Genetic diversity of modern Japanese malting barley was assessed by RNA-sequencing of transcribed genes in immature seeds. The work aims to identify genes underlying malting-quality and agronomic characteristics. We also attempt to clarify unique genetic features of Japanese barley germplasm in relevance to barley collections in other geographical regions. Barley has unique morphology in seed and spikes including hulled vs hulless (naked) caryopses and two-row vs six-row. Barley has diverse utilities, such as human food, animal feed and brewery. In addition, viral and fungal disease resistance genes and high and stable yield potential and abiotic stress tolerance, such as water logging, drought, and pre-harvest sprouting, are our scopes. The goal is to dissecting genes beneficial for quality improvement and unique morphology.