Genome-Wide-Epidemiological-Climatic-Analyses: a new tool for crop resistance to diseases in the face of climate change (GWECAs)

Infectious diseases in crops and domestic animals are a significant burden on agriculture, as they have both direct effects on yields or production losses and indirect effects such as quality losses. Climate change and global trade increase the likelihood of devastating epidemics and thus the unpredictability of production and yields because

1. rising temperatures increase the geographical range of infectious diseases and the severity of epidemics
2. pathogen strains travel easily between locations with favourable environmental conditions for epidemics and
3. new epidemics emerge due to the increasing frequency of host jumps.

There is now overwhelming evidence of devastating epidemics in crops (Ug99 wheat stem rust), livestock (H5N1 bird flu) and humans (Covid-19). Modern breeding for disease resistance in crops or livestock is therefore an arms race between humans and pathogens, which is further accelerated and complicated by climate change. The susceptibility/resistance of hosts and the severity of epidemics are determined by the interaction of a particular genotype of the host (crop or livestock) with a particular genotype of the pathogen (viruses, bacteria, fungi) in a particular climate/environmental context (referred to as GxGxE interactions). New resistance genes must therefore be found to increase the resistance of crop plants and animals to epidemics. In order to optimise the spatial and temporal deployment of resistant varieties in the agricultural landscape, the effects of genetic diversity of pathogens and climate change on GxGxE interactions must also be quantified and predicted.

The Tellier lab is developing mathematical models of coevolution between hosts and pathogens and has recently developed a novel genome-wide association (Bayesian) system to combine the genomes of European humans and hepatitis C virus (HCV) to uncover a novel human locus for resistance to the virus. Dr Spannagl from the Helmholtz Zentrum München specialises in the assembly and analysis of large plant genomes such as barley or maize and is currently creating the barley pan-genome based on 76 varieties. Dr Herz is responsible for barley breeding at the Bavarian State Research Centre for Agriculture (LfL) with a focus on resistance to pathogens and carries out field work throughout Bavaria to uncover the effects of environmental conditions on disease severity. Professor Franziska Wespel from the University of Applied Sciences Weihenstephan-Triesdorf (HSWT) contribute her experience in barley breeding and pathogenes. The laboratories at the HSWT and the LfL have the expertise and the necessary infrastructure for carrying out field trials and collecting plant and pathogen samples from barley fields throughout Bavaria. In addition, Dr Herz at the LfL and Prof Wespel at the HSWT are the perfect partners to translate the results of this project into the development of new resistant barley varieties. The team thus unites theoretical biologists, plant pathologists, plant breeders and genomics experts in a unique way. As a pilot project and proof of concept for Genome-Wide Epidemiological Climatic Analyses (GWECAs), the team of experts will focus on spring barley and Fusarium fungal pathogens that produce toxins.

The project has three objectives:

1. To develop a novel GWECA framework to discover new resistance genes in crops and to identify the pathogen genes for infectivity and to assess/predict the impact of the environment (climate) on the occurrence and severity of local epidemics
2. Obtaining genome data of spring barley and Fusarium sp. from various field trials in Bavaria as evidence for the application of our GWECA method,
3. Establishment of a Bavarian and European network of interested researchers and breeders to further develop the method and implement this GWECA scheme of gene discovery and breeding in various important crops (barley, wheat, maize) and livestock (poultry, cattle, pigs).
   

Information from whole genome data will be used to decipher the genetic and environmental basis of disease severity in space and time (across fields, years and varieties). The project is timely as modern breeding tends to reduce the genetic diversity of most major crops and climate change increases the unpredictability of disease epidemics. The project is unique and ambitious in its scope: it ranges from the development of genomic methods to the analysis of epidemiological and climatic data and the application to the genome analysis of barley and Fusarium sp. This project is only possible due to the interdisciplinary collaboration between the four groups of TUM, Helmoltz Centre, HSWT and LfL. The results of this project will be far-reaching and ground-breaking, benefiting many crops beyond barley and contributing to food security in Bavaria and the EU.