# GWAS-based identification of multi-trait genetic loci conferring salinity tolerance in barley under hydro- and nanoparticle-priming conditions

## TL;DR

This study identifies genetic markers in barley linked to salt tolerance under hydro and nano priming, offering insights for improving barley production in saline conditions.

## Contribution

The study discovers pleiotropic markers associated with multiple traits of salinity tolerance in barley under different priming conditions.

## Key findings

- Hydro and nano priming significantly improved seed germination and seedling traits under salinity.
- 137 significant SNPs were identified at p ≤ 0.0001, with 30 pleiotropic markers linked to salt tolerance across conditions.
- Specific SNPs like BOPA1_1518 − 624 and SCRI_RS_168580 were associated with multiple germination and seedling traits.

## Abstract

Salinity is one of the most detrimental abiotic stressors, harming agricultural plants and reducing production. Barley (Hordeum vulgare L.) is the fourth most produced cereal crop in the world, which tolerates salt stress conditions. However, the genetic basis of salinity tolerance under hydro and nano priming in barley remains poorly understood. Therefore, understanding the genetics of seed germination under salt stress can aid in improving the development and production of barley. This study aimed to detect the genetic associations underpinning the impact of hydro and zinc oxide nanoparticles (100 ppm) priming compared to unprimed conditions on 170 spring barley cultivars that were exposed to 200 mM sodium chloride during seed germination and seedling growth using GWAS (MLM + K, p-value ≤ 0.0001 and FDR α = 0.01).

High phenotypic variations were detected among all genotypes under control and salinity for all studied traits under all treatments. The reduction rate in root length and shoot length was lower in nano and hydro priming compared to unprimed conditions. The reduction rates were higher in the nano priming compared to hydropriming and unprimed conditions for fresh weight. GWAS analysis reveals 137 and 79 significant SNPs at p ≤ 0.0001 and FDR ≤ 0.01, respectively. Thirty pleiotropic markers linked with salt tolerance at p ≤ 0.0001 for unprimed and priming conditions. For instance, on chr 7 H at position 111,292,841 bp, the SNP marker BOPA1_1518 − 624 was significantly associated with twelve traits related to germination under hydro and nano priming was found near the gene HORVU.MOREX.r3.7HG0670060 coding for F-box family protein (protein turnover). Also, five SNPs were detected that control seven germination-related traits under all treatments. For seedling-related traits, the SNP marker SCRI_RS_168580 on 4 H was found to be associated with the salt tolerance index of both root and shoot length under unprimed conditions, which lies near the gene model HORVU.MOREX.r3.4HG0345880 coding for peroxidase (ROS detoxification).

Hydro and nano priming significantly enhanced seed germination and the seedling establishment traits under salinity. This study highlights the potential of employing pleiotropic markers linked to multiple traits to advance our understanding and improvement of salinity tolerance in barley.

The online version contains supplementary material available at 10.1186/s12870-025-07898-5.