The deployment of heterosis in the form of hybrid rice varieties has boosted grain yield, but grain quality improvement still remains a challenge. Here we show that a quantitative trait locus for rice grain quality, qGW7, reflects allelic variation of GW7, a gene encoding a TONNEAU1-recruiting motif protein with similarity to C-terminal motifs of the human centrosomal protein CAP350. Upregulation of GW7 expression was correlated with the production of more slender grains, as a result of increased cell division in the longitudinal direction and decreased cell division in the transverse direction. OsSPL16 (GW8), an SBP-domain transcription factor that regulates grain width, bound directly to the GW7 promoter and repressed its expression. The presence of a semidominant GW7TFA allele from tropical japonica rice was associated with higher grain quality without the yield penalty imposed by the Basmati gw8 allele. Manipulation of the OsSPL16-GW7 module thus represents a new strategy to simultaneously improve rice yield and grain quality.
At a glance
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- Supplementary Figure 2: The contrasting phenotype and grain yield of hybrid combinations ZS97A/MH63 and TFA/MH63. (91 KB)
(a) The number of tillers per plant. (b) The number of grains per panicle. (c) 1,000-grain weight. (d) The overall grain yield per plant. All data were measured from plants grown with a spacing of 20 × 20 cm in paddies under normal cultivation conditions. Data are shown as means ± s.e.m. (n = 180). A Student’s t test was used to generate the P values.
- Supplementary Figure 3: The semidominant qGW7 allele from TFA was correlated with the formation of more slender grains. (116 KB)
(a) Segregation of the BC1F2 population derived from TFA and HJX74 (recurrent parent). (b–d) Comparisons of grain width (b), grain length (c) and ratio of grain length to width (d) among homozygotes for the TFA qGW7 allele, heterozygotes for the TFA qGW7 allele and the HJX74 qgw7 allele, and homozygotes for the HJX74 qgw7 allele. Data are shown as means ± s.e.m. (n = 120). The same lowercase letter denotes a non-significant difference between the means (P > 0.05).
- Supplementary Figure 4: Phylogenetic tree of TRM family proteins based on the protein sequences. (230 KB)
The names of Arabidopsis and rice TRM genes were downloaded from the Arabidopsis Functional Genomics Network (http://www.dbg-afgn.de) and the Rice Annotation Project Database (http://rapdb.dna.affrc.go.jp).
- Supplementary Figure 5: C-terminal motifs of the GW7 protein are present in CAP350. (150 KB)
A significant match was obtained with a human centrosomal protein CAP350, which contains the three conserved motifs M3-M4-M2 in the same configuration as in both rice GW7 and Arabidopsis TRM1. The numbers on the right indicate the position of the residues in the full-length protein. Identical residues are indicated by dark boxes, conserved residues are indicated by gray boxes and variant residues are indicated by light boxes. The C-terminal motifs of human centrosomal protein CAP350 (NP_055625.4) are from NCBI (http://www.ncbi.nlm.nih.gov).
- Supplementary Figure 6: Comparison of GW7 transcription between NIL-GW7TFA and NIL-gw7HJX74 plants in vegetable growth stage. (34 KB)
SAM, shoot apical meristem. Expression levels were expressed as the relative copies of rice actin3. Data are shown as means ± s.e.m. (n = 3). The same lowercase letter denotes a non-significant difference between the means (P > 0.05).
- Supplementary Figure 7: Comparison of GW7 transcription between NIL-GW7TFA and NIL-gw7HJX74 plants in developing rice endosperms. (44 KB)
Total RNA was extracted from the developing rice endosperms. DAP, days after pollination. Expression levels were expressed as the relative copies of rice actin3. Data are shown as means ± s.e.m. (n = 3). The same lowercase letter denotes a non-significant difference between the means (P > 0.05).
- Supplementary Figure 8: The effect of GW7 on the average length and width of the outer epidermal cells of spikelet hulls. (39 KB)
Data are shown as means ± s.e.m. (n = 30). A Student’s t test was used to generate the P values.
- Supplementary Figure 9: The GW7 protein interacts with both OsTON1b and OsTON2. (51 KB)
(a) The colored boxes correspond to the position of the motif present in the GW7 and TRM1/LNG2 proteins. (b) The M2 motif of GW7 was involved in the interaction between GW7 and OsTON1b, and the M3 motif of GW7 was involved in the interaction between GW7 and OsTON2. The schematic shows the GW7 fragments tested for interaction using yeast two-hybrid assays.
- Supplementary Figure 10: Different transcriptional levels of starch biosynthesis genes in the developing rice endosperm between NIL-GW7TFA and NIL-gw7HJX74 plants. (45 KB)
Total RNA was extracted from the developing rice endosperms on day 9 after pollination. BEI, branching enzyme I; BEII, branching enzyme II; AGPL1, AGP large subunit; AGPL2, AGP large subunit; AGPS1, AGP small subunit; SSI, soluble starch synthase; SSIIa, soluble starch synthase; SSIIIa, soluble starch synthase; GBSS, granule-bound starch synthase; ISA1, isoamylase; PUI, pullulanase; SuSy2, sucrose synthase; UGP1, UDP-glucose pyrophosphorylase1. Expression levels are expressed as the relative copies of rice actin3, and the values are expressed relative to the level of transcript in NIL-gw7HJX74, which was set to 1. Data are shown as means ± s.e.m. (n = 3). The same lowercase letter denotes a non-significant difference between the means (P > 0.05).
- Supplementary Figure 11: The effect of GW7 transcript abundance on scanning electron microscopy images of the transverse sections of starch granules. (111 KB)
(a) NIL-gw7HJX74 plants. (b) NIL-GW7TFA endosperm comprised largely sharp-edged, compactly arranged polygonal starch granules when compared to NIL-gw7HJX74 ones. (c) Transgenic NIL-gw7HJX74 plants overexpressing the TFA GW7 cDNA driven by its native promoter.
- Supplementary Figure 12: EMSA assays. (38 KB)
(a,b) The DNA fragment (F8) containing two GATC motifs (a) or two mutated ATAC motifs (b) was incubated with GST-OsSPL16 as indicated. Competition for OsSPL16 binding was performed with 10×, 20×, 30× and 50× cold probes containing the GTAC motif.
- Supplementary Figure 13: Yeast one-hybrid assays. (45 KB)
The 0.5-kb TFA promoter fragments and mutated promoters, which contained an 18-bp deletion and/or an 11-bp insertion located in the F8 region, were used to analyze the binding activity of OsSPL16 to the GW7 promoter. Data are shown as means ± s.e.m. (n = 3). The presence of the same lowercase letter denotes a non-significant difference between the means (P > 0.05).
- Supplementary Figure 14: Appearance of the NIL grains. (74 KB)
The four contrasting allelic combinations of the qGW7 and qGW8 loci were assembled on a near-isogenic HJX74 background. Scale bar, 2 mm.
- Supplementary Figure 15: Improving appearance quality of the rice grain by QTL pyramiding. (68 KB)
The four contrasting allelic combinations of the qGW7 and qGS3 loci were assembled on a near-isogenic HJX74 background. Scale bar, 2 mm.
- Supplementary Text and Figures (4,650 KB)
Supplementary Figures 1–15 and Supplementary Tables 1–10.