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.
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We appreciate Dr. Caiyan Chen for the critical advice of the manuscript and Dr. David Zaitlin for language improvement. We would like to express our gratitude to anonymous reviewers and editor for their careful work and thoughtful suggestions that have helped improve this paper substantially.
This work was supported by grants from the National Natural Science Foundation of China (31371603) and partly supported by Youth Innovation Promotion Association of Chinese Academy of Sciences (2018398).
The authors declare that they have no competing interests.
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Electronic supplementary material
Flow diagram showing the population development strategy used in this study. MAS, marker-assisted selection; 9311, an indica rice cultivar; Nipponbare, a japonica rice cultivar; 9311-SD1NpSD1Np, the NIL for SD1Np in the indica rice cultivar ‘9311’; Np-SD19311SD19311, the NIL for SD19311 in the japonica rice cultivar ‘Np’; F1-SD1NpSD1Np, F1-SD19311SD19311, F1-SD1NpSD19311, and F1-SD19311SD1cr: four kinds of F1 hybrids carrying different genotypes of SD1, the two homozygous types SD1NpSD1Np and SD19311SD19311, and the heterozygous type SD1NpSD19311 and SD19311SD1cr, respectively (JPG 95 kb)
Morphology of a CRISPR/Cas9 knockout mutant, the two SD1 NILs, of the parental lines 9311 and ‘Np’ grown in the field at Sanya city in the summer of 2018 and 2020. a WT, wild-type ‘Np’; cr-sd1-1, the CRISPR/Cas9 SD1 knockout mutant; 9311-SD1NpSD1Np, the ‘9311’ backcross line carrying SD1NpSD1Np; Np-SD19311SD19311, the ‘Np’ backcross line carrying SD19311SD19311. In the field at Sanya city in the summer of 2018, b 9311-SD1NpSD1Np, the ‘9311’ backcross line carrying SD1NpSD1Np; CK1, a rice cultivar as control check 1 in the same field; CK2, another rice cultivar as control check 2 in the same field. In the field at Sanya city in the summer of 2020 (JPG 442 kb)
Phenotypic comparisons and statistical analyses of the F1 hybrids with different SD1 genotypes, the homozygous NILs, and the parental inbred lines ‘Np’ and ‘9311’. The dotted line represents the mid-parent value (MPV) (JPG 257 kb)
Statistical analyses of plant height and yield-related traits in two hybrid rice lines. F1-SD19311SD1cr, the F1 hybrid derived from a cross between ‘9311’ and cr-sd1-1; F1-SD1NpSD19311, the F1 hybrid derived from a cross between ‘9311’ and ‘Np’. ns, no significant difference; *p < 0.05 and **p < 0.01, as determined by Student’s t test (JPG 76 kb)
Comparison of plant heights between Np-SD19311SD19311 and the CRISPR/Cas9 knockout line cr-sd1-1. ns, no significant difference at the 0.05 level (Student’s t test) (JPG 19 kb)
Hypothetical model showing how SD1 regulates plant height, tiller number, and spikelet number in rice (JPG 167 kb)
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Yu, Y., Hu, X., Zhu, Y. et al. 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. Mol Breeding 40, 84 (2020). https://doi.org/10.1007/s11032-020-01164-2
- OsGA20ox-2 (SD1)
- Tiller number
- Spikelets per panicle