Abstract
Wheat (Triticum aestivum L.) is the second most important cereal crop after rice. Improving yield is crucial to address population growth and food security. Enhancing crop productivity requires structural modification in plant architecture, mainly the canopy, which improves photosynthetic activity and mitigates stresses such as heat and drought. In this study, we evaluated 161 wheat genotypes for canopy architecture traits, performed marker-trait association to identify genetic factors influencing canopy structure. Precision phenotyping using imaging was conducted for traits including flag leaf area, flag leaf length, flag leaf width, flag leaf angle, canopy inclination angle, and ground cover. Genome-wide association study identified 230 significant quantitative trait nucleotides (QTNs) across all chromosomes for six traits in both years. Stable SNPs were detected on chromosomes 3B and 6B for flag leaf area and on 5 A for flag leaf width. Seven ortholog candidate genes i.e., OsDEP1, OsSPL14, ZmCLA4, ZmNA2, OsBZR1, OsHD1, and OsLIC were explored based on QTN proximity and transcriptome profiling for studied canopy related traits. This study helped to understand the prevalence of natural variations in Pakistan’s germplasm, and ortholog candidate genes involved in the wheat canopy architecture. These findings delivered the genome-based pre-breeding information for erect canopy lines which can be used in future for the development of new cultivars with efficient photosynthetic system. These findings will also assist the breeders in formulating the climate-resilient wheat varieties.
Data availability
The data that supports the findings of this study are available in the supplementary material of this article.
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Acknowledgements
The authors are thankful to CIMMYT seed bank for providing Pakistan’s landraces and historical cultivars.
Funding
The research was funded by the Public Sector Development Program (PSDP) “Sino-Pak Agricultural Breeding Innovations Project for Rapid Yield Enhancement” PSDP-857 Project at the National Institute for Genomics and Advanced Biotechnology (NIGAB), NARC and Polish National Agency for Academic Exchange (NAWA) under the Ulam Program (BPN/ULM/2022/1/00147/U/00001).
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Conceptualization, Muhammad Farhan and Muhammad Kashif Naeem; Data curation, Muhammad Farhan, Muhammad Kashif Naeem, Amna Muhammad and Bilal Saleem; Formal analysis, Muhammad Farhan, Marcin Kiedrzyński, Muhammad Uzair and Bilal Saleem; Funding acquisition, Muhammad Ramzan Khan; Investigation, Amna Muhammad, Bilal Saleem and Zahid Mahmood; Methodology, Muhammad Kashif Naeem, Amna Muhammad, Muhammad Uzair, Bilal Saleem and Zahid Mahmood; Project administration, Muhammad Ramzan Khan; Resources, Muhammad Kashif Naeem, Muhammad Uzair, Zahid Mahmood, Asif Mir and Muhammad Ramzan Khan; Software, Muhammad Farhan and Bilal Saleem; Supervision, Asif Mir, Muhammad Ramzan Khan and Aamir Hamid Khan; Validation, Muhammad Ramzan Khan; Visualization, Muhammad Uzair; Writing – original draft, Muhammad Farhan; Writing – review & editing, Muhammad Kashif Naeem, Aamir Hamid Khan, Amna Muhammad, Muhammad Uzair, Bilal Saleem, Zahid Mahmood, Asif Mir and Muhammad Ramzan Khan. All authors have read and agreed to the published version of the manuscript.
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Farhan, M., Naeem, M.K., Muhammad, A. et al. Genome-wide association analysis reveals natural genetic variations controlling canopy architecture traits in bread wheat. Sci Rep (2026). https://doi.org/10.1038/s41598-026-37433-x
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DOI: https://doi.org/10.1038/s41598-026-37433-x
