A Novel and Pleiotropic Factor SLENDER GRAIN3 Is Involved in Regulating Grain Size in Rice

doi:10.1016/j.rsci.2018.02.004

Abstract

Abstract:

Grain size is frequently selected during domestication and breeding. It influences the preferences of consumers, thus affecting the commercial value of rice. In present study, a mutant named as SLENDER GRAIN3 (sg3) was identified from cultivar Zhenong 41 (Oryza sativa L. ssp. indica) with ethyl methanesulfonate (EMS) treatment. Histological analysis showed that the slender grain of sg3 mutant resulted from increased cell division longitudinally and decreased cell division horizontally. Compared with the wild type Zhenong 41, starch granules in sg3 mutant were more closely packed, thus decreasing the chalkiness. Moreover, grain yield per plant in sg3 mutant was improved by 14%. By map-based cloning, SG3 was located on the long arm of chromosome 3 with a physical distance of 82 kb, and a 9-bp deletion in the 5′-UTR of LOC_Os03g27110 was identified, which upregulated the expression level significantly. Moreover, a molecular marker for SG3 was developed to identify the grain size during the early generation breeding in rice. The novel factor SG3 regulated the grain size mainly through changing the cell division and the endosperm formation in rice.

Key words: grain size, gene mapping, phenotype analysis, rice

Zhongkang Wang, Dongdong Zeng, Ran Qin, Jialin Liu, Chunhai Shi, Xiaoli Jin. A Novel and Pleiotropic Factor SLENDER GRAIN3 Is Involved in Regulating Grain Size in Rice[J]. Rice Science, 2018, 25(3): 132-141.

Figures/Tables 6

Table 1 Comparison of agronomic traits between sg3 and wild type.

Trait	Wild type	sg3 mutant
GL (mm) (n = 30)	8.28 ± 0.12	10.13 ± 0.10**
GW (mm) (n = 30)	3.17 ± 0.12	2.60 ± 0.14**
L/W (n = 30)	2.61 ± 0.10	3.89 ± 0.17**
GT (mm) (n = 30)	2.04 ± 0.11	1.99 ± 0.14
PL (cm) (n = 10)	23.16 ± 0.57	23.50 ± 0.50
PH (cm) (n = 10)	93.37 ± 1.80	83.12 ± 1.52**
PN (n = 10)	7.33 ± 0.81	10.83 ± 0.74**
TGW (g) (n = 6)	26.07 ± 0.12	25.92 ± 0.16
NGP (n = 10)	225.33 ± 10.02	216.33 ± 12.85
SSR (%) (n = 10)	87.02 ± 3.60	77.33 ± 4.70**
YPP (g) (n = 5)	32.18 ± 1.31	36.90 ± 0.93**

Fig. 1. Comparisons of different traits between wild type (WT) and sg3 mutant. A, Mature grains. Scale bar, 1 mm. B, Mature panicles. Scale bar, 2 cm. C, Plants during anthesis. Scale bar, 10 cm. D, Chalkiness of the polished rice. Scale bar, 1 mm. E, Cross section of the polished rice. Scale bar, 1 mm. F, Degree of chalkiness. G, Amylose content. All data represent Means ± SD (n = 3). ** represents significant difference at the 0.01 level by the Student’s t-test.

Fig. 2. Spikelet hulls of wild type (WT) and sg3 mutant. A and B, Spikelets of WT and sg3 mutant, respectively. Scale bar, 2 mm. C and D, Glume outer surfaces of WT and sg3 mutant, respectively. Scale bar, 10 μm. E and F, Cross section of outer parenchyma layer from the dotted line position in A and B, respectively. Scale bar, 10 μm. G, Cell length of outer glumes. H, Cell width of outer glumes. I, Cell length of outer parenchyma layer of spikelet hulls. J, Cell size of outer parenchyma layer of spikelet hulls. All data represent Means ± SD (n = 10).

Fig. 3. Development process of rice grains of sg3 mutant and wild type (WT). A, Representative rice grains at 3 days after fertilization (DAF), 5 DAF, 7 DAF, 10 DAF and 17 DAF, respectively. Scale bar, 2 mm. B, Dry weight of rice kernel. C, Length of rice kernel. D, Width of rice kernel. All data represent Means ± SD (n = 20).

Fig. 4. Scanning electron microscope of the cross section of grains and the physiological changes of wild type (WT) and sg3 mutant. A and B, Cross section of grains. Scale bar, 100 μm. The arrows in A and B show the position of images for C to F. C and D, Starch granules in the central endosperm cell. Scale bar, 3 μm. E and F, Starch granules in the abdominal endosperm cell, Scale bar, 3 μm. G, Relative expression levels of genes related to starch biosynthesis. H, Starch content in the leaf sheath before heading. I, Net photosynthesis rate of flag leaves after heading. All data represent Means ± SD (n = 6). ** represents significant difference at the 0.01 level by the Student’s t-test.

Fig. 5. Map-based cloning of SG3. A, Primary mapping of SG3 on chromosome 3 based on 15 individuals; B, SG3 was fine-mapped to an interval of 82 kb by 591 individuals; C, Thirteen genes were annotated on the 82 kb region; D, Structure of LOC_ Os03g27110; E, Mutation locus in LOC_ Os03g27110; F, The differences in 5′-UTR region of sg3, wild type (WT) and the F2 population derived from sg3/Zhenongda 104; G, LOC_ Os03g27110 expression levels of young panicles at 3 cm in length; H, LOC_ Os03g27110 expression levels of young panicles at 5 cm in length.M, Marker. All data represent Means ± SD (n = 3). ** represents significant difference at the 0.01 level by the Student’s t-test.

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