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Journal of Experimental Botany logoLink to Journal of Experimental Botany
. 2018 Jun 28;69(20):4703–4713. doi: 10.1093/jxb/ery243

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

Zhigang Wu 1,2,#, Ding Tang 3,#, Kai Liu 4,#, Chunbo Miao 3, Xiaoxuan Zhuo 1, Yafei Li 3, Xuelin Tan 2, Mingfa Sun 4,✉, Qiong Luo 1,✉, Zhukuan Cheng 3,✉
PMCID: PMC6137977  PMID: 29955878

Dwarf germplasms are very important for genetic breeding. Here, we characterize a new semi-dominant dwarf allele of SLR1 and show its potential application in hybrid rice breeding.

Keywords: Giberellin, rice, semi-dominant dwarf, SLR1, yield

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.

Introduction

Dwarfism is one of the most important agronomic traits in crop breeding programs. Dwarf cultivars are not only improved in lodging resistance and harvest index, but also have better responses to fertilizers (Khush, 2001). The introduction of two well-known dwarf genes, semi-dwarf1 (sd1) in rice (Oryza sativa) and reduced height1 (Rht1) in wheat (Triticum aestivum), to create semi-dwarf varieties has greatly increased crop yields and initiated the ‘Green Revolution’ in the 1960s (Hedden, 2003). Since then, efforts have been made by breeders to collect novel dwarf germplasms and reveal their dwarf mechanisms. More than 70 dwarf mutants have been characterized in rice so far (Liu et al., 2018; https://shigen.nig.ac.jp/rice/oryzabase/).

Dwarfism in plants is mainly caused by deficiency in various endogenous hormones. Gibberellin (GA) is one of the most important phytohormones determining plant height (Wang and Li, 2005; Yamaguchi, 2008; Sun, 2011). GAs are a group of diterpenoid compounds that act as regulators in a range of growth and developmental processes in higher plants, including stem elongation, leaf differentiation, photomorphogenesis, pollen development, and flowering (Richards et al., 2001; Fleet and Sun, 2005). Dwarf mutants deficient in GA biosynthesis or signaling usually exhibit a dn-type dwarf phenotype accompanied by deep green and rough leaves (Sakamoto et al., 2004). Several genes, namely d18 (Itoh et al., 2001), d35 (Itoh et al., 2004), sd1 (Monna et al., 2002), and eui (Zhu et al., 2006), that contribute to a defective GA biosynthetic pathway have been cloned in rice. In addition, genes encoding the GA receptor GA-INSENSITIVE DWARF1 (GID1) (Ueguchi-Tanaka et al., 2005), DELLA proteins (Peng et al., 1997; Silverstone et al., 1998; Ikeda et al., 2001), and the F-box protein GA-INSENSITIVE DWARF2 (GID2) (Gomi et al., 2004) have also been isolated, and an integrated GA signaling pathway has started to emerge (Sun, 2010, 2011). DELLA protein acts as a GA signaling repressor that restrains the expression of GA-responsive genes in the absence of GA (Eckardt, 2007; Schwechheimer, 2008). When GA is present, GID1 binds to GA and subsequently interacts with DELLA proteins in the nucleus, resulting in the recognition of DELLA proteins by the SCFGID2/SLY1 complex, degradation of DELLA proteins via the 26S proteasome pathway, and consequently activation of the expression of GA-responsive genes (Sun and Gubler, 2004). Despite the fact that numerous dwarf or semi-dwarf mutants have been reported, only sd1 and its alleles act as useful dwarf sources and thus have been widely used for rice breeding (Asano et al., 2007).

Intervarietal hybrid rice yields 10–20% more than inbred varieties, and it covers >50% of the total rice-planting area in China (Cheng et al., 2007). Two-line intersubspecific (indica/japonica) hybrids could further increase yield potential, exceeding the yield plateau reached by intervarietal hybrid rice. However, in hybrid breeding programs, both male and female parents must carry the same recessive dwarf gene sd1 to solve the problem of higher plant stature due to heterosis, which is time consuming and labor intensive. Moreover, the extensive use of limited dwarf sources may cause ‘bottleneck effects’ in the genetic background when breeding new varieties, which would cause genetic vulnerability to pests or diseases (Kikuchi and Futsuhara, 1997). If one parent has a dominant dwarf gene, there will be no restriction on whether or not the other parent has a recessive dwarf gene, which would greatly expand the genetic backgrounds that can be selected for both parents and save time and labor costs in breeding high yield rice hybrids. Thus, the identification of dominant dwarf germplasms is urgent for hybrid rice breeding. However, there have only been a few dominant or semi-dominant dwarf mutants, including D53, Dx, D-h, LBD4, Sdd(t), Slr1-d, Ssil, and Tid1, characterized in rice so far (Wei et al., 2006; Liu et al., 2008; Qin et al., 2008; Asano et al., 2009; Miura et al., 2009; Sunohara et al., 2009; Hirano et al., 2010; Liang et al., 2011; Piao et al., 2014; Zhang et al., 2016). In addition, these dwarf mutants are not available for practical breeding due to their unfavorable phenotypes, such as severe dwarfism, low fertility, and short grains. In rice, there are currently no dominant dwarfing sources with high breeding value that are being used in practical production.

Five alleles of Slr1-d mutants have been previously reported in rice. They showed ~50–70% reduction in plant height when compared with their wild types (Asano et al., 2009; Hirano et al., 2010; Zhang et al., 2016). In the present study, we characterized a new mutant allele of Slr1-d, Slr1-d6. The Slr1-d6 mutant reduces plant height by 37%, which is much milder dwarfism than previously reported alleles. Map-based cloning revealed that the mutation site in Slr1-d6 is less conserved in the TVHYNP domain of SLR1, which is thought to be the reason for the milder dwarf phenotype in Slr1-d6. Expression of SLR1 and five key GA biosynthetic genes is disturbed in the Slr1-d6 mutant. The S97L substitution in SLR1 leads to a decreased interaction with GID1. In the genetic background of cultivar 9311 with sd1 eliminated, Slr1-d6 homozygous plants showed suitable plant height and decent seed setting for sterile line production. Moreover, Slr1-d6 heterozygous plants also showed significant yield potential compared with normal 9311 plants.

