Predictive models and wild progenitor-derived introgression lines dissect the population dynamics of domestication syndrome traits associated with crop mimicry in weedy rice

Weedy-rice, causing 15-90% yield loss of rice across continents, is a conspecific weed originating from natural outcrossing between Oryza sativa and its wild-progenitors. Bidirectional gene flow and phenotypic mimicry of cultivated ecotypes in early growth stages enable evasion of manual weeding, and facilitate rapid proliferation in cultivated ecosystems. Their sustainable management requires understanding of population dynamics in a crop-weed continuum which is challenging in field-populations due to genetic admixtures and multidimensional selection pressures. To resolve this, we generated bulked backcross-derived inbred lines (BILs) and chromosome-segment substitution lines (CSSLs) from Oryza rufipogon using syntenic microsatellite and SNP markers.Leaf-sheath pigmentation and short-term seed dormancy traits were fine-mapped and BILs mimicking weedy-rice populations were selected for awns, seed shattering, and dormancy, but differing in leaf-sheath pigmentation and plant height. A near-isogenic line (NIL) with purple leaf sheath was also developed to facilitate application of bidirectional selection pressure. Simulated models of population dynamics under different levels of gene flow (5 and 10%) and selection pressures were developed after baseline-surveys in natural populations. Using an experimental population of the weedy-derivatives and the recurrent parent or its purple-sheathed NIL at 40:60 ratio, population dynamics under different degree and directions of selection were characterized in field trials. While resurgence of weedy-derivatives was 59.20–64.27% in the absence of selection, it could be restricted to 16.27–19.60% by applying unidirectional selection pressure and further to 3.94–4.33% through bidirectional selection. These findings highlight the effectiveness of population-dynamics guided breeding and agronomic strategies to reduce weedy-rice load.