Current Research

• Defining daily, seasonal and annual changes in gene expression in long-lived perennials (Douglas-fir Transcriptome Observatory; Fragaria polyploids).
• Linking spatial genetic differentiation in Port-Orford Cedar and Yellow Cedar to migration, climatic and selective pressure from pathogens.
• Developing genetic markers for domestic and international trees, plants and animals of management concern.
• Adopting new genomics technologies for applications in forest management.

Research Interests

• studying the genetic basis of adaptation through the integration of gene expression and quantitative variation.
• studying the population and evolutionary genetic history of North American members of the pine family.
• defining patterns of neutral and adaptive differentiation as a foundation for understanding quantitative variation in restoration plant species.

Past Research

• population and evolutionary genetics of wild cottons
• gene evolution and gene expression in polyploid plant genomes
• biochemistry of antiretroviral agents targeting immune deficiency viruses

Why This Research is Important

Genes -- the DNA codes present in all living organisms -- are the basis of adaptive traits that make species resilient to a changing climate and an array of diseases. The genes of plants are poorly understood, and this is especially true for genes that help plants adapt to changes in seasonal and annual weather. This research applies new genomics methods to address a fundamental question: What genes do plants use to sense seasonal changes in light quality, temperature, and water availability? By defining genes that have a large impact on growth and health, we can use this information to guide breeding methods and plant selections that result in broadly adapted trees that contribute to resilient forest communities.

The same genomics approaches used for identifying adaptive genomic variation can also be used to identify the species and geographic source of plant products, such as wood and wood products. We are using these approaches to define taxonomically- and spatially-informative genetic markers that can be used to track and manage products from economically and ecologically important forest trees.  

Education

• Iowa State University, Ph.D. Genetics Evolutionary and population genetics 1997

Featured Publications & Products

• Schroeder, Hilke; Cronn, Richard; Yanbaev, Yulai; Jennings, Tara; Mader, Malte; Degen, Bernd; Kersten, Birgit; Gomory, Dusan. 2016. Development of molecular markers for determining continental origin of wood from White Oaks (Quercus L. sect. Quercus).
• Weitemier, Kevin; Straub, Shannon C.K.; Cronn, Richard C.; Fishbein, Mark; Schmickl, Roswitha; McDonnell, Angela; Liston, Aaron. 2014. Hyb-Seq: combining target enrichment and genome skimming for plant phylogenomics.
• Cronn, Richard; Knaus, Brian J.; Liston, Aaron; Maughan, Peter J.; Parks, Matthew; Syring, John V.; Udall, Joshua. 2012. Targeted enrichment strategies for next-generation plant biology.
• Jennings, Tar N.; Knaus, Brian J.; Alderman, Katherine; Hennon, Paul E.; D’Amore, David V.; Cronn, Richard. 2013. Microsatellite primers for the Pacific Northwest conifer Callitropsis nootkatensis (Cupressaceae).
• Howe, Glenn R.; Yu, Jianbin; Knaus, Brian; Cronn, Richard; Kolpak, Scott; Dolan, Peter; Lorenz, W. Walter; Dean, Jeffrey F.D. 2013. A SNP resource for douglas-fir: de novo transcriptome assembly and SNP detection and validation.
• Knaus, Brian J.; Cronn, Richard; Liston, Aaron; Pilgrim, Kristine; Schwartz, Michael K. 2011. Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore.
• Stritch, Larry; Olwell, Peggy; Lambert, Scott; Horning, Matthew E.; Cronn, Richard. 2010. What are the best seed sources for ecosystem restoration on BLM and USFS lands.

