Seed shattering in a North American Oryzeae grain: Developmental and genomic signatures of early domestication

Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic grain endemic to North America and a member of the Oryzeae tribe. As an outcrossing crop with a short breeding history, domestication progress in cultivated NWR (cNWR) is ongoing, and seed shattering remains a major barrier to yield stability. In this study, we investigated the developmental and genetic mechanisms underlying seed retention by integrating phenotypic, anatomical, and molecular analyses across wild and cultivated populations. Time-course phenotyping using four methods revealed a ∼90% reduction and 2-week delay in shattering in cNWR relative to wild populations. Histological analysis indicated differential anatomical reorganization of the abscission layer in cNWR compared to the wild type. Comparative genomic analyses identified multiple NWR homologs of key Oryza sativa shattering genes, revealing lineage-specific gene duplication, pseudogenization, and divergence from Zizania latifolia. Expression profiling of candidate genes via reverse transcription quantitative polymerase chain reaction across floret developmental stages identified the gene ZpSh5c as a potential regulator of seed shattering. Together, these findings provide new insights into the anatomical and molecular basis of seed shattering in NWR and demonstrate the utility of comparative frameworks for accelerating trait improvement in emerging, non-model crops.