Genome-wide association study identifies candidate genes for early seedling traits in barley

The natural salinity of soil is a crucial environmental and agricultural issue caused by excessive evaporation rates, insufficient rainfall, and seawater intrusion into overexploited aquifers. The coastal and interior areas in Qatar, is characterized by high salinity such as Sabkha, which often naturally inhibits vegetation growth. This study seeks to investigate the phenotypic variation and genetic architecture of early seedling traits in 184 barley accessions from around the world using a genome-wide association study (GWAS) approach. Two types of soil were used: a naturally saline soil with severe hypersalinity (pH 8.5 and 55.6 mS/cm) and a low-salinity soil as a control (pH 6.9 and 6.6 mS/cm). However, after two weeks, no germination or seedling growth was observed under the soil’s natural salinity, indicating that none of the accessions carried salt-tolerant features and lacked the genetic and physiological adaptation mechanisms. Ample significant phenotypic variation was observed among accessions under controled soil conditions, with all traits displaying continuous distributions, revealing polygenic inheritance. GWAS analyses using the FarmCPU model identified significant single-nucleotide polymorphisms (SNPs) distributed across the genome, with major genomic regions detected on chromosomes 1 and 6. These regions were linked with multiple traits, suggesting shared genetic control. The GWAS analysis was conducted under low-salinity soil conditions with sufficient phenotypic variation. Candidate gene analysis identified genes involved in key biological processes, including cell wall biosynthesis, hormonal regulation, signal transduction, and transcriptional control. The co-localization of these genes supports the existence of coordinated regulatory networks that govern early seedling development. These findings provide a foundation for improving seedling vigor through modern breeding strategies, including marker-assisted selection and genomic selection, contributing to the development of salt-tolerant barley cultivars.