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 two-week delay in shattering in cNWR relative to wild populations. Histological analysis indicated anatomical reorganization of the abscission layer in cNWR, consistent with selection for seed retention. Comparative genomic analyses identified multiple NWR orthologs of key Oryza sativa shattering genes, revealing lineage-specific gene duplication, pseudogenization, and divergence from Z. latifolia . Expression profiling of candidate genes via RT-qPCR across floret developmental stages suggested a regulatory role for ZpSh5c , a putative OsSh5 ortholog, in modulating seed shattering. In cNWR, delayed and reduced expression of ZpSh5c mirrored observed differences in shattering timing, highlighting its potential involvement in abscission zone development. 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.