu5v3xga4

Genomics Researches and Their Applications in Plant Breeding at PAG XXIV Conference

Franz Marielle Nogoy, Shadi Rahimi, Kwon-Kyoo Kang, Yong-Gu Cho
2016 Plant Breeding and Biotechnology  
PAG XXIV demonstrated different works about the extensive use of genomic databases accompanied by bioinformatics tools to accelerate breeding methods, discovery of new approaches to genomics, further increasing  ...  By the way, the genome annotation and assembly is an essential key for breeding of stress-tolerant plants.  ...  ACKNOWLEDGEMENTS This work was supported by a grant from the Next-Generation BioGreen 21 Program (National Center for GM Crops No. PJ01191601), Rural Development Administration, Republic of Korea.  ... 
doi:10.9787/pbb.2016.4.1.16 fatcat:s5afsbtmsfeqviyycxkh4gscvi

A Reference Genome Sequence for Giant Sequoia

Alison D Scott, Aleksey V Zimin, Daniela Puiu, Rachael Workman, Monica Britton, Sumaira Zaman, Madison Caballero, Andrew C Read, Adam J Bogdanove, Emily Burns, Jill Wegrzyn, Winston Timp (+2 others)
2020 G3: Genes, Genomes, Genetics  
This giant sequoia reference genome sequence represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management  ...  The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains.  ...  ACKNOWLEDGMENTS This project was supported by a grant from Save The Redwoods League for the Redwood Genome Project (to DN), and by grants from the National Institute of Food and Agriculture of the U.S.  ... 
doi:10.1534/g3.120.401612 pmid:32948606 pmcid:PMC7642918 fatcat:o7chi7h47vcknn4fhoalrtaghi

Genetic characterization of chestnut (Castanea sativa Mill.) orchards and traditional nut varieties in El Bierzo, a glacial refuge and major cultivation site in northwestern Spain

Julia Quintana, Angela Contreras, Irene Merino, Alvaro Vinuesa, Gabriela Orozco, Felipe Ovalle, Luis Gomez
2014 Tree Genetics & Genomes  
Seven nuclear microsatellite markers were selected to analyze the genetic variability and structure of 169 local trees grafted for nut production. We analyzed in the same manner 62 local nuts.  ...  with broader geographical scope but based on limited local sampling (Pereira-Lorenzo et al., Tree Genet Genomes 6: 701-715, 2010a).  ...  Data archiving statement The allelic profiles for chestnut varieties have been deposited in the TreeGenes database with accession number TGDR034.  ... 
doi:10.1007/s11295-014-0826-x fatcat:ool3bog7rrep3esn4yhfh2fpua

275 years of forestry meets genomics in Pinus sylvestris

Tanja Pyhäjärvi, Sonja Tuulia Kujala, Outi Savolainen
2019 Evolutionary Applications  
For forest breeding and long-term management purposes, genomic data can help in assessing the genetic basis of inbreeding depression and the application of genomic tools for genomic prediction and relatedness  ...  Here, we explore how genomic characteristics of P. sylvestris, such as rare alleles and the low extent of linkage disequilibrium, impact the applicability and power of the tools.  ...  In Finland and Sweden, breeding efforts on P. sylvestris were started in the late 1940s by collecting phenotypically superior plus trees from natural and cultivated forests.  ... 
doi:10.1111/eva.12809 pmid:31988655 pmcid:PMC6966708 fatcat:b3qtzsciszbldikk2nnm64qwfy

Genetic diversity and genetic structure of Persian walnut (Juglans regia) accessions from 14 European, African, and Asian countries using SSR markers

Aziz Ebrahimi, Abdolkarim Zarei, Shaneka Lawson, Keith E. Woeste, M. J. M. Smulders
2016 Tree Genetics & Genomes  
STRUCTURE software confirmed these results and divided the accessions into two main groups, separating accessions collected from Europe and North Africa from those from Greece and the Near East.  ...  Two populations from Iran (Alborz and Ardabil) had the highest number of private alleles (7 and 5), but they were quite different as they also had the lowest genetic identity when compared to the remaining  ...  Data archiving If the manuscript is accepted, genotype data will be submitted to TreeGenes database.  ... 
doi:10.1007/s11295-016-1075-y fatcat:crwzzwq4znes3fxswsdoatjdru

Breeding Climate-Resilient Bananas [chapter]

Allan Brown, Sebastien C. Carpentier, Rony Swennen
2020 Genomic Designing of Climate-Smart Fruit Crops  
Acknowledgements This study has been supported by Grants Nº 19308/PI/14 and Nº 19879/GERM/15 of the Seneca Foundation of the Region of Murcia and the Apricot Breeding project Converse (1987) , Tzanetakis  ...  (2010) , Petrzik et al. (1998), Thompson and Jelkman (2003) , , Tzanetakis et al. (2007) , Yoshikawa et al. (1986) , Yoshikawa and Inouye (1988) , Ratti et al. (2006) Nematode Jones and Wood  ...  From another side, such infrastructure is compatible with the infrastructure of other databases like TreeGene sand FruitBreedomics.  ... 
doi:10.1007/978-3-319-97946-5_4 fatcat:cqzcfw6fnfcjtbnsw2bchzkx3q

Expression Divergence Is Correlated with Sequence Evolution but Not Positive Selection in Conifers

Kathryn A. Hodgins, Sam Yeaman, Kristin A. Nurkowski, Loren H. Rieseberg, Sally N. Aitken
2016 Molecular biology and evolution  
) to elucidate the evolutionary forces that shape their genomes and their plastic responses to abiotic stress.  ...  The evolutionary and genomic determinants of sequence evolution in conifers are poorly understood, and previous studies have found only limited evidence for positive selection.  ...  This work is part of the AdapTree Project funded by the Genome Canada Large Scale Applied Research Project program, with co-funding from Genome BC, the BC Ministry of Forests, Lands and Natural Resources  ... 
doi:10.1093/molbev/msw032 pmid:26873578 fatcat:7orscwtrajhundz2jocjcdctve

National Institute of Food and Agriculture Bioeconomy-Bioenergy-Bioproducts Portfolio Strategic Plan 2014 Progress and Implementation Report Point of Contact

William Goldner
unpublished
reference of loblolly pine.  The TreeGenes database was improved with the addition of the complete conifer repeat library generated by the team.  ...  In addition, TreeGene resources for viewing genome annotations were developed in Gbrowse and WebApollo.  ... 
fatcat:yrq5ija2enbxbeuj7bho7fp7dq