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Journal article
Genome-Wide Association Study and Transcriptome Analysis Reveal Alkaline Stress-Responsive Genes in Bread Wheat ( Triticum aestivum L.)
International journal of molecular sciences, Vol.26(17), 8659
2025
PMID: 40943578
Abstract
Alkaline stress, driven by high pH and carbonate accumulation, results in severe physiological damage in plants. While the molecular mechanisms underlying alkaline tolerance have been partially elucidated in many crops, they remain largely unexplored in wheat. We hypothesize that alkaline stress tolerance in wheat is genotype-dependent. This study employed an integrated multi-omics approach to assess alkaline stress responses, combining genome-wide association study (GWAS) and RNA-seq analyses. Systematic phenotyping revealed severe alkaline stress-induced root architecture remodeling-with 57% and 73% length reductions after 1- and 3-day treatments, respectively-across 258 accessions. Analysis of the GWAS results identified nine significant alkaline tolerance QTLs on chromosomes 1A, 3B, 3D, 4A, and 5B, along with 285 associated candidate genes. Using contrasting genotypes-Dingxi 38 (tolerant) and TDP.D-27 (sensitive)-as experimental materials, physiological analyses demonstrated that root elongation was less inhibited in Dingxi 38 under alkaline stress compared to TDP.D-27, with superior root integrity observed in the tolerant genotype. Concurrently, Dingxi 38 exhibited enhanced reactive oxygen species (ROS) scavenging capacity. Subsequent RNA-seq analysis identified differentially expressed genes (DEGs) involved in ion homeostasis, oxidative defense, and cell wall remodeling. Integrated GWAS and RNA-seq analyses allowed for the identification of seven high-confidence candidate genes, including transcription factors (MYB38, bHLH148), metabolic regulators (ATP-PFK3), and transporters (OCT7), elucidating a mechanistic basis for adaptation to alkaline conditions. These findings advance our understanding of alkaline tolerance in wheat and provide candidate targets for molecular breeding of saline- and alkaline-tolerant crops.
Details
- Title
- Genome-Wide Association Study and Transcriptome Analysis Reveal Alkaline Stress-Responsive Genes in Bread Wheat ( Triticum aestivum L.)
- Authors/Creators
- Xuelian Sun - Qingdao Agricultural UniversityXin Kang - Qingdao Agricultural UniversityJiayan Wang - Qingdao Agricultural UniversityXiaoyan He - Qingdao Agricultural UniversityWenxing Liu - Qingdao Agricultural UniversityDengan Xu - Qingdao Agricultural UniversityXuehuan Dai - Qingdao Agricultural UniversityWujun Ma - Qingdao Agricultural UniversityJianbin Zeng - Qingdao Agricultural University
- Publication Details
- International journal of molecular sciences, Vol.26(17), 8659
- Publisher
- MDPI
- Number of pages
- 23
- Grant note
- YDZX2021078 / the Special Projects of the Central Government Guiding Local Science and Technology Development No Grant Number / Shandong Province First-class Discipline Construction "811" Project 32171976 / National Natural Science Foundation of China 2023LZGC009 / Shandong Provincial Key Research and Development Plan
- Identifiers
- 991005813418007891
- Copyright
- © 2025 by the authors.
- Murdoch Affiliation
- Centre for Crop and Food Innovation
- Language
- English
- Resource Type
- Journal article
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- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.49 Plant Stress Responses
- Web Of Science research areas
- Biochemistry & Molecular Biology
- Chemistry, Multidisciplinary
- ESI research areas
- Chemistry