Wheat can adapt to most agricultural conditions across temperate regions. This success is the result of phenotypic plasticity conferred by a large and complex genome composed of three homoeologous genomes (A, B, and D). Although drought is a major cause of yield and quality loss in wheat, the adaptive mechanisms and gene networks underlying drought responses in the field remain largely unknown. Here, we addressed this by utilizing an interdisciplinary approach involving field water status phenotyping, sampling, and gene expression analyses. Overall, changes at the transcriptional level were reflected in plant spectral traits amenable to field-level physiological measurements, although changes in photosynthesis-related pathways were found likely to be under more complex post-transcriptional control. Examining homoeologous genes with a 1:1:1 relationship across the A, B, and D genomes (triads), we revealed a complex genomic architecture for drought responses under field conditions, involving gene homoeolog specialization, multiple gene clusters, gene families, miRNAs, and transcription factors coordinating these responses. Our results provide a new focus for genomics-assisted breeding of drought-tolerant wheat cultivars.

Bioinformatics Unit SCAI Campus Rabanales University of Córdoba 14014 Córdoba Spain

Biological and Environmental Science and Engineering Division King Abdullah University of Science and Technology Thuwal 23955 6900 Kingdom of Saudi Arabia

Departamento de Bioquímica y Biología Molecular Campus de Excelencia Internacional Agroalimentario Universidad de Córdoba Campus Rabanales C6 1 E17 14071 Córdoba Spain

Departamento de Lenguajes y Ciencias de la Computación ETSI Informática Campus de Teatinos Universidad de Málaga 29071 Málaga Spain

Department of Economic Development AgriBio Centre for AgriBioscience Jobs Transport and Resources La Trobe University 5 Ring Rd Bundoora Victoria 3083 Australia

Department of Plant Sciences and Plant Pathology Montana State University Bozeman MT 59717 3150 USA

Institute of Experimental Botany Centre of Plant Structural and Functional Genomics CZ 78371 Olomouc Czech Republic

Instituto de Agricultura Sostenible Alameda del Obispo s n 14004 Córdoba Spain

John Innes Centre Norwich Research Park Norwich NR4 7UH UK

Veterinary and Agricultural Sciences University of Melbourne Gratten St Parkville Victoria 3010 Australia

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Capturing Wheat Phenotypes at the Genome Level