Integration of genome‐wide association study, linkage analysis, and population transcriptome analysis to reveal the TaFMO1‐5B modulating seminal root growth in bread wheat.

SUMMARY: Bread wheat, one of the keystone crops for global food security, is challenged by climate change and resource shortage. The root system plays a vital role in water and nutrient absorption, making it essential for meeting the growing global demand. Here, using an association‐mapping population composed of 406 accessions, we identified QTrl.Rs‐5B modulating seminal root development with a genome‐wide association study and validated its genetic effects with two F5 segregation populations. Transcriptome‐wide association study prioritized TaFMO1‐5B, a gene encoding the flavin‐containing monooxygenases, as the causal gene for QTrl.Rs‐5B, whose expression levels correlate negatively with the phenotyping variations among our population. The lines silenced for TaFMO1‐5B consistently showed significantly larger seminal roots in different genetic backgrounds. Additionally, the agriculture traits measured in multiple environments showed that QTrl.Rs‐5B also affects yield component traits and plant architecture‐related traits, and its favorable haplotype modulates these traits toward that of modern cultivars, suggesting the application potential of QTrl.Rs‐5B for wheat breeding. Consistently, the frequency of the favorable haplotype of QTrl.Rs‐5B increased with habitat expansion and breeding improvement of bread wheat. In conclusion, our findings identified and demonstrated the effects of QTrl.Rs‐5B on seminal root development and illustrated that it is a valuable genetic locus for wheat root improvement. Significance Statement: Accelerating bread wheat functional genomic studies with the rapidly increasing amounts of genomic and multi‐omics data is challenging. Here, we identified the QTrl.Rs‐5B and its causal gene TaFMO1‐5B modulating seminal root development by integrating genome‐wide association study, linkage analysis, and population transcriptomes. Its favorable haplotype also improves the yield component and plant architecture‐related traits in the field and was increased in terms of frequency during modern wheat breeding. [ABSTRACT FROM AUTHOR]