Materials and methods

Plant materials and growth conditions

The semi-dominant dwarf mutant Slr1-d6 is a spontaneous mutant identified from the indica rice (Oryza sativa L.) cultivar Zhongxian 3037 (ZX3037). The F2 mapping populations were generated by crossing Slr1-d6+/− plants with the japonica variety Nipponbare. The indica variety Nanjing 6, with no dwarf genes, was used as one donor parent. Four 9311 plant lines with different genotypes of dwarf genes, namely SD1SD1/SLR1SLR1, sd1sd1/SLR1SLR1, SD1SD1/Slr1-d6SLR1, and SD1SD1/Slr1-d6Slr1-d6, were generated with the following steps: first, Slr1-d6+/− plants were crossed with Nanjing 6, and SD1SD1/Slr1-d6Slr1-d6 plants were chosen at the segregation generation; secondly, SD1SD1/Slr1-d6Slr1-d6 plants were crossed with 9311, and then SD1SD1/Slr1-d6Slr1-d6 plants were chosen at the segregation generation; and, thirdly, SD1SD1/Slr1-d6Slr1-d6 plants were backcrossed six times with 9311 followed by a final selfing generation. All plant materials were cultivated in paddy fields in Beijing or Yangzhou in the summer and in Hainan in the winter, with spacing of 13.3 cm between plants within each row and 25 cm between rows, under normal rice production practices.

Culm anatomical observation

At the filling stage, the second internodes under the panicle of wild-type ZX3037 and Slr1-d6 plants were fixed in FAA solution (5% formaldehyde, 5% glacial acetic acid, and 63% ethanol) for 2 d at 4 °C after they were vacuum pumped for 30 min. After dehydration in a graded ethanol series (30–50–70–85–90–100%; 30 min per step), the samples were infiltrated and embedded in Technovit 7100 resin (RM2265, Germany). Transverse and longitudinal sections (4 µm thick) were cut with a Leica (Wetzlar, Germany) microtome. These sections were stained with 0.25% toluidine blue and then observed under a light microscope (DM500, Leica, Germany).

GA induction of shoot elongation

Seed glumes were removed and sterilized with 75% ethanol for 5 min, then sterilized with 25% NaClO for 40 min, and finally washed five times with sterile distilled water and put onto sterilized filter paper to remove residual moisture. The seeds were cultivated on 1/2 Murashige and Skoog (MS) solid medium containing different concentrations of GA3 and grown at 28 °C with 12 h of light from fluorescent lights. Ten days later, the length of the second leaf sheath of each plant was measured.

Map-based cloning and sequence analysis of Slr1-d6

A total of 523 plants with a severe dwarf phenotype segregated from the F2 population from a cross between Slr1-d6 and Nipponbare were selected for isolating the mutated gene. Sequence-tagged site (STS) markers were developed according to sequence differences between the japonica variety Nipponbare and the indica variety 9311, according to the data published on the NCBI website (http://www.ncbi.nlm.nih.gov). Orthologs of rice DELLA protein, SLR1, were downloaded from the NCBI website by homology blasting. Multiple sequence alignment was conducted using the online software Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de/#/).

Functional complementation test

The complementary plasmid was constructed by cloning a 6.06 kb genomic DNA fragment, containing 2541 bp promotor sequences, the entire 1878 bp coding region of Slr1-d6, and 1669 bp downstream sequences, into the pCAMBIA1300 vector. The control plasmid contained a 2541 bp promotor sequence, the entire 1878 bp coding region of SLR1, and 1669 bp downstream sequences. Transformation of the embryonic callus of ZX3037 was conducted using the recombinant plasmids constructed above. Genotypes of the transgenic plants were identified by sequencing.

Quantitative real-time PCR (qRT-PCR) for transcript expression assay

Total RNA was extracted from root, internode, young leaf, leaf sheath, and panicle of ZX3037 and Slr1-d6 at the elongation stage using the classical TRIZOL RNA isolation protocol (Chomczynski and Mackey, 1995); RNA was further purified with DNase I. The mRNAs were reverse transcribed into cDNA with oligo(dT)18 primer. Real-time PCR was performed using the Bio-Rad CFX96 real-time PCR instrument and EvaGreen (Biotium, http://www.biotium.com/) with gene-specific primer pairs (SLR1-RT-F/R, OsCPS1-RT-F/R, OsKS1-RT-F/R, OsKAO-RT-F/R, OsGA3ox2-RT-F/R, and SD1-RT-F/R) and an internal control primer OsActin-RT-F/R. The results were analyzed using OPTICONMONITOR 3.1 (Bio-Rad, USA). Each experiment had three replicates.

Yeast two-hybrid assay

The Matchmaker Two-Hybrid System (Clontech, USA) was used for the yeast two-hybrid assay. pGADT7-SLR1 and pGADT7-Slr1-d6 served as the prey, and pGBKT7-GID1 as the bait. Plate assays (–His) and β-galactosidase (β-gal) liquid assays were conducted according to the manufacturer’s protocol (Clontech) with 10–4 M GA3 added or not added (control). The yeast strain Y2H gold was used for growth tests on –His plates. Serial 1:10 dilutions were prepared in ddH2O, and 10 µl of each dilution was used per spot; Y187 was used to detect β-gal activity by liquid assay.

Measurement and statistical analysis of yield-associated agronomic traits

All of the following recordings and measurements were carried out at the maturity stage. Effective tillers of 20 and 100 plants of each sample were evaluated in Beijing and Yangzhou, respectively. The length from the ground surface to the top of the highest panicle was measured as the plant height of rice, and 20 and 50 plants for each sample were investigated in Beijing and Yangzhou, respectively. Yield per plant was represented by the average product of 10 plants that were randomly selected in the middle field. Spikelets per panicle were calculated by: total spikelets of one plant/effective tiller number, with 10 replications. Seed setting (%) was calculated by: filled grains per panicle/spikelets per panicle×100%. Kilo-grain weight was measured for each sample with five replications. All analyses were conducted using the statistical data analyses software SPSS.

