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Carolyn Young

Professor and Department Head

Varsity Research Building, Module 6, Suite 1535


Dr. Carolyn Young was a Professor at the Noble Research Institute, in Ardmore, Oklahoma for 15 years and spent 6 months as Principal Scientist at Nature’s Fynd in Bozeman Montana. She is internationally recognized for research on seed transmitted fungal endophytes and their impact on forage grazing systems, endophyte diversity in native grasses and crop wild relatives, pecan scab and a root rot pathogen of alfalfa. She has discovered genes for the synthesis of bioprotective alkaloids, identified and described new endophyte species, and developed genomic and culture resources. She established educational activities centered on the inconspicuous symbiosis and provided knowledge and tools to stakeholders. Carolyn is originally from New Zealand, where she completed her studies at Massey University in Palmerston North. She moved to the USA in 2004 for a postdoctoral fellowship with Dr. Sophien Kamoun at the OARDC, Ohio State University. In 2006 she started her research lab at the Noble Research Institute. Carolyn has two sons who are now embarking on their own tertiary education journey. She was the founding Editor-in-Chief for the Phytobiomes Journal, which was established in 2017 by the American Phytopathological Society. Carolyn is passionate about mentoring and providing professional socialization and personal support to enhance early career development. She values the relationships with her mentors who have enriched her career, and as a result, she strives to pay forward similar experiences to others.


Diversity Matters: Endophytes and pathogens that impact agriculture

Sustainable plant productivity is greatly influenced by biotic and abiotic stresses that result in ongoing economic losses for stakeholders. My lab has addressed these problems by: (1) overcoming plant stress responses with beneficial endophytes that improve host persistence and (2) by understanding the biology of important regional pathogens to manage disease. I work on diverse plant associated fungal systems but link them by exploring fungal diversity (e.g. bioactive alkaloids, pathogenicity factors) at a population level and understanding their life-history strategies.

The success and resilience of cool-season forage grasses (e.g. tall fescue and perennial ryegrass) is attributed to a fungal seedborne symbiont from the genus Epichloë, which is a dominant and stable member of the grass microbiome. Epichloë species represent a dynamic group of endophytes that systemically infect above ground host tissue and vary in transmission strategies (horizontal, vertical or both), reproduction (sexual or asexual), and genome content (nonhybrid or hybrid). These endophytes are capable of producing a range of alkaloids that can protect the host from herbivory, but some alkaloids reduce livestock quality. Considerable genotypic and chemotypic diversity exist within the symbiont alkaloid biosynthetic pathways. We have shown through genome sequencing and genotyping that significant symbiont variation exists within a host and between host populations. Erosion from the chromosome end has provided natural diversity of indole-diterpenes produced by Epichloë species.

In contrast to these beneficial symbionts, fungal pathogen life-history strategies of Venturia effusa, causative agent of pecan scab, and the root pathogen Phymatotrichopsis omnivora are poorly understood. V. effusa is widely distributed across the southeastern USA and is treated as an asexual pathogen by pecan growers. We have recently shown that V. effusa is sexually active, with mating type idiomorphs in equilibrium in pecan orchards. Recent genome sequencing has helped elucidate the similarity between Venturia found on Carya illinoinensis (pecan) and other Carya species (hickory), and possible gene flow that may occur between the taxa. P. omnivora is considered a natural born killer of dicotyledonous plants, including cotton, pecan and Medicago sativa (alfalfa/lucerne). This pathogen is endemic to southwestern USA and dramatically reduces alfalfa stand productivity, with no known mechanisms of resistance. Aerial imaging has been used to identify areas of stand loss, follow disease progression, and determine the cost of production losses caused by P. omnivora. Recent genome sequencing of P. omnivora revealed the presence of a heterothallic mating type system but spatial distance between distinct isolates within a field would likely limit the existence of the sexual stage. Understanding genetic diversity within and between populations has provided insight into these diverse fungi-host systems that will help with development of management tools to maintain plant productivity.


