Genetic variation in seed shattering and awn length in a core collection of Japanese local upland rice, Oryza sativa L.

Upland rice is cultivated in dry and rain-fed fields and is grown primarily in regions with limited water resources. Due to the development of irrigation systems and the comparatively lower yield and eating quality of upland rice relative to paddy rice, its cultivated area has decreased in Japan over the years. However, upland rice is known to carry genes controlling important agricultural traits such as drought tolerance and disease resistance. Therefore, they have a large potential serving as genetic resource to improve modern paddy cultivars. Although upland rice is cross-compatible with most paddy rice and shares a close genetic background, its evolutionary history and introduction pathways into Japan remain unclear. In this study, we employed a core collection of Japanese local upland rice to evaluate two domestication-related traits: seed shattering and awn length. Large variations were observed in the degree of seed shattering and awn length. Genetic analyses at known loci controlling these traits indicated that several upland cultivars may carry unidentified loci explaining their seed shattering and awn length. The Japanese local upland rice core collection represents a valuable genetic resource for elucidating genetic alterations in domestication-related traits and clarifying their introduction into Japan.