Results

Identification and characterization of a novel semi-dominant dwarf mutant in rice

A rice spontaneous dwarf mutant was isolated from ZX3037. The mutant plant showed a 37% reduction in plant height compared with the normal ZX3037 (Supplementary Table S1 at JXB online), with wide and shortened dark green leaf blades (Fig. 1A). When the mutant plant was crossed with the normal ZX3037, the F1 plants showed intermediate plant height relative to both parents (Fig. 1A). Ten-day-old seedlings of Slr1-d6 were also shorter than those of ZX3037, but had more developed roots (Fig. 1B). Transverse and longitudinal sections of the penultimate internode of the dwarf mutant showed that the cell length was significantly reduced and the internode was obviously thickened with increased cell layers (Fig. 1C). In the subsequent F2 population, the segregation ratio of dwarf plants (including semi-dwarf phenotype like the F1 plants) to normal plants was 73:25, which is consistent with the expected 3:1 segregation ratio of a single dominant gene. In comparison with ZX3037, the lengths of different internodes of the dwarf mutant were all reduced (Fig. 1D; Supplementary Table S1), characteristic of the dn-type rice dwarf mutants (Takeda, 1977). These results indicated that this dwarf mutant was a semi-dominant dwarf mutant belonging to the dn-type rice dwarf mutants, and that cell length reduction may be the immediate cause of the shortened culm length in the dwarf mutant plant.

Fig. 1.

Fig. 1.

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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.

Defects in GA biosynthesis and/or perception are the major determinants of plant height, despite various causes of dwarfism in plants. In the present study, the response of the dwarf mutant to exogenous GA3 was examined using a shoot elongation test. Elongation of the second leaf sheath of the wild type was clear with the application of 10–8–10–7 M GA3, while such effects were not observed in the mutant until 10–7–10–6 M GA3 was applied (Fig. 1E). When treated with 10–5 M GA3, the length of the second leaf sheath in ZX3037 was elongated up to ~13.5 cm, whereas that in the mutant was only elongated to ~6 cm (Fig. 1E). These results suggest that the dwarf mutant is responsive to GA, although to a reduced extent.

Map-based cloning and molecular analysis of Slr1-d6

To isolate the mutated gene in Slr1-d6 that controls the dwarf phenotype, map-based cloning was carried out using the F2 population generated by crossing the dwarf mutant with Nipponbare. In total, 523 plants with severe dwarf phenotypes that segregated from the F2 population were selected and used for gene mapping. Preliminarily, the mutated gene locus was located between two STS markers, C3S10 and C3S12, on the long arm of chromosome 3 (Fig. 2A). Using adjacent insertion/dletion (InDel) markers (Supplementary Table S2), we further narrowed its locus to a 356 kb candidate region that contains 52 predicted genes (Fig. 2A). Scanning this candidate region, we found that the gene Os03g0707600 that encodes the sole rice DELLA protein, SLR1, is located within this region. Five dominant dwarf mutant alleles of SLR1, including Slr1-d1-d5, showing dominant dwarf and delayed GA response or GA-insensitive phenotypes, have been reported in rice (Asano et al., 2009; Hirano et al., 2010; Zhang et al., 2016). Thus, Os03g0707600 was considered as the most likely candidate gene and was sequenced. Sequence analysis revealed that a single base transition, C290T, occurred in SLR1 in the dwarf mutant, leading to substitution of the 97th amino acid serine (S) of SLR1 with leucine (L) (Fig. 2B). Multiple sequence alignment of the conserved N-terminal domains of DELLA proteins showed that, unlike previously reported Slr1-d alleles, the substituted amino acid residue site of SLR1 in the dwarf mutant was less conserved (Fig. 2C). We named the semi-dominant dwarf mutant Slr1-d6 and suspected that the single base transition C290T of SLR1 conferred the dwarf phenotypes described above.

Fig. 2.

Fig. 2.

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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.

To confirm the above speculation, transgenic plants expressing SLR1 (ZX3037SLR1) and Slr1-d6 (ZX3037Slr1-d6) under the control of their own promoters were generated, and 19 and 14 transgenic lines were obtained, respectively. Ten-day-old seedlings and mature plants of transgenic lines expressing Slr1-d6 had a dwarf phenotype, while transgenic lines expressing SLR1 were not obviously different from the wild-type ZX3037 (Supplementary Fig. S1). These results further confirmed that the gain-of-function mutant of the rice DELLA protein SLR1 caused the semi-dominant dwarf phenotypes described in Slr1-d6.

Expression of SLR1 and five key GA biosynthetic genes was disturbed in Slr1-d6

DELLA protein is one of the key components of the GA signaling pathway and acts as a suppressor of GA responses. To reveal the dwarfism mechanism of Slr1-d6 at the transcription level, we first detected the expression pattern of SLR1 in both the mutant and its wild type by qRT-PCR at the jointing–booting stage. In the wild-type ZX3037 plants, SLR1 was expressed in all five detected tissues, namely root, internode, leaf, sheath, and panicle, of which sheath showed the highest expression level (Fig. 3A). In the Slr1-d6 plants, transcripts of the mutated DELLA-encoding gene were also detected in all five tissues by gene-specific qRT-PCR primers of SLR1 (Supplementary Table S3). However, its expression was significantly down-regulated in leaf and sheath, and conversely up-regulated in root (Fig. 3A). These results seem to conflict: Slr1-d6 showed reduced plant height and sheath length while the DELLA-encoding gene had a lower expression level than the wild type in leaf and sheath.

Fig. 3.

Fig. 3.

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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).

Numerous studies have shown that DELLA protein also plays a role in maintaining GA homeostasis by feedback regulation of the GA biosynthesis pathway (Sun and Gubler, 2004; Yamaguchi, 2008). Thus we further detected the expression patterns of five key GA biosynthetic genes, OsCPS1, OsKS1, OsKAO, SD1 (OsGA20ox2), and OsGA3ox2, in Slr1-d6 at the same stage by gene-specific primers (Supplementary Table S3). OsCPS1 and OsKS1 encode enzymes that catalyze early steps in the conversion of GGDP to ent-kaurene in the plastids; OsKAO encodes an enzyme that catalyzes the conversion of ent-kaurene acid to GA12 in the endoplasmic reticulum; while SD1 and OsGA3ox2 encode enzymes that catalyze late steps in the synthesis of bioactive GAs in the cytoplasm (Yamaguchi, 2008). In the wild-type ZX3037 plants, OsCPS1, OsKS1, OsKAO, and OsGA3ox2 are all mainly expressed in young leaves (Fig. 3B–D, F), but not SD1 which is mainly expressed in both root and young leaves (Fig. 3E). In the Slr1-d6 plants, the expression levels of OsCPS1, OsKS1, and OsGA3ox2 were significantly down-regulated in young leaves (Fig. 3B, C, F), and, conversely, the expression levels of OsCPS1, OsKS1, and SD1 in internode and sheath, OsKAO in sheath, and OsGA3ox2 in root and internode were significantly up-regulated (Fig. 3B–F). These results suggest that the expression patterns of the five key GA biosynthetic genes were disturbed in Slr1-d6.

