Re-evaluation of the rice ‘Green Revolution’ gene: the weak allele SD1-EQ from japonica rice may be beneficial for super indica rice breeding in the post-Green Revolution era

The Green Revolution of the 1960s introduced semi-dwarf cultivars of rice that had reduced lodging and increased harvest indexes. The mutant allele of Semi Dwarf 1 (SD1) is the gene underlying the Green Revolution advances in rice yield. Since that time, most of the commercial semi-dwarf cultivars carry a mutation in SD1. Unlike japonica rice cultivars containing weak functional SD1 alleles, indica rice cultivars owed their diminished stature to a null mutation in SD1. It has been proposed recently that increasing plant height and subsequently plant biomass will increase grain production in semi-dwarf cultivars used in super rice breeding programs. In this study, we evaluated the potential benefit of the weak functional allele of SD1 from japonica rice on yield improvement in the indica rice background. We found that the Green Revolution gene SD1 has pleiotropic effects on tiller number and spikelets per panicle, in addition to plant height in rice. The introduction of the weak allele SD1-EQ from the japonica cultivar ‘Nipponbare (Np)’ led not only to a substantial increase in plant height but also to an increase in yield per plant in the indica cultivar ‘9311’. This result was further confirmed in CRISPR/Cas9-mediated knockout mutants. In addition, heterosis for yield-related traits was detected at the SD1 locus, and SD1-EQ exhibited a potential improved yield in hybrid rice lines. This study provides evidence that the weak functional SD1 allele from japonica rice cultivar ‘Np’, SD1-EQ, is an excellent genetic resource for the improvement of indica rice lines with null alleles of SD1, in the post-Green Revolution era.