Recent Publications

  1. Quenu M, Treindl A, Lee K, Takemoto D, Thunen T, Ashrafi S, Winter D, Ganley ARD, Leuchtmann A, Young CA, Cox M. (2022). Telomere-to-telomere genome sequences along a fungal genus transect reveals highly variable chromosome rearrangement rates but absolute stasis of chromosome number. Journal of Fungi. 8: 670 DOI: 3390/jof8070670
  2. Bock CH, Frusso E, Zoppolo R, Ortiz E, Shiller J, Charlton ND, Young CA, Randall J. (2022). Population genetic characteristics and mating type frequency of Venturia effusa from pecan in South America. Phytopathology DOI: 10.1094/PHYTO-01-22-0031-R.
  3. Prince S, Anower MR, Motes CM, Hernandez TD, Liao F, Putman L, Mattson R, Seethapalli A, Shah K, Komp M, Mehta P, York LM, Young C, Monteros MJ. (2022). Intraspecific variation for leaf physiological and root morphological adaptation to drought stress in Alfalfa (Medicago sativa). Frontiers in Plant Science. DOI: 10.3389/fpls.2022.795011
  4. Bock CH, Charlton ND, Shiller J, Randall JJ, Young CA. (2022). Population genetic diversity and structure of the pecan scab pathogen, Venturia effusa, on cv. Desirable and native seedlings and the impact of marker number. Plant Pathology. 71: 1103-1119.
  5. Mattupalli C, Proaño Cuenca F, Shiller JB, Watkins T, Hansen K, Garzon CD, Marek SM, Young CA. (2022). Genetic diversity of Phymatotrichopsis omnivora based on mating type and microsatellite markers reveal heterothallic mating system. Plant Disease. DOI: 10.1094/PDIS-01-22-0013-RE
  6. Berry D, Lee K, Winter D, Mace W, Becker Y, Nagabhyru P, Treindl A, Valverde-Bogantes E, Young CA, Leuchtmann A, Johnson L, Johnson R, Cox M, Schardl CL, Scott B. (2022). Cross-species transcriptomics identifies core regulatory changes differentiating the asymptomatic asexual and virulent sexual life cycles of grass-symbiotic Epichloë G3: Genes, Genomes, Genetics 12: jkac043
  7. Von Cräutlein, M, Helander M, Korpelalnen H, Leinonen PH, Válzquez de Aldana BR, Young CA, Zabalgogeazcoa I, Saikkonen K. (2021). Genetic diversity of the symbiotic fungus Epichloë festucae in naturally occurring grass populations. Frontiers in Microbiology 3567 DOI: 10.3389/fmicb.2021.756991
  8. Mattupalli C, Shiller J, Kankanala P, Krom N, Marek SM, Mysore KS, Young CA (2021). The first genomic resources for Phymatotrichopsis omnivora, a soil-borne Pezizomycete pathogen with a broad host range. Phytopathology 11: 1897-1900 DOI: 10.1094/PHYTO-01-21-0014-A
  9. Bock CH, Young CA, Zhang M, Chen C, Brennan P, Adaskaveg J, Charlton ND (2021). Mating type idiomorphs, heterothallism and high genetic diversity in Venturia carpophila, cause of peach scab. Phytopathology 111: 408-424 DOI: 1094/PHYTO-12-19-0485-R
  10. Bock CH, Alarcon Y, Conner P, Young C, Stokes U, Randall J, Pisani C, Grauke L, Wang X, Monteros M. (2020) Foliage and fruit susceptibility of a pecan provenance collection to scab, caused by Venturia effusa. Target: CABI Agriculture and Bioscience 1:19 DOI: 1186/s43170-020-00020-9
  11. Roberts CA, Andrae JG, Smith SR, Poore MH, Young CA, Hancock DW, Pent GJ (2020). The Alliance for Grassland Renewal: A model for teaching endophyte technology. International Journal of Animal and Veterinary Sciences. 14:50-54.
  12. Charlton ND, Yi M, Bock CH, Zhang M, Young CA. (2020) First description of the sexual stage of Venturia effusa, causal agent of pecan scab. Mycologia DOI: 10.1080/00275514.2020.1759998
  13. Krauss J, Vikuk V, Young CA, Chrischke M, Muller MJ, Baerenfaller K (2020). Epichloë endophyte infection rates and alkaloid content in commercially available grass seed mixtures in Europe. Microorganisms 8:498 DOI: 10.3390/microorganisms8040498
  14. Shymanovich T, Crowley G, Ingram S, Steen C, Panaccione DG, Watson W, Young CA, Poore M (2020). Endophytes matter: Variation of dung beetle performance across different endophyte-infected tall fescue cultivars. Applied Soil Ecology 152:103561 DOI: 10.1016/j.apsoil.2020.103561
  15. Gundel PE, Sun P, Charlton ND, Young CA, Miller TEX, Rudgers JA (2020). Simulated folivory increases vertical transmission of fungal endophytes that deter herbivores and alter tolerance to herbivores in Poa autumnalis. Annals of Botany DOI: /10.1093/aob/mcaa021
  16. Winter DJ, Charlton ND, Krom N, Shiller JB, Bock C Cox MP, Young CA (2020). Chromosome-level reference genome of Venturia effusa, causative agent of pecan scab. Molecular Plant-Microbe Interactions 33:149-152 (DJW and NCD contributed equally to the work)