Interaction between Slr1-d6 and GID1

DELLA protein interacted with the GA receptor, GID1, in a GA-dependent manner, which is the key step in GA signaling and is necessary for subsequent degradation of DELLA proteins (Gomi and Matsuoka, 2003; Eckardt, 2007; Sun, 2010; Davière and Achard, 2013). The interaction abilities of Slr1-d mutant proteins with GID1 were reduced in Slr1-d mutants, which caused their dwarf phenotypes (Asano et al., 2009). A yeast two-hybrid assay was performed to test whether the interaction between Slr1-d6 and GID1 was affected in the Slr1-d6 mutants. Both yeast cells, those expressing SLR1 and GID1 and those expressing Slr1-d6 and GID1, grew on –His plates in the presence of GA3, whereas none of the yeast cells grew on –His plates without GA3 (Fig. 4A). However, yeast cells expressing Slr1-d6 and GID1 grew much more slowly and less than yeast cells expressing SLR1 and GID1; both types of cells only had dispersed and small yeast colonies on –His plates with GA3 (Fig. 4A). These results suggest that Slr1-d6 could interact with GID1 in a GA-dependent manner just like the wild-type SLR1 and other Slr1-d proteins, but the interaction ability between Slr1-d6 and GID1 was affected.

Fig. 4.

Fig. 4.

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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).

To confirm further the above speculation, β-galactosidase activity was measured with a liquid assay using yeast strain Y187, with or without 10–4 M GA3 treatment. The β-gal activity of yeast strain Y187 expressing Slr1-d6 and GID1 was significantly lower than that of yeast strain Y187 expressing SLR1 and GID1 in the presence of GA3, and no β-galactosidase activity was detected in either strain in the absence of GA3 (Fig. 4B). These results further confirmed that the interaction between Slr1-d6 and GID1 is in a GA-dependent manner and their interaction ability is decreased.

Yield trait performance of Slr1-d6

Slr1-d mutants showed 50–70% reduction in plant height in previous studies (Asano et al., 2009; Hirano et al., 2010; Zhang et al., 2016). In the present study, Slr1-d6 had a 37% reduction in plant height. The Slr-d6 mutant thus has much milder dwarfism than previously reported alleles, which stimulated our interest in investigating its potential application in rice breeding. Statistical analyses of yield traits, including effective tillers per plant, spikelets per panicle, seed setting, kilo-grain weight, and yield per plant of Slr-d6 and ZX3037, were carried out at the mature stage. Compared with ZX3037, the number of effective tillers per plant of Slr-d6 was significantly increased (Fig. 5A), while the spikelets per panicle, seed setting, and kilo-grain weight of Slr-d6 were significantly decreased (Fig. 5B–D). Surprisingly, the yield per plant of Slr-d6 showed no significant difference from ZX3037 (Fig. 5E). These results suggest that the Slr1-d6 mutant may have some negative influences on agronomy traits, but its yield would not be affected for the compensation effects by increased tillers, suggesting that Slr1-d6 may have potential application value.

Fig. 5.

Fig. 5.

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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.

Comparison of dwarfing ability between Slr1-d6 and sd1

The Slr1-d6 mutant in the ZX3037 genetic background showed milder dwarfism, which may be useful in rice dwarf breeding. However, the cultivar ZX3037 intrinsically has the semi-dwarf gene sd1, making it difficult to assess the dwarfism effects of Slr1-d6 accurately in the ZX3037 genetic background. To exclude the influence of sd1 and accurately evaluate the dwarfing effects of Slr1-d6, we constructed plant lines with different genotypes of dwarf genes in the same genetic background of cultivar 9311 (see the Materials and Methods for details). The line without any dwarf genes (SD1SD1/SLR1SLR1) had the highest plant height; the line with the green revolution gene sd1 (sd1sd1/SLR1SLR1), the wild-type cultivar 9311, had a semi-dwarf phenotype accompanied by dark-green and erect leaves; the line with heterozygous genotype of Slr1-d6 (SD1SD1/Slr1-d6SLR1) was similar to normal 9311 in plant height but matured earlier; the line with the homozygous genotype of Slr1-d6 (SD1SD1/Slr1-d6Slr1-d6) had the lowest plant height, with leaves that were shorter and greener than the wild type 9311 (Fig. 6A). Further measurement of plant height revealed that the plant heights of SD1SD1/SLR1SLR1, sd1sd1/SLR1SLR1, SD1SD1/Slr1-d6SLR1, and SD1SD1/Slr1-d6Slr1-d6 were 165.85 ± 7.07, 104.60 ± 4.19, 102.18 ± 2.62, and 68.02 ± 2.69 cm, respectively (Fig. 6B; Supplementary Table S4). The Slr1-d6 homozygous plants were shorter than the sd1 homozygous plants in the same genetic background of 9311, suggesting that the dwarfing ability of Slr1-d6 is stronger than that of sd1. The height of Slr1-d6 homozygous plants was close to 70 cm, which is not too short for sterile line production. In addition, the plant height of Slr1-d6 heterozygotes was equivalent to the normal semi-dwarf height of 9311 plants carrying sd1. These results suggest that Slr1-d6 may have potential application value in rice hybrid breeding.

Fig. 6.

Fig. 6.

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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.

