Wild rice GL12 regulated by GIF1 and WRKY53 synergistically improves grain length and salt tolerance in cultivated rice

Abstract The abounding variations in wild rice (Oryza rufipogon) provided potential reservoirs of beneficial genes for rice breeding. Maintaining stable and high yields under environmental stresses is a long-standing goal of rice breeding but is challenging due to internal trade-off mechanisms. Here, we reported a gene in wild rice as a candidate target for achieving this goal in cultivated rice. Wild rice GL12W improves grain length, grain weight, and salt tolerance in both indica and japonica genetic backgrounds. GL12W alters cell length by regulating grain size related genes including GS2, and positively regulates the salt tolerance related genes, such as NAC5, NCED3, under salt stresses. We found that a G/T variation in GL12 promoter determined its binding to coactivator GIF1 and transcript factor WRKY53. GIF1 promotes GL12W expression in young panicle and WRKY53 represses GL12W expression under salt stresses. The near isogenic line of GL12W showed longer grain length and higher salt tolerance than its overexpression lines, demonstrated that GL12W has a stronger effect under its native promoter. Additionally, the G/T variation contributes to the divergence of indica and japonica subspecies, most of japonica harbor G genotype and the majority of indica are T genotype. Generally, GL12W synergistically controls rice yield and salt tolerance through different spatio-temporal expression patterns, which regulated by GIF1 and WRKY53. Our results provided novel resources for modern rice breeding and insights for yield and salt tolerance trade-off mechanism.