  17. Berry D, Mace W, Grage K, Wesche F, Gore S, Schardl CL, Young CA, Dijkwel PP, Leuchtmann A, Bode HB, Scott B (2019). Efficient nonenzymatic cyclization and domain shuffling drive pyrrolopyrazine diversity from truncated variants of a fungal NRPS. Proceedings of the National Academy of Sciences (USA) 116:25614-25623. DOI: 10.1073/pnas.1913080116
  18. Leuchtmann A, Young CA, Stewart AV, Simpson WR, Scott B (2019). Epichloë novae-zelandiae, a new endophyte from the endemic New Zealand grass Poa matthewsii. New Zealand Journal of Botany 57: 271-288 DOI: 1080/0028825X.2019.1651344
  19. Vikuk V, Young CA, Lee ST, Nagabhyru P, Krischke M, Muller MJ, Krauss J (2019). Infection rates and alkaloid patterns of different grass species with systemic Epichloë Applied and Environmental Microbiology 85: e00465-19 DOI: 10.1128/AEM.00465-19
  20. Dinkins RD, Nagabhyru P, Young CA, West CP, Schardl CL (2019). Transcriptome analysis and differential expression in tall fescue harboring different endophyte strains in response to water deficit. The Plant Genome DOI:10.3835/plantgenome2018.09.0071
  21. Mattupalli C, Seethepalli A, York LM, Young CA (2019). Digital imaging to evaluate root system architectural changes associated with soil biotic factors. Phytobiomes Journal 3: 102-11 DOI: 10.1094/PBIOMES-12-18-0062-R
  22. Kenyon SL, Roberts CA, Lory JA, Bailey EA, Kallenbach R, Rottinghaus G, Young CA, Davis D (2019). Comparison and diet preference of novel endophyte-infected tall fescue cultivars. Crop Science DOI: 10.2135/cropsci2018.10.0626
  23. Sneck ME, Rudgers JA, Young CA, Miller TEX (2019). Does host outcrossing disrupt compatibility with heritable symbionts? Oikos 128: 892-903 DOI: 1111/oik.06182
  24. Berry D, Mace W, Rehner SA, Grage K, Dijkwel PP, Young CA, Scott DB (2019). Orthologus peramine and pyrrolopyrazine-producing biosynthetic gene clusters in Metarhizium rileyi, Metarhizium majus and Cladonia grayi. Environmental Microbiology DOI: 1111/1462-2920.14483
  25. Bushman BS, Singh D, Lamp R, Robins JG, Young CA, Charlton ND, Anderson N (2019). Variation among orchardgrass (Dactylis glomerata) germplasm for choke incidence caused by Epichloë typhina. Plant Disease. 103:324-330 DOI:org/10.1094/PDIS-05-18-0867-RE
  26. Buckley H, Young CA, Charlton ND, Hendricks WQ, Haley B, Nagabhyru P, Rudgers JA (2018). Leaf endophytes mediate fertilizer effects on plant yield and traits in northern oat grass (Trisetum spicatum). Plant and Soil DOI:10.1007/s11104-018-3848-6
  27. Winter DJ, Ganley ARD, Young CA, Liachko I, Schardl CL, Dupont P-Y, Berry D, Ram A, Scott B, Cox MP (2018). Repeat elements organize 3D genome structure in the filamentous fungus Epichloë festucae and mediate transcription of symbiosis genes. PLoS Genetics DOI: 10.1371/journal.pgen.1007467
  28. Mattupalli C, Moffet C, Shah K, Young CA (2018). Supervised classification of RGB aerial imagery acquired by manned and unmanned aircrafts to evaluate a root rot disease. Remote Sensing 10: 917. DOI:org/10.3390/rs10060917
  29. Bock CH, Young CA, Stevenson KL, Charlton ND (2018). Fine scale population genetic structure and within tree distribution of mating types of Venturia effusa, cause of pecan scab in the U.S.A. Phytopathology 108:1326-1336 DOI:10.1094/PHYTO-02-18-0068-R
  30. Yi M, Hendricks WQ, Kaste J, Charlton ND, Nagabhyru P, Panaccione DG, Young CA (2018). Molecular identification and characterization of endophytes from uncultivated barley. Mycologia 110:453-472 DOI:10.1080/00275514.2018.1464818
  31. Trammell MA, Butler TJ, Young CA, Widdup K, Amadeo J, Hopkins AA, Nyaupane NP, Biermacher JT (2018). Registration of ‘Chisholm’ summer dormant tall fescue. Journal of Plant Registrations. 12:293-299
  32. Young CA, Bock CH, Charlton ND, Mattupalli C, Krom ND, Bowen JK, Templeton M, Plummer KM, Wood BW (2018). Evidence for sexual reproduction: identification, frequency and spatial distribution of Venturia effusa (pecan scab) mating type idiomorphs. Phytopathology 108:837-846 DOI:10.1094/PHYTO-07-17-0233-R
  33. Shi C, An S, Yao Z, Young CA, Panaccione DG, Lee ST, Schardl CL, Li C (2018). Toxin-producing Epichloë bromicola symbiotic with the forage grass, Elymus dahuricus, in China. Mycologia 109:847-859. DOI: 10.1080/00275514.2018.1426941
  34. Mitic M, Berry D, Brassell E, Green K, Young CA, Saikia S, Rakonjac J, Scott B (2018). Disruption of calcineurin catalytic subunit (cnaA) in Epichloë festucae induces symbiotic defects and intrahyphal hyphae formation. Molecular Plant Pathology 19:1414-1426. DOI: 1111/mpp.12624


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Ph.D., Molecular Biology, Massey University, New Zealand (2005)
M.Sc., Genetics, Massey University, New Zealand (1999)
B.Sc., Massey University, New Zealand (1993)