In addition, the responses of Slr1-d6 and sd1 mutants to exogenous GA3 treatment were also tested in the same genetic background of 9311. Lines SD1SD1/SLR1SLR1 and sd1sd1/SLR1SLR1 had the same response tendency to exogenous GA3 treatment: obvious elongation of the second leaf sheath was observed with the application of 10–8–10–7 M GA3 (Fig. 6C). Similar to Slr1-d6, this response of the SD1SD1/Slr1-d6Slr1-d6 plant line was not observed until the application of 10–7–10–6 M GA3 (Fig. 6C). These results further confirmed that the Slr1-d6 mutant is responsive to GA, although to a reduced extent, which is not affected by the presence or absence of sd1.

Yield trait performance of Slr1-d6 in the genetic background of 9311

To evaluate further the practical application value of Slr1-d6 in rice hybrid breeding, a comparison of yield traits between Slr1-d6 and sd1 was also carried out in the same genetic background of 9311 at the mature stage (Supplementary Table S4). Effective tillers per plant of SD1SD1/Slr1-d6Slr1-d6 and SD1SD1/Slr1-d6SLR1 plants were 10.04 ± 1.22 and 8.70 ± 1.06, respectively, both significantly higher than 7.03 ± 1.09 in sd1sd1/SLR1SLR1 plants (Fig. 7A). Spikelets per plant of sd1sd1/SLR1SLR1 and SD1SD1/Slr1-d6SLR1 plants were 205.30 ± 12.66 and 214.80 ± 14.59, respectively, significantly higher than 176.50 ± 15.91 in SD1SD1/Slr1-d6Slr1-d6 plants (Fig. 7B). The seed setting rates of SD1SD1/Slr1-d6Slr1-d6 and SD1SD1/Slr1-d6SLR1 plants were 87.06 ± 5.17% and 87.65 ± 2.96%, respectively, significantly higher than 79.08 ± 5.02% in SD1SD1/Slr1-d6Slr1-d6 plants (Fig. 7C). Kilo-grain weights of sd1sd1/SLR1SLR1 and SD1SD1/Slr1-d6SLR1 plants were 31.37 ± 0.03 g and 31.33 ± 0.02 g, respectively, higher than 30.89 ± 0.04 g in the SD1SD1/Slr1-d6Slr1-d6 plants (Fig. 7D). Yield per plant of sd1sd1/SLR1SLR1 plants was 31.75 ± 6.67 g, and in SD1SD1/Slr1-d6Slr1-d6 plants it was 28.35 ± 5.70 g. In contrast, the yield per plant of SD1SD1/Slr1-d6SLR1 plants was as high as 39.95 ± 6.59 g, a significant increase of 25% compared with sd1sd1/SLR1SLR1 plants (Fig. 7E; Supplementary Table S5).

Fig. 7.

Fig. 7.

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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.

The number of effective tillers per plant increased dramatically, but spikelets per panicle, seed setting rate, kilo-grain weight, yield per plant, and yield per square meter of Slr1-d6 homozygous plants were all significantly lower than in sd1 homozygous plants. The seed setting of Slr1-d6 homozygous plants is close to 80%, which is sufficient for F1 hybrid seed production. In addition, Slr1-d6 heterozygous plants showed great yield-increasing potential when compared with sd1 homozygous plants. These results suggest that Slr1-d6 is a valuable dominant dwarf allele that has potential application value in rice hybrid breeding.

Discussion

Currently, >70 rice dwarf mutants and 24 wheat dwarfing genes have been reported (Tian et al., 2017; Liu et al., 2018). However, most of these dwarf mutants are accompanied by unfavorable phenotypes such as severe dwarfism, low fertility, and short grains; thus sd1 and Rht1 are still the dwarf sources predominantly used to produce modern semi-dwarf varieties in rice and wheat, respectively (Hedden, 2003; Asano et al., 2007). Both sd1 and Rht1 are related to GA. SD1 encodes the GA biosynthetic enzyme, GA20 oxidase 2, catalyzing late steps of gibberellin biosynthesis, and its mutation reduces the endogenous GA level, causing the semi-dwarf phenotypes in sd1 mutants (Sasaki et al., 2002; Spielmeyer et al., 2002). In contrast, the RHT1 encodes a GA signaling repressor DELLA protein; deletion in the N-terminal region constitutively suppresses GA signaling and consequently results in a dominant, semi-dwarf phenotype (Peng et al., 1999). Both cases highlight the pivotal role of GA in regulating plant height, making the GA pathway a prime target for generating useful dwarf sources for crop breeding (Hedden, 2003).

In this study, we isolated and characterized a new allele of rice Slr1-d mutants, Slr1-d6. Similar to the five previously reported alleles of Slr1-d mutants, Slr1-d6 had wide, dark-green leaf blades, with reduced response to exogenous GA treatment, and reduced elongation of all internodes. Slr-d6 is inherited in a semi-dominant dwarf manner. Based on anatomical observations of the culm, we concluded that cell length reduction was the immediate reason for plant height reduction in Slr1-d6. However, the Slr1-d1, -d2, -d3, -d4, and -d5 mutants had ~50–70% reduction in plant height (Asano et al., 2009; Hirano et al., 2010; Zhang et al., 2016), while Slr-d6 mutant plants only led to a 37% reduction in plant height, which is much milder dwarfism than for previously reported alleles. Slr1-d6 has a 1 bp substitution resulting in the amino acid substitution S97L in the conserved TVHYNP motif of SLR1. Based on multiple sequence alignment of the conserved DELL1/TVHYNP domain of DELLA protein orthologs, we found that the amino acid of the mutation site in Slr1-d6 is less conserved than other alleles, which might be the reason for milder dwarfism in Slr1-d6.

