Image-based phenotyping to understand the genetic basis of waterlogging barley

Barley (Hordeum vulgare L.) is a vital staple crop globally, significantly contributing to food security and the malting industry in Europe. However, its production is increasingly jeopardized by climate change, particularly through challenges such as waterlogging. This thesis aims to expedite the breeding of waterlogging-tolerant barley while advancing methodologies for analysing complex phenotyping datasets. A two-row European spring barley collection, named European HerItage Barley collection (ExHIBiT), was assembled, characterized, and phenotyped for waterlogging tolerance in both controlled and field conditions. Cutting-edge imaging technologies, including unmanned aerial vehicles (UAVs), were employed to capture detailed phenotypic data, which was subsequently analysed through Genome-Wide Association Studies (GWAS). This analysis led to the identification of potential candidate genes associated with waterlogging tolerance across various stress and developmental phases. The second chapter provides a comprehensive background on barley’s significance and the complexities of breeding for waterlogging tolerance. The third chapter details the creation of the ExHIBiT core collection, emphasizing its genetic diversity and statistical power for GWAS analysis. The fourth chapter investigates the ExHIBiT collection through a waterlogging trial conducted under field conditions, employing both traditional phenotyping methods and UAV-based imaging technologies. The fifth chapter discusses the selection of resilient accessions, highlighting the challenges faced in translating resilience classifications across years. The sixth chapter focuses on phenotyping the ExHIBiT core collection under controlled conditions using a 21-day protocol that included stress and recovery phases. An automated high-throughput phenotyping facility was utilized to capture detailed phenotypic data, and a new visualization tool, Genomic Visualizer 3D, was introduced to enhance the analysis of longitudinal GWAS studies. GWAS analyses in Chapters 4 and 6 resulted in the identification of several candidate genes associated with waterlogging tolerance during both the early stress phase and the recovery period. Altogether, this thesis provides a new insight into the genetics of barley tolerance to waterlogging in both field and controlled conditions.