RAD-Seq analysis of wild Japanese garlic (Allium macrostemon Bunge) growing in Japan revealed that this neglected crop was previously actively utilized

Abstract

Abstract Wild Japanese garlic (Allium macrostemon Bunge), commonly referred to as "no-biru" in Japan, is a widespread wild onion species found across the country. Despite being deeply entwined in ancient Japanese culture, as evidenced by numerous references in classical literature, it remains an underutilized crop in Japan, contrasting its culinary applications in China and Korea. Determining the origins of its domestic populations and understanding their genetic composition is crucial to highlighting the plant's historical significance in Japan. This study aims to bridge this knowledge gap by examining the genetic diversity of 47 A. macrostemon samples from various regions in Japan using restriction site-associated DNA sequencing (RAD-Seq). Our analysis distinguished unique population structures, dividing the samples into three distinct groups: A, B, and C. Notably, Groups A and B showed clear evidence of bulb propagation, while Group C diverged from this pattern, forming four subgroups C1, C2, C3, and C4. Hybridization between subgroup C1 and either Group A, B, or both, gave rise to subgroups C2, C3, and C4. Thus, Groups A, B, and C1 are posited as the ancestral populations. Additionally, our morphological observations indicated distinct differences among these three groups. Our findings also suggest that human migration may have influenced the plant's distribution, hinting at active usage in the past that later waned, causing its current underutilized status. Gaining insight into the genetic diversity of A. macrostemon has significant implications. It could improve its desirable traits, such as bulb and leaf quality for culinary purposes, potentially triggering a renaissance in its use as a food source in Japan.