DELLA protein is one of the key components of the GA signaling pathway and acts as a suppressor of GA responses. The expression of SLR1 in the root of Slr1-d6 was up-regulated, which is consistent with the dwarf phenotype. Conversely, the expression of SLR1 in both the leaf and internode of Slr1-d6 was down-regulated, which is not consistent with the dwarf phenotype. This conflicting result suggests that the dwarf mechanism hidden in Slr1-d6 could not be explained by its mutated DELLA-encoding gene at the transcriptional level. DELLA protein also plays a role in maintaining GA homeostasis by feedback regulation of the GA biosynthesis pathway (Sun and Gubler, 2004; Yamaguchi, 2008). When a loss-of-function mutation occurs in DELLA protein, the transcript levels of GA20ox and/or GA3ox genes are lower than in the wild type. Conversely, gain-of-function mutations in DELLA protein often result in up-regulation of GA20ox and GA3ox gene expression. Slr1-d6 is a gain-of-function mutant of rice DELLA protein. The expression of SD1 in the internode and sheath and OsGA3ox2 in the root and internode of Slr1-d6 was up-regulated, consistent with previous studies. In contrast, SD1 in the root and OsGA3ox2 in the leaf of Slr1-d6 were down-regulated. There are two possible reasons to explain this paradoxical phenomenon: first, the feedback regulation of the GA biosynthesis pathway mediated by gain-of-function mutation in DELLA protein has tissue specificity, which mainly happened in the rapidly elongated tissues such as internode and sheath in rice at the jointing–booting stage; secondly, the changed expression of one GA biosynthetic gene in one tissue may also have a feedback regulation on its expression in the other tissues to maintain GA homeostasis. Similar to SD1 and OsGA3ox2, the expression of OsCPS1, OsKS1, and OsKAO was mainly up-regulated in internode and/or sheath, and down-regulated in leaf. This is consistent with the current opinion that downstream steps usually regulate feedback on upstream steps in the same biosynthesis pathway. Previous studies have mainly focused on one tissue to illustrate the feedback regulation of DELLA protein on the GA biosynthesis pathway. Whether the feedback regulation of DELLA protein on the GA biosynthesis pathway has tissue specificity still needs to be confirmed.

DELLA protein may interact with the GA receptor, GID1, in a GA-dependent manner, which guides its degradation via the 26S proteasome pathway (Sun and Gubler, 2004). Based on a yeast two-hybrid assay and a β-gal activity test, we found that the mutated SLR1 protein, Slr1-d6, still interacted with GID1 in a GA-dependent manner, but with decreased interaction ability. Previous studies have also revealed that DELLA proteins interact with GID1 via the N-terminal DELLA/TYHYNP domain of DELLA protein (Ueguchi-Tanaka et al., 2007; Willige et al., 2007), especially the valine and proline residues of the TVHYNP motif that directly binds to GID1 (Murase et al., 2008). The S97L substitution in Slr1-d6 is adjacent to the important proline residues of the TVHYNP motif; thus we speculate that the 97th serine residue of the TVHYNP motif also plays a role in the interaction between SLR1 and GID1. Taken together, the semi-dominant dwarf phenotypes of Slr1-d6 might be caused by inefficient degradation of the mutated DELLA protein, Slr1-d6.

Dominant dwarf germplasms possess special advantages in rice hybrid breeding programs. When one parent carries a dominant dwarf gene, it does not matter whether the other parent has a recessive dwarf gene, meaning that a higher number of parental genetic backgrounds can be used, which promotes the use of heterosis. Modern rice varieties are basically semi-dwarf cultivars, intrinsically carrying a recessive dwarf gene. The overwhelming majority of rice dwarf mutants are generated from rice varieties already containing a dwarf gene, which makes it difficult to evaluate the dwarfism effects of new dwarf germplasms accurately for additive effects. Here, we evaluated the dwarfism effects of Slr1-d6 in the genetic background of 9311 with sd1 eliminated. In the same genetic background of 9311, Slr1-d6 showed stronger dwarfism ability than sd1. The production of F1 hybrid seeds requires sterile parents that are 10–20 cm shorter than the pollen donor parents to increase pollen shedding on the female panicle (Virmani and Edwards, 1983).

Here we provide strong evidence that Slr1-d6 is of great practical application value in rice hybrid breeding. First, the Slr1-d6 homozygous plants, with heights of ~70 cm, are not much shorter than the main cultivated varieties of rice with plant height of between 80 cm and 120 cm (http://www.ricedata.cn/). Thus, the Slr1-d6 homozygous plants could be used as the sterile parents, while most rice cultivars could be used as the pollen donor parents. Secondly, the seed-setting rate of Slr1-d6 homozygous plants is ~80%, which is sufficient for production of F1 hybrid seeds. Moreover, the yield per plant of Slr1-d6 heterozygous plants increased by 25% when compared with the normal 9311. Theoretically, if Slr1-d6 is used in the sterile parents as a dominant dwarf source, the genetic backgrounds of the pollen donor parents will not be restricted, and the F1 hybrid plants will gain the standard sd1 semi-dwarf plant height and have a higher yield potential for carrying the heterozygous genotype of Slr1-d6. The Slr1-d6 heterozygous plants that have been selected for yield testing had less competition pressure for space from their neighbors in the segregation population, which would contribute to their yield just like a marginal effect. However, the exact yield-increasing potential of Slr1-d6 in heterosis utilization still needs to be fully evaluated with more cross-combinations.

In rice, mutants of SLR1 located in DELLA/TYHYNP and SAW subdomains may lead to dominant dwarf phenotypes (Asano et al., 2009; Hirano et al., 2010; Zhang et al., 2016). In addition, overexpression of SLR1 variants that are mutated in LHRI, VHIID, LHRII, and PFYRE subdomains could also generate dwarfing transgenic seedlings (Hirano et al., 2012). These studies indicate that mutation of SLR1 in multiple subdomains could lead to the generation of dominant dwarf mutants, making SLR1 the prime target gene for generating dominant dwarf sources. In light of great yield-increasing potential of Slr1-d6 and gene-editing techniques developed in rice (Shan et al., 2014; Hu et al., 2016), we propose that the rice DELLA protein-encoding gene, SLR1, is a potential target for gene editing in rice molecular breeding.

Supplementary data

Supplementary data are available at JXB online.

Fig. S1. Gross morphology of transgenic seedlings and mature plants of ZX3037SLR1 and ZX3037Slr1-d6.

Table S1. Plant height and internode length comparison between ZX3037 and Slr1-d6.

Table S2. List of the PCR-based molecular markers developed for gene mapping.

Table S3. Primers used for sequencing identification, qRT-PCR, and yeast two-hybrid assay.

Table S4. Statistics of agronomic traits of different 9311 lines.

Table S5. Agronomic trait performance of the Slr1-d6 homozygotes and heterozygote compared with 9311.

Supplementary Material

Supplementary Figure S1 and Table S1-s5
Click here for additional data file. (129.4KB, pdf)

Acknowledgements

This work was supported by grants from the Ministry of Sciences and Technology of China (2014ZX0800939B and 2016ZX08009-003), and the Jiangsu Province Science Foundation (BK20161308).

