High-throughput field phenotyping reveals that selection in breeding has affected the phenology and temperature response of wheat in the stem elongation phase

Roth, Lukas; Kronenberg, Lukas; Aasen, Helge; Walter, Achim; Hartung, Jens; van Eeuwijk, Fred; Piepho, Hans-Peter; Hund, Andreas

doi:10.1093/jxb/erad481

Cited by 4 publications

References 63 publications

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A genome-wide association study identifies markers and candidate genes affecting tolerance to the wheat pathogenZymoseptoria tritici

Mikaberidze,

McDonald,

Kronenberg

2024

Preprint

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Plants defend themselves against pathogens using either resistance, measured as the host’s ability to limit pathogen multiplication, or tolerance, measured as the host’s ability to reduce the negative effects of infection. Tolerance is a promising trait for crop breeding, but its genetic basis has rarely been studied and remains poorly understood. Here, we reveal the genetic basis of leaf tolerance to the fungal pathogenZymoseptoria triticithat causes the globally important septoria tritici blotch disease on wheat. Leaf tolerance toZ. triticiis a quantitative trait that was recently discovered in wheat by using automated image analyses that quantified the symptomatic leaf area and counted the number of pycnidia found on the same leaf. A genome-wide association study including both tolerance and resistance to STB found a strong negative genetic correlation between these traits, indicative of a trade-off. We identified four chromosome intervals associated with tolerance and a separate chromosome interval associated with resistance. Within these intervals, we identified candidate genes, including wall-associated kinases similar toStb6, the first cloned STB resistance gene. A trade-off between tolerance and resistance would hinder breeding simultaneously for both traits, but our findings suggest a way forward using marker-assisted breeding. We expect that the methods described here can be used to characterize tolerance to other fungal diseases that produce visible fruiting bodies, such as speckled leaf blotch on barley, potentially unveiling conserved tolerance mechanisms shared among plant species.

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A genome-wide association study identifies markers and candidate genes affecting tolerance to the wheat pathogenZymoseptoria tritici

Mikaberidze,

McDonald,

Kronenberg

2024

Preprint

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The FIP 1.0 Data Set: Highly Resolved Annotated Image Time Series of 4,000 Wheat Plots Grown in Six Years

Roth,

Boss,

Kirchgessner

et al. 2024

Preprint

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Background: Understanding genotype-environment interactions of plants is crucial for crop improvement, yet limited by the scarcity of quality phenotyping data. This data note presents the Field Phenotyping Platform 1.0 data set, a comprehensive resource for winter wheat research that combines imaging, trait, environmental, and genetic data. Findings: We provide time series data for more than 4,000 wheat plots, including aligned high-resolution image sequences totaling more than 148,000 aligned images across six years. Measurement data for eight key wheat traits is included, namely canopy cover values, plant heights, wheat head counts, senescence ratings, heading date, final plant height, grain yield, and protein content. Genetic marker information and environmental data complement the time series. Data quality is demonstrated through heritability analyses and genomic prediction models, achieving accuracies aligned with previous research. Conclusions: This extensive data set offers opportunities for advancing crop modeling and phenotyping techniques, enabling researchers to develop novel approaches for understanding genotype-environment interactions, analyzing growth dynamics, and predicting crop performance. By making this resource publicly available, we aim to accelerate research in climate-adaptive agriculture and foster collaboration between plant science and computer vision communities.

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Accelerating wheat improvement through trait characterization: advances and perspectives

Roychowdhury,

Ghatak,

Kumar

et al. 2024

Physiologia Plantarum

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Wheat (Triticum spp.) is a primary dietary staple food for humanity. Many wheat genetic resources with variable genomes have a record of domestication history and are widespread throughout the world. To develop elite wheat varieties, agronomical and stress‐responsive trait characterization is foremost for evaluating existing germplasm to promote breeding. However, genomic complexity is one of the primary impediments to trait mining and characterization. Multiple reference genomes and cutting‐edge technologies like haplotype mapping, genomic selection, precise gene editing tools, high‐throughput phenotyping platforms, high‐efficiency genetic transformation systems, and speed‐breeding facilities are transforming wheat functional genomics research to understand the genomic diversity of polyploidy. This review focuses on the research achievements in wheat genomics, the available omics approaches, and bioinformatic resources developed in the past decades. Advances in genomics and system biology approaches are highlighted to circumvent bottlenecks in genomic and phenotypic selection, as well as gene transfer. In addition, we propose conducting precise functional genomic studies and developing sustainable breeding strategies for wheat. These developments in understanding wheat traits have speed up the creation of high‐yielding, stress‐resistant, and nutritionally enhanced wheat varieties, which will help in addressing global food security and agricultural sustainability in the era of climate change.

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High-throughput field phenotyping reveals that selection in breeding has affected the phenology and temperature response of wheat in the stem elongation phase

Cited by 4 publications

References 63 publications

A genome-wide association study identifies markers and candidate genes affecting tolerance to the wheat pathogenZymoseptoria tritici

A genome-wide association study identifies markers and candidate genes affecting tolerance to the wheat pathogenZymoseptoria tritici

The FIP 1.0 Data Set: Highly Resolved Annotated Image Time Series of 4,000 Wheat Plots Grown in Six Years

Accelerating wheat improvement through trait characterization: advances and perspectives

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