Publications

• Hauck, Laura L.; Weitemier, Kevin A.; Penaluna, Brooke E.; Garcia, Tiffany S.; Cronn, Richard . 2019. Casting a broader net: Using microfluidic metagenomics to capture aquatic biodiversity data from diverse taxonomic targets.
• Schmitz, Nele , (ed.).; Blanc-Jolivet, Céline ; Boner, Markus ; Cervera, María Teresa; Chavesta, Manuel ; Cronn, Richard ; Degen, Bernd ; Deklerck, Victor ; Diaz-Sala, Carmen ; Dormontt, Eleanor ; Ekué, Marius ; Espinoza, Edgard O.; Gasson, Peter ; Gehl, David ; Gehre, Matthias ; Haag, Volker ; Hermanson, John C.; Honorio-Coronado, Eurídice ; Koch, Gerald ; Lancaster, Cady ; Lens, Fredric ; Liendo-Hoyos, Estephanie Patricia; Martínez-Jarquín, Sandra ; Montenegro, Rolando ; Paredes-Villanueva, Kathelyn ; Pastore, Tereza ; Ramananantoandro, Tahiana ; Rauber-Coradin, Vera T.; Ravaomanalina, Harisoa ; Rees, Gareth ; Sebbenn, Alexandre Magno; Tysklind, Niklas ; Vlam, Mart ; Watkinson, Charlie ; Wiemann, Michael . 2019. General sampling guide for timber tracking: How to collect reference samples for timber identification.
• Coble, Ashley A.; Flinders, Camille A.; Homyack, Jessica A.; Penaluna, Brooke E.; Cronn, Richard C.; Weitemier, Kevin . 2019. eDNA as a tool for identifying freshwater species in sustainable forestry: A critical review and potential future applications.
• Baker, Ethan A. G.; Wegrzyn, Jill L.; Sezen, Uzay U.; Falk, Taylor ; Maloney, Patricia E.; Vogler, Detlev R.; Delfino-Mix, Annette ; Jensen, Camille ; Mitton, Jeffry ; Wright, Jessica ; Knaus, Brian ; Rai, Hardeep ; Cronn, Richard ; Gonzalez-Ibeas, Daniel ; Vasquez-Gross, Hans A.; Famula, Randi A.; Liu, Jun-Jun ; Kueppers, Lara M.; Neale, David B. 2018. Comparative transcriptomics among four white pine species.
• Young, Michael K.; McKelvey, Kevin S.; Jennings, Tara ; Carter, Katie ; Cronn, Richard ; Keeley, Ernest R.; Loxterman, Janet L.; Pilgrim, Kristine L.; Schwartz, Michael K. 2018. The phylogeography of westslope cutthroat trout.
• Holman, Garth; Del Tredici, Peter; Havill, Nathan; Lee, Nam Sook; Cronn, Richard; Mathews, Sarah; Raubeson, Linda; Campbell, Christopher S. 2017. A new species and introgression in eastern Asian hemlocks (Pinaceae: Tsuga).
• Pham, Kasey K.; Hipp, Andrew L.; Manos, Paul S.; Cronn, Richard C. 2017. A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny.
• Wegrzyn, Jill; Staton, Meg; Grau, Emily; Cronn, Richard; Nelson, C. Dana. 2017. Community standards for genomic resources, genetic conservation, and data integration.
• Finch, Kristen; Espinoza, Edgard; Jones, F. Andrew; Cronn, Richard. 2017. Source identification of western Oregon Douglas-Fir wood cores using mass spectrometry and random forest Classification.
• Neale, David B.; McGuire, Patrick E.; Wheeler, Nicholas C.; Stevens, Kristian A.; Crepeau, Marc W.; Cardeno, Charis; Zimin, Aleksey V.; Puiu, Daniela; Pertea, Geo M.; Sezen, U. Uzay; Casola, Claudio; Koralewski, Tomasz E.; Paul, Robin; Gonzalez-Ibeas, Daniel; Zaman, Sumaira; Cronn, Richard; Yandell, Mark; Holt, Carson; Langley, Charles H.; Yorke, James A.; Salzberg, Steven L.; Wegrzyn, Jill L. 2017. The Douglas-fir genome sequence reveals specialization of the photosynthetic apparatus in Pinaceae.
• Cronn, Richard; Dolan, Peter C.; Jogdeo, Sanjuro; Wegrzyn, Jill L.; Neale, David B.; St. Clair, J. Bradley; Denver, Dee R. 2017. Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles.
