Association analysis identified superior haplotypes for improved salt stress tolerance in wheat (Triticum aestivum L.)

Authors: GUDI, SANTOSH - North Dakota State University; GILL, HARSIMARDEEP - South Dakota State University; COLLINS, SERENA - University Of California, Riverside; SINGH, JATINDER - North Dakota State University; Sandhu, Devinder; SEHGAL, SUNISH - South Dakota State University; UPINDER, GILL - North Dakota State University; Gupta, Rajeev

Submitted to: Plant Stress
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/19/2025
Publication Date: 5/23/2025
Citation: Gudi, S., Gill, H., Collins, S., Singh, J., Sandhu, D., Sehgal, S., Upinder, G., Gupta, R. 2025. Association analysis identified superior haplotypes for improved salt stress tolerance in wheat (Triticum aestivum L.). Plant Stress. 16. Article 100900. https://doi.org/10.1016/j.stress.2025.100900.
DOI: https://doi.org/10.1016/j.stress.2025.100900

Interpretive Summary: Wheat is a globally important cereal crop affected by various abiotic stresses including salt stress. Wheat is affected by salt stress at various developmental stages; however, the seedling stage is the most vulnerable among all. Salinization is the overaccumulation of soluble salts in soil beyond the crop tolerance level and globally, 833 million hectares of land is affected by salinity, which accounts for around 20% of the cultivable area. Understanding the genetic basis of salt tolerance can help in breeding resilient wheat cultivars with improved productivity. In this study we evaluated a diverse panel of spring wheat landraces and cultivars under salt stress which revealed large phenotypic and genetic variations. Genomic regions, candidate genes, and superior alleles identified in this study hold promise for developing resilient wheat cultivars through use of gene-specific molecular markers.

Technical Abstract: Understanding genetic and molecular mechanisms regulating salt stress tolerance is crucial to develop salt resilient wheat cultivars for saline soils. In this study, 228 genetically, phenotypically, and geographically diverse panel of hexaploid spring wheat accessions were evaluated under control (electrical conductivity of irrigation water (ECiw) = 1.46 dS/m) and saline (ECiw = 14 dS/m) irrigation water in greenhouse lysimeter system at US Salinity Laboratory, Riverside, CA. Salt stress had a pronounced negative impact on several seedling traits, reducing shoot height (17.45%), root length (15.51%), tiller number (43.83%), shoot weight (44.61%), and root weight (35.82%). However, salt stress increased root length-by-shoot height ratio (3.75%) and root weight-by-shoot weight ratio (28.02%), highlighting greater adverse effect on shoots compared to roots. Based on phenotypic variations, contrasting lines with hyper or hypo sensitive response to salt stress were identified. Notably, the salt-tolerant lines were mainly landraces originating from seashores, ocean banks, or coastal marshes, whereas salt-sensitive lines were either landraces collected from the freshwater-irrigated regions or modern breeding lines. Multi-locus genome-wide association studies (GWAS) using 297,104 SNPs and linkage disequilibrium (LD)-based grouping identified 25 high-confidence quantitative trait loci (QTLs). Candidate gene mining from flanking genomic regions spanning these QTLs, combined with expression analysis, revealed eight putative genes associated with salt stress tolerance. Haplotype analysis identified superior haplotypes of genes encoding sodium symporter (TraesCS1B02G413800) and peptide transporter (TraesCS5A02G004400). Superior haplotypes are mainly present in landraces but often lost in modern cultivars due to artificial selection pressure during breeding. In summary, this study identified salt tolerant genotypes and associated genomic regions, providing invaluable resources for breeding programs aimed at developing salt-resilient wheat varieties.