References

  1. Asano K, Hirano K, Ueguchi-Tanaka M, Angeles-Shim RB, Komura T, Satoh H, Kitano H, Matsuoka M, Ashikari M. 2009. Isolation and characterization of dominant dwarf mutants, Slr1-d, in rice. Molecular Genetics and Genomics 281, 223–231. [DOI] [PubMed] [Google Scholar]
  2. Asano K, Takashi T, Miura K, Qian Q, Kitano H, Matsuoka M, Ashikari M. 2007. Genetic and molecular analysis of utility of sd1 alleles in rice breeding. Breeding Science 57, 53–58. [Google Scholar]
  3. Cheng SH, Zhuang JY, Fan YY, Du JH, Cao LY. 2007. Progress in research and development on hybrid rice: a super-domesticate in China. Annals of Botany 100, 959–966. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chomczynski P, Mackey K. 1995. Short technical reports. Modification of the TRI reagent procedure for isolation of RNA from polysaccharide- and proteoglycan-rich sources. Biotechniques 19, 942–945. [PubMed] [Google Scholar]
  5. Davière JM, Achard P. 2013. Gibberellin signaling in plants. Development 140, 1147–1151. [DOI] [PubMed] [Google Scholar]
  6. Eckardt NA. 2007. GA perception and signal transduction: molecular interactions of the GA receptor GID1 with GA and the DELLA protein SLR1 in rice. The Plant Cell 19, 2095–2097. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Fleet CM, Sun TP. 2005. A DELLAcate balance: the role of gibberellin in plant morphogenesis. Current Opinion in Plant Biology 8, 77–85. [DOI] [PubMed] [Google Scholar]
  8. Gomi K, Matsuoka M. 2003. Gibberellin signalling pathway. Current Opinion in Plant Biology 6, 489–493. [DOI] [PubMed] [Google Scholar]
  9. Gomi K, Sasaki A, Itoh H, Ueguchi-Tanaka M, Ashikari M, Kitano H, Matsuoka M. 2004. GID2, an F-box subunit of the SCF E3 complex, specifically interacts with phosphorylated SLR1 protein and regulates the gibberellin-dependent degradation of SLR1 in rice. The Plant Journal 37, 626–634. [DOI] [PubMed] [Google Scholar]
  10. Hedden P. 2003. The genes of the green revolution. Trends in Genetics 19, 5–9. [DOI] [PubMed] [Google Scholar]
  11. Hirano K, Asano K, Tsuji H, Kawamura M, Mori H, Kitano H, Ueguchi-Tanaka M, Matsuoka M. 2010. Characterization of the molecular mechanism underlying gibberellin perception complex formation in rice. The Plant Cell 22, 2680–2696. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hirano K, Kouketu E, Katoh H, Aya K, Ueguchi-Tanaka M, Matsuoka M. 2012. The suppressive function of the rice DELLA protein SLR1 is dependent on its transcriptional activation activity. The Plant Journal 71, 443–453. [DOI] [PubMed] [Google Scholar]
  13. Hu X, Wang C, Fu Y, Liu Q, Jiao X, Wang K. 2016. Expanding the range of CRISPR/Cas9 genome editing in rice. Molecular Plant 9, 943–945. [DOI] [PubMed] [Google Scholar]
  14. Ikeda A, Ueguchi-Tanaka M, Sonoda Y, Kitano H, Koshioka M, Futsuhara Y, Matsuoka M, Yamaguchi J. 2001. Slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8. The Plant Cell 13, 999–1010. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Itoh H, Tatsumi T, Sakamoto T, Otomo K, Toyomasu T, Kitano H, Ashikari M, Ichihara S, Matsuoka M. 2004. A rice semi-dwarf gene, Tan-Ginbozu (D35), encodes the gibberellin biosynthesis enzyme, ent-kaurene oxidase. Plant Molecular Biology 54, 533–547. [DOI] [PubMed] [Google Scholar]
  16. Itoh H, Ueguchi-Tanaka M, Sentoku N, Kitano H, Matsuoka M, Kobayashi M. 2001. Cloning and functional analysis of two gibberellin 3 beta-hydroxylase genes that are differently expressed during the growth of rice. Proceedings of the National Academy of Sciences, USA 98, 8909–8914. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Khush GS. 2001. Green revolution: the way forward. Nature Reviews. Genetics 2, 815–822. [DOI] [PubMed] [Google Scholar]
  18. Kikuchi F, Futsuhara Y. 1997. Inheritance of morphological characters. 2. Inheritance of semi-dwarf. Science of the Rice Plant 3, 300–308. [Google Scholar]
  19. Liang F, Xin X, Hu Z, Xu J, Wei G, Qian X, Yang J, He H, Luo X. 2011. Genetic analysis and fine mapping of a novel semidominant dwarfing gene LB4D in rice. Journal of Integrative Plant Biology 53, 312–323. [DOI] [PubMed] [Google Scholar]
  20. Liu BM, Wu YJ, Fu XD, Qian Q. 2008. Characterizations and molecular mapping of a novel dominant semi-dwarf gene Sdd(t) in rice (Oryza sativa). Plant Breeding 127, 125–130. [Google Scholar]
  21. Liu C, Zheng S, Gui J, et al. 2018. Shortened basal internodes encodes a gibberellin 2-oxidase and contributes to lodging resistance in rice. Molecular Plant 11, 288–299. [DOI] [PubMed] [Google Scholar]
  22. Miura K, Wu J, Sunohara H, Wu X, Matsumoto T, Matsuoka M, Ashikari M, Kitano H. 2009. High-resolution mapping revealed a 1.3-Mbp genomic inversion in Ssi1, a dominant semidwarf gene in rice (Oryza sativa). Plant Breeding 128, 63–69. [Google Scholar]
  23. Monna L, Kitazawa N, Yoshino R, et al. 2002. Positional cloning of rice semidwarfing gene, sd-1: rice ‘green revolution gene’ encodes a mutant enzyme involved in gibberellin synthesis. DNA Research 9, 11–17. [DOI] [PubMed] [Google Scholar]
  24. Murase K, Hirano Y, Sun TP, Hakoshima T. 2008. Gibberellin-induced DELLA recognition by the gibberellin receptor GID1. Nature 456, 459–463. [DOI] [PubMed] [Google Scholar]
