Hordeum spontaneum Koch, the progenitor of cultivated barley, shares the same number of chromosomes as cultivated barley and can be easily crossed without any biological barriers. This study focuses on a collection of H. spontaneum obtained from natural habitats in the Zagros basin, Iran. This collection demonstrates a wide range of variations in seed quality, which were analyzed based on various parameters such as malting efficiency, cold and hot water extract, brix, reducing sugar, and color intensity. Additionally, the nutritional characteristics of the straw produced by each genotype of this germplasm were evaluated under rainfed and irrigated conditions, including crude protein (%CP), crude fiber (%CF), acid detergent fiber (%ADF), dry matter digestibility (%DMD), metabolism energy (ME), digestible energy (DE), and total digestible nutrient (TNT) characteristics. The genetic structure of the population was assessed using 97 different alleles amplified for 35 simple sequence repeat (SSR) and expressed sequence tag (EST)-derived SSR markers. The analysis revealed the presence of seven distinct sub-populations within this diverse panel of wild barley. Marker-trait association analysis identified the markers BeMAG0323 and GBM1461 as highly informative loci for the seed quality traits under both conditions. The markers SCSSR15864 and BMAC0154 were found to have the most significant association with the quality characteristics of the straw. This study is the first to establish a connection between straw traits and seed quality in barley by utilizing SSR and EST-SSR markers. By introducing new plant material that has been thoroughly studied for its economic qualitative characteristics in terms of seed and straw of barley, this research serves as a pre-breeding effort to enhance the quality of barley cultivars and to utilize the informative markers introduced here for future genomic selection programs.
