Characterization of a new semi-dominant dwarf allele of SLR1 and its potential application in hybrid rice breeding

Abstract

The widespread introduction of semi-dwarf1 (sd1), also known as the 'Green Revolution' gene, has dramatically increased rice yield. However, the extensive use of limited sources of dwarf genes may cause 'bottleneck' effects in breeding new rice varieties. Alternative dwarf germplasms are quite urgent for rice breeding. Here, we characterized a new allele of the rice Slr1-d mutant, Slr1-d6, which reduced plant height by 37%, a much milder allele for dwarfism. Slr-d6 was still responsive to gibberellin (GA) to a reduced extent. The mutation site in Slr1-d6 was less conserved in the TVHYNP domain, leading to the specific semi-dominant dwarf phenotype. Expression of SLR1 and five key GA biosynthetic genes was disturbed in Slr1-d6, and the interaction between Slr1-d6 and GID1 was decreased. In the genetic background of cultivar 9311 with sd1 eliminated, Slr1-d6 homozygous plants were ~70 cm tall. Moreover, Slr1-d6 heterozygous plants were equivalent in height to the standard sd1 semi-dwarf 9311, but with a 25% yield increase, showing its potential application in hybrid rice breeding.

Fig. 1.

Characterization of the phenotype and response to exogenous GA₃ treatment of the semi-dominant dwarf mutant Slr1-d6. (A) Gross morphology of ZX3037 (left), F₁ plant between ZX3037 and Slr1-d6 (middle), and homozygous mutant Slr1-d6 (right). Scale bar=10 cm. (B) Morphology of 10-day-old seedlings of ZX3037 (left) and Slr1-d6 (right). Scale bar=2 cm. (C) Transverse and longitudinal sections of the penultimate internode from ZX3037 (left) and Slr1-d6 (right). Scale bars=100 µm. (D) Panicle and internode length comparison between ZX3037 and Slr1-d6. (E) Elongation of the second leaf sheath of Slr1-d6 in response to exogenous treatment with different concentrations of GA₃. ZX3037 was used as a control. Data are means ±SD; n=10.

Fig. 2.

Map-based cloning of Slr1-d6. (A) The Slr1-d6 locus was mapped to a 356 kb candidate region on the long arm of chromosome 3. The vertical bars represent molecular markers, and the adjacent numbers indicate recombinant plants. (B) Gene structure and mutation site on the candidate gene Os030707600. White boxes with black frames indicate exons, and black bold lines on both sides represent the 5'- and 3'-untranslated regions. Boxes with different gray levels indicate different motifs deduced in the rice DELLA protein, SLR1. (C) Multiple sequence alignment of the conserved N-terminal domains of different DELLA proteins. DELLA proteins from rice (SLR1), maize (D8), sorghum (SlD8), barley (SLN1), wheat (Rht1-D1), Arabidopsis (GAI1 and RGA1), soybean (GmDELLA1), alfalfa (MtDELLA1), pear (PpDELLA1), and grape (VvDELLA). The black triangle indicates the mutation site of Slr1-d6. The white triangles indicate the mutation sites of other Slr1-d allele mutants.

Fig. 3.

Expression patterns of SLR1 and five key GA biosynthetic genes in Slr1-d6. * represents a significance level of P<0.05; ** represents a significance level of P<0.01; *** represents a significance level of P<0.005. Error bars are the mean ±SD (n=3).

Fig. 4.

Slr1-d6 shows decreased interaction ability with GID1. (A) Yeast two-hybrid tests between Slr1-d6 and GID1. Growth of yeast strain Y2Hgold on a –His plate with 10^–4 M GA₃ (+) or without (–). (B) Interaction between Slr1-d6 and GID1 in an in vitro β-galactosidase activity tested in a liquid assay using yeast strain Y187 with (+) or without (–) 10^–4 M GA₃. Error bars are the mean ±SD (n=3).

Fig. 5.

Yield trait performance of Slr1-d6. Sample size: n=10 for spikelets per panicle, seed setting, and yield per plant; n=20 for effective tillers per plant; n=5 for kilo-grain weight. Error bars are the mean ±SD. ** represents a highly significant difference (P<0.01), and *** represents an extremely significant difference (P<0.005) by t-test.

Fig. 6.

Dwarfing ability comparison between Slr1-d6 and sd1. (A) Gross morphology of 9311 plants with different genotypes of dwarf genes at the mature stage. (B) Plant height in the 9311 genetic background with different dwarf genes. Plant heights were measured at the mature stage. Data are means ±SD; n=50. (C) Elongation of the second leaf sheath of different 9311 lines in response to GA₃ treatment. Data are means ±SD; n=10.

Fig. 7.

Yield trait performance of Slr1-d6 in the genetic background of 9311. (A) Number of effective tillers per plant, means ±SD; n=100. (B) Spikelets per panicle, means ±SD; n=10. (C) Seed setting, means ±SD; n=10. (D) Kilo-grain weight, means ±SD; n=5. (E) Yield per plant, means ±SD; n=10. * represents a significant difference (P<0.05), ** represents a highly significant difference (P<0.01) and *** represents an extremely significant difference (P<0.005) by t-test.