• Schmickl, Roswitha; Liston, Aaron; Zeisek, Vojtěch; Oberlander, Kenneth; Weitemier, Kevin; Straub, Shannon C. K.; Cronn, Richard C.; Dreyer, Léanne L.; Suda, Jan. 2016. Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae).
• Syring, John V.; Tennessen, Jacob A.; Jennings, Tara N.; Wegrzyn, Jill; Scelfo-Dalbey, Camille; Cronn, Richard. 2016. Targeted capture sequencing in Whitebark pine reveals range-wide demographic and adaptive patterns despite challenges of a large, repetitive genome.
• Staton, Margaret ; Best, Teodora ; Khodwekar, Sudhir ; Owusu, Sandra ; Xu, Tao ; Xu, Yi ; Jennings, Tara ; Cronn, Richard ; Arumuganathan, A. Kathiravetpilla; Coggeshall, Mark ; Gailing, Oliver ; Liang, Haiying ; Romero-Severson, Jeanne ; Schlarbaum, Scott ; Carlson, John E. 2015. Preliminary genomic characterization of ten hardwood tree species from multiplexed low coverage whole genome sequencing.
• DeGiorgio, Michael; Syring, John; Eckert, Andrew J.; Liston, Aaron; Cronn, Richard; Neale, David B.; Rosenberg, Noah A. 2014. An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines.
• Hayden, Katherine J.; Garbelotto, Matteo; Knaus, Brian J.; Cronn, Richard C.; Rai, Hardeep; Wright, Jessica W. 2014. Dual RNA-seq of the plant pathogen phytophthora ramorum and its tanoak host.
• Straub, Shannon C.K.; Cronn, Richard C.; Edwards, Christopher; Fishbein, Mark; Liston, Aaron. 2013. Horizontal transfer of DNA from the mitochondrial to the plastid genome and its subsequent evolution in milkweeds (Apocynaceae).
• Njunguna, Wambui; Liston, Aaron; Cronn, Richard; Ashman, Tia-Lynn; Bassil, Nahla. 2013. Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing.
• Rai, Hardeep S.; Mock, Karen E.; Richardson, Bryce A.; Cronn, Richard C.; Hayden, Katherine J.; Wright, Jessica W.; Knaus, Brian J.; Wolf, Paul G. 2013. Transcriptome characterization and detection of gene expression differences in aspen (Populus tremuloides).
• Ross-Davis, A. L.; Stewart, J. E.; Hanna, J. W.; Kim, M.-S.; Knaus, B. J.; Cronn, R.; Rai, H.; Richardson, B. A.; McDonald, G. I.; Klopfenstein, N. B. 2013. Transcriptome of an Armillaria root disease pathogen reveals candidate genes involved in host substrate utilization at the host -pathogen interface.
• Hayden, Katherine J.; Garbelotto, Matteo; Fai, Hardeep; Knaus, Brian; Cronn, Richard; Wright, Jessica W. 2012. Gene expression in the tanoak-Phytophthora ramorum interaction.
• Alexander, Alana; Steel, Debbie; Slikas, Beth; Hoekzema, Kendra; Carraher, Colm; Parks, Matthew; Cronn, Richard; Baker, C. Scott. 2012. Low diversity in the mitogenome of sperm whales revealed by next-generation sequencing.
• Magbanua, Zenaida V.; Ozkan, Seval; Bartlett, Benjamin D.; Chouvarine, Philippe; Saski, Christopher A.; Liston, Aaron; Cronn, Richard C.; Nelson, C. Dana; Peterson, Daniel G. 2011. Adventures in the enormous: a 1.8 million clone BAC library for the 21.7 Gb genome of loblolly pine.
• Straub, Shannon C.K.; Fishbein, Mark; Livshult, Tatyana; Foster, Zachary; Parks, Matthew; Weitemier, Kevin; Cronn, Richard C.; Liston, Aaron. 2011. Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing.
• Parks, Matthew; Liston, Aaron; Cronn, Rich. 2011. Newly developed primers for complete YCF1 amplification in Pinus (Pinaceae) chloroplasts with possible family-wide utility.
• Bajgain, Prabin; Richardson, Bryce A.; Price, Jared C.; Cronn, Richard C.; Udall, Joshua A. 2011. Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata).
