Identification of marker genes for drought stress tolerance in wheat (Triticum aestivum) through carbon isotope composition

Abstract

Improving drought adaptation in wheat requires robust physiological traits that can be genetically dissected and translated into breeding tools. Carbon isotope composition (δ¹³C) is a stable proxy for intrinsic water-use efficiency (iWUE) and enables the identification of genetic factors underlying drought-stress responses. In this study, δ¹³C was measured in the Bavarian MAGIC Wheat (BMW) population, and quantitative trait locus (QTL) mapping at the drought-prone Morgenrot field site identified six significant loci on chromosomes 1D, 2B, 4B, 4D, 6A, and 6B. Based on phenotypic extremes at this site, eight genetically diverse lines with contrasting δ¹³C/iWUE values (four high δ¹³C and four low δ¹³C) were selected for detailed characterization. These extreme lines were evaluated under controlled greenhouse conditions using high-throughput phenotyping under both well-watered and drought-stress treatments.

Transcriptomic analyses revealed pronounced drought-induced expression changes, with enrichment of genes involved in abscisic acid signaling, stress perception, stomatal regulation, and energy metabolism. To identify robust molecular targets, QTL mapping results were integrated with differential gene expression (DGE) and weighted gene co-expression network analysis in a multi-layer framework. This approach prioritized 18 high-confidence candidate genes located mainly on chromosomes 1D, 4B, 4D, 6A, and 6B. These genes are embedded in regulatory networks dominated by transcription factors such as WRKY and NAC. Collectively, this study provides genetically anchored candidate genes for iWUE and drought adaptation, offering valuable resources for marker-assisted selection in wheat breeding.