Jonathan Cope

Jonathan Cope is a researcher specialising in underground crop ecology and Genotype × Environment interactions in Martin Weih's Plant Ecology group.

Previous work has included identification of genetic regions involved in tolerances to different biotic (e.g. fungal diseases) and abiotic (e.g. salt stress and nutrient differences) in a Scottish landrace of Barley - "Bere". 

The current focus of his work is on underground crop ecology: root system architecture (RSA), how managment practices affect this, and how this interacts with the nutrient cycle and microbial community to affect yield.

My main research is on Underground Crop Ecology, with projects including:

• HeRo (SLU Grogrund), where I develop and apply approaches to study how environmental factors - such as region and preceding crop - shape RSA, and how these changes, in turn, influence nutrient accumulation and the composition of the root-associated microbial community. 
• InterRoot (Ekhagastiftelsen), where I coordinate and carry out the project’s work on intercropping root complementarity, with the goal of maximising cereal–legume intercropping under organic conditions.
• DIVERSOW (Ekhagastiftelsen), where I investigate how landrace-based inter- and intra-cropping affects organic crop performance through RSA, nutrient accumulation and fungal disease, and relate these responses to the broader project’s holistic assessment of the root-associated microbiome, weeds, and insect dynamics.

Additionally, I contribute to projects including:

• RhizoLupin (Ekhagastiftelsen), where I advise on links between RSA, rhizobia establishment, nitrogen fixation and Lupin crop performance, and coordinate experiments investigating whether introduced rhizobia can survive, adapt, and fix nitrogen effectively under organic Swedish conditions.
• Robust Wheat (SLU Grogrund), where I advise on how RSA contributes to wheat robustness under diverse environmental conditions, including water stress.
• N2CROP (Novo Nordisk Foundation), where I advise on how RSA affects nitrogen-use efficiency and performance in faba bean–cereal intercropping systems, and co-supervise a PhD student in work aiming to use legume symbiotic nitrogen fixation to produce high-quality and nutritious plant protein in sustainable agri-food systems.

Previously I have been involved in:

• NewP (Formas), where I co-supervised a PhD student working on how early root growth and root-to-shoot allocation relate to nitrogen economy during grain filling in spring wheat, as part of work identifying traits for improved nutrient use and yield under Swedish conditions.
• Identifying traits from Scots Bere and other landraces to develop stress tolerant barley (AHDB), where I conducted the work identifying genetic regions associated with tolerance to biotic stresses, such as fungal diseases, and abiotic stresses, such as salt stress and nutrient differences, in the Scottish barley landrace “Bere”.

I am currently co-course leader for the BSc level course "Sustainable food production - challenges and cropping system solutions" (MX0146) as of 2024.

I am also a guest lecturer on the MSc level courses:

• "Experimental approaches in plant growth analysis and phenotyping" (BI1339), where I teach Basic Statistics (2022 ), Root Phenotyping (2022 ), and supervise the practical in Growth Dynamics (2023)
• "Sustainable Plant Production - from Molecular to Field Scale" (BI1295) where I teach Gene Pools and their Role in Breeding for Sustainability (2023-25)

I have been working at the SLU (Department of Crop Production Ecology) as a Postdoktor/Forskare since Oct 2020. Prior to SLU I undertook my PhD at University of Aberdeen & The James Hutton Institute (2015-2019) with my dissertation entitled “Characterising Resilience and Resource Use Efficiency Traits from Scots Bere and Additional Landraces for Development of Stress Tolerant Barley”.

My MSc was undertaken at the University of East Anglia & The John Innes Centre (2013-2014), with my thesis evaluating pathogen interactions on Brachypodium. My BSc (Hons) was at the University of St Andrews (2009-2013), with my thesis investigating signiling activity of self-cleaving proteins in plant cells.

2026-Ongoing: PhD Student, Inge van de Wiel, Co-supervisor  

2020-2025: PhD Student, Lorena Guardia Velarde, Co-supervisor  

2020-2022: MSc Student, Co-supervisor

2022-Ongoing: BSc and MSc level internships

The full list can be found in the "Research and EMA Database" profile above.

Postdoktor/Forskare:

Cope JE, and Newton AC (2025). Performance of elite and heritage germplasm in barley genotype mixtures: effects on yield and disease under diverse management scenarios. Agronomy for Sustainable Development 45:52.

Guardia-Velarde L, Cope JE, Metzler H, Westerbergh A, and Weih M (2025). Same with less: a method to reduce destructive sampling to estimate nitrogen use efficiency components using allometric relationships in spring wheat (Triticum aestivum). Functional Plant Biology, 52:FP24201.

Cope JE, Berckx F, Galinski A, Lentz J, Nagel KA, Fiorani F, and Weih M (2024). Precrop-treated Soil Influences Wheat (Triticum aestivum L.) Root System Architecture and its Response to Drought. Frontiers in Plant Science, 15:1389593.

Cope JE, Berckx F, Lundmark J, Henriksson T, Karlsson I, and Weih M (2024). Clear effects on root system architecture of winter wheat cultivars (Triticum aestivum L.) from cultivation environment and practices. Scientific Reports, 14:11099.

Guardia-Velarde L, Liu H, Cope JE, Westerbergh A, and Weih M (2023). Differential breeding targets in wheat influence non-target traits related to grain quality, but not crop nitrogen requirement. Frontiers in Agronomy, 5.

Doctorate:

Cope JE, Norton GJ, George TS, and Newton AC (2022). Evaluating Variation in Germination and Growth of Landraces of Barley (Hordeum vulgare L.) Under Salinity Stress. Frontiers in Plant Science,  13:863069.

Cope JE, Norton GJ, George TS, and Newton AC (2021). Identifying potential novel resistance to the foliar disease ‘Scald’ (Rhynchosporium commune) in a population of Scottish Bere barley landrace (Hordeum vulgare L.). Journal of Plant Diseases and Protection, 128: 999–1012.

Amaro TMMM, Cope J, and Franco-Orozco B (2021). Current status of plant pathogens of agricultural importance for Colombia. A review. Revista Colombiana de Ciencias Hortícolas, 15:e12425.

Cope JE, Russell J, Norton GJ, George TS, and Newton AC (2020). Assessing the variation in Manganese Use Efficiency Traits in Scottish Barley Landrace Bere (Hordeum vulgare L.). Annals of Botany, 126: 289-300.

Bachelors & Masters:

Cope JE, and Peraldi A (2026). Genetic insights into root disease resistance using the model cereal Brachypodium distachyon. Phytopathology Research, 8.

Roulston C, Luke GA, Felipe P, Ruan L, Cope J, Nicholson J, Sukhodub A, Tilsner J, and Ryan MD (2016). ‘2A‐Like’ Signal Sequences Mediating Translational Recoding: A Novel Form of Dual Protein Targeting. Traffic, 17: 923-939.