  25. Peng J, Carol P, Richards DE, King KE, Cowling RJ, Murphy GP, Harberd NP. 1997. The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses. Genes & Development 11, 3194–3205. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Peng J, Richards DE, Hartley NM, et al. 1999. ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature 400, 256–261. [DOI] [PubMed] [Google Scholar]
  27. Piao R, Chu SH, Jiang W, Yu Y, Jin Y, Woo MO, Lee J, Kim S, Koh HJ. 2014. Isolation and characterization of a dominant dwarf gene, D-h, in rice. PLoS One 9, e86210. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Qin RZ, Qiu Y, Cheng ZJ, Shan XY, Guo XP, Zhai HQ, Wan JM. 2008. Genetic analysis of a novel dominant rice dwarf mutant 986083D. Euphytica 160, 379–387. [Google Scholar]
  29. Richards DE, King KE, Ait-Ali T, Harberd NP. 2001. How gibberellin regulates plant growth and development: a molecular genetic analysis of gibberellin signaling. Annual Review of Plant Physiology and Plant Molecular Biology 52, 67–88. [DOI] [PubMed] [Google Scholar]
  30. Sakamoto T, Miura K, Itoh H, et al. 2004. An overview of gibberellin metabolism enzyme genes and their related mutants in rice. Plant Physiology 134, 1642–1653. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Sasaki A, Ashikari M, Ueguchi-Tanaka M, et al. 2002. Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416, 701–702. [DOI] [PubMed] [Google Scholar]
  32. Schwechheimer C. 2008. Understanding gibberellic acid signaling—are we there yet?Current Opinion in Plant Biology 11, 9–15. [DOI] [PubMed] [Google Scholar]
  33. Shan Q, Wang Y, Li J, Gao C. 2014. Genome editing in rice and wheat using the CRISPR/Cas system. Nature Protocols 9, 2395–2410. [DOI] [PubMed] [Google Scholar]
  34. Silverstone AL, Ciampaglio CN, Sun T. 1998. The Arabidopsis RGA gene encodes a transcriptional regulator repressing the gibberellin signal transduction pathway. The Plant Cell 10, 155–169. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Spielmeyer W, Ellis MH, Chandler PM. 2002. Semidwarf (sd-1), ‘green revolution’ rice, contains a defective gibberellin 20-oxidase gene. Proceedings of the National Academy of Sciences, USA 99, 9043–9048. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Sun TP. 2010. Gibberellin–GID1–DELLA: a pivotal regulatory module for plant growth and development. Plant Physiology 154, 567–570. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Sun TP. 2011. The molecular mechanism and evolution of the GA–GID1–DELLA signaling module in plants. Current Biology 21, R338–R345. [DOI] [PubMed] [Google Scholar]
  38. Sun TP, Gubler F. 2004. Molecular mechanism of gibberellin signaling in plants. Annual Review of Plant Biology 55, 197–223. [DOI] [PubMed] [Google Scholar]
  39. Sunohara H, Kawai T, Shimizu-Sato S, Sato Y, Sato K, Kitano H. 2009. A dominant mutation of TWISTED DWARF 1 encoding an alpha-tubulin protein causes severe dwarfism and right helical growth in rice. Genes & Genetic Systems 84, 209–218. [DOI] [PubMed] [Google Scholar]
  40. Takeda K. 1977. Internode elongation and dwarfism in some graminaeous plants. Gamma Field Symposia 16, 1–18. [Google Scholar]
  41. Tian X, Wen W, Xie L, et al. 2017. Molecular mapping of reduced plant height gene Rht24 in bread wheat. Frontiers in Plant Science 8, 1379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Ueguchi-Tanaka M, Ashikari M, Nakajima M, et al. 2005. GIBBERELLIN INSENSITIVE DWARF1 encodes a soluble receptor for gibberellin. Nature 437, 693–698. [DOI] [PubMed] [Google Scholar]
  43. Ueguchi-Tanaka M, Nakajima M, Katoh E, et al. 2007. Molecular interactions of a soluble gibberellin receptor, GID1, with a rice DELLA protein, SLR1, and gibberellin. The Plant Cell 19, 2140–2155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Virmani SS, Edwards IB. 1983. Current status and future prospects for breeding hybrid rice and wheat. Advances in Agronomy 36, 145–214. [Google Scholar]
  45. Wang Y, Li J. 2005. The plant architecture of rice (Oryza sativa). Plant Molecular Biology 59, 75–84. [DOI] [PubMed] [Google Scholar]
  46. Wei LR, Xu JC, Li XB, Qian Q, Zhu LH. 2006. Genetic analysis and mapping of the dominant dwarfing gene D-53 in rice. Journal of Integrative Plant Biology 48, 447–452. [DOI] [PubMed] [Google Scholar]
  47. Willige BC, Ghosh S, Nill C, Zourelidou M, Dohmann EM, Maier A, Schwechheimer C. 2007. The DELLA domain of GA INSENSITIVE mediates the interaction with the GA INSENSITIVE DWARF1A gibberellin receptor of Arabidopsis. The Plant Cell 19, 1209–1220. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Yamaguchi S. 2008. Gibberellin metabolism and its regulation. Annual Review of Plant Biology 59, 225–251. [DOI] [PubMed] [Google Scholar]
  49. Zhang YH, Bian XF, Zhang SB, Ling J, Wang YJ, Wei XY, Fang XW. 2016. Identification of a novel gain-of-function mutant allele, slr1-d5, of rice DELLA protein. Journal of Integrative Agriculture 15, 1441–1448. [Google Scholar]
  50. Zhu Y, Nomura T, Xu Y, et al. 2006. ELONGATED UPPERMOST INTERNODE encodes a cytochrome P450 monooxygenase that epoxidizes gibberellins in a novel deactivation reaction in rice. The Plant Cell 18, 442–456. [DOI] [PMC free article] [PubMed] [Google Scholar]

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Supplementary Materials

Supplementary Figure S1 and Table S1-s5
Click here for additional data file. (129.4KB, pdf)

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