Harnessing salt tolerance and C4-like traits from the halophyte wild species Oryza coarctata into cultivated rice (Oryza sativa L.)

Developing rice varieties suitable for salt-affected coastal regions is critical for ensuring food security in the face of rising sea levels and a growing global population. Oryza coarctata, a halophytic wild species with a KKLL genome, thrives in coastal seawater environments and possesses exceptional traits for salt tolerance and C₄-like photosynthesis. In this study, we successfully hybridized the genomes between AA (O. sativa) and KKLL and further introgressed these unique traits into cultivated rice (Oryza sativa, AA genome) by overcoming hybridization barriers between the two species. Through 36,000 interspecific crosses and optimized embryo-rescue protocols, we generated AKL hybrid and advanced backcross progenies in the indica rice cultivar IR56 background. To confirm the true hybridizations and introgressions, we developed genome-wide polymorphic InDel marker set (132 markers) across 12 chromosomes through direct sequence comparisons. We subsequently developed monosomic alien addition lines (MAALs) and disomic introgression lines (DILs), confirmed using genome-specific InDel markers and SNP genotyping. The F1 and BC1F1 lines exhibited remarkable salinity tolerance, surviving up to EC 24 ds m−1 (240 mM NaCl), whereas the standard salt-tolerant checks (Nonabokra, FL478 and Pokkali) survived only up to EC 12 ds m−1 (120 mM NaCl). This enhanced tolerance is associated with efficient improved Na+/K+ homeostasis, with salt gland-mediated secretion in early hybrids and internal ion regulation in advanced introgression lines. These lines also displayed C₄-like anatomical features, including reduced mesophyll cell rows between bundle sheath cells and enlarged bundle sheath cells traits linked to enhanced carbon assimilation and reduced photorespiration. Furthermore, the disomic introgression lines showed salinity tolerance at EC 12 ds m−1 and retained stable C₄-like leaf characteristics. This work demonstrates the successful transfer of novel salt-tolerance and C₄-like anatomical features from O. coarctata into cultivated rice, offering a promising genetic resource for breeding climate-resilient, high-yielding rice varieties suitable for saline coastal agro-ecosystems.