• Zapiola, Maria L.; Cronn, Richard C.; Mallory-Smith, Carol A. 2010. Development of novel chloroplast microsatellite markers to identify species in the Agrostis complex (Poaceae) and related genera..
• Whittall, J.B.; Syring, J.; Parks, M.; Buenrostro, J.; Dick, C.; Liston, A.; Cronn, R. 2010. Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines.
• Njuguna, W.; Liston, A.; Cronn, R.; Bassil, N.V. 2010. Multiplexed fragaria chloroplast genome sequencing.
• Parks, Matthew; Cronn, Richard; Liston, Aaron. 2009. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes.
• Hersch-Green, Erika l.; Cronn, Richard. 2009. Tangled trios Characterizing a hybrid zone in Castilleja (Orobanchaceae).
• Cronn, Richard; Liston, Aaron; Parks, Matthew; Gernandt, David S.; Shen, Rongkun; Mockler, Todd. 2008. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology.
• Syring, John; del Castillo, Rafael F.; Cronn, Richard; Liston, Aaron. 2007. Multiple nuclear loci reveal the distinctiveness of the threatened, Neotropical Pinus chiapensis.
• Horning, Matthew E.; Cronn, Richard C. 2006. Length polymorphism scanning is an efficient approach for revealing chloroplast DNA variation..
• Syring, John; Willyard, Ann; Cronn, Richard; Liston, Aaron. 2005. Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci..
• Johnson, GR; Sorensen, Frank C; St Clair, J Bradley; Cronn, Richard C. 2004. Pacific Northwest forest tree seed zones: a template for native plants.
• Wendel, Jonathan F.; Cronn, Richard C.; Jonhston, J. Spencer; Price, H. James. 2002. Feast and famine in plant genomes..
• Cronn, Richard C.; Cedroni, M.; Haselkorn, T.; Grover, C.; Wendel, Jonathan F. 2002. PCR-mediated recombination in amplification products derived from polyploid cotton..
• Cronn, Richard C.; Small, Randall L.; Hanselkorn, Tamara; Wendel, Jonathan F. 2002. Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes..
• Cronn, Richard C.; Small, Randall L.; Wendel, Jonathan F. 1999. Duplicated genes evolve independently in allopolyploid cotton..

Research Highlights

Highlight	Title	Year
PNW-2015-37	A Climate Adaptation Strategy for Conservation and Management of Yellow-Cedar in Alaska A new report assesss past, current, and expected future condition of yellow-cedar forests on all land ownerships where yellow-cedar grows in Ala ...	2015
PNW-2017-230	Combatting illegal logging with technology Chemical fingerprints can determine the geographic origin of wood.	2017
PNW-2014-094	Genetic Analysis Shows the Scale and Pattern of Spatial Genetic Variation in Yellow-Cedar Genetic analysis shows that yellow-cedar is a diverse and highly mobile species.	2014
PNW-2011-05	Genetic studies reveal population structure of fisher predate management This research is being used to aid management decisions about whether these populations warrant protection under the Endangered Species Act. Sci ...	2011
PNW-2019-49	Invisible eDNA Reveals Stream and Riparian Ecosystem Biodiversity Environmental DNA is a powerful new approach that, with a single water sample, can detect a host of stream and riparian species—from pathogens ...	2019
PNW-2010-011	New genome sequencing method reveals a species evolutionary history Organelle genomes from plants, animals, and fungi are used as genetic markers to track maternal diversity, historical migration, and maternally ...	2010