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Grain weight is a key trait that determines rice quality and yield, and it is primarily controlled by quantitative trait loci (QTL). Recently, attention has been paid to minor QTLs. A minor effect QTL

Polyamines, including putrescine, spermidine, and spermine, play essential roles in a wide variety of prokaryotic and eukaryotic organisms. Rice (Oryza sativa) contains four putative spermidine/spermine synthase (SPMS)-encoding genes (OsSPMS1, OsSPMS2, OsSPMS3, and OsACAULIS5), but none have been functionally characterized. In this study, we used a reverse genetic strategy to investigate the biological function of OsSPMS1 We generated several homozygous RNA interference (RNAi) and overexpression (OE) lines of OsSPMS1 Phenotypic analysis indicated that OsSPMS1 negatively regulates seed germination, grain size, and grain yield per plant. The ratio of spermine to spermidine was significantly lower in the RNAi lines and considerably higher in the OE lines than in the wild type, suggesting that OsSPMS1 may function as a SPMS. S-Adenosyl-l-methionine is a common precursor of polyamines and ethylene biosynthesis. The 1-aminocyclopropane-1-carboxylic acid (ACC) and ethylene contents in seeds increased significantly in RNAi lines and decreased in OE lines, respectively, compared with the wild type. Additionally, the reduced germination rates and growth defects of OE lines could be rescued with ACC treatment. These data suggest that OsSPMS1 affects ethylene synthesis and may regulate seed germination and plant growth by affecting the ACC and ethylene pathways. Most importantly, an OsSPMS1 knockout mutant showed an increase in grain yield per plant in a high-yield variety, Suken118, suggesting that OsSPMS1 is an important target for yield enhancement in rice.

Background The heterotrimeric G protein β subunit RGB1 plays an important role in plant growth and development. However, the molecular mechanisms underlying the regulation of rice growth by RGB1 remain elusive. Results Here, the rgb1 mutants rgb1–1 (+ 1 bp), rgb1–2 (− 1 bp), and rgb1–3 (− 11 bp) were isolated using the CRISPR/Cas9 system, and they were arrested at 1 day after germination and ultimately exhibited seedling lethality. The dynamic anatomical characteristics of the embryos of the rgb1 seedlings and WT during early postgermination and according to TUNEL assays showed that the suppressed growth of the rgb1 mutants was caused by cell death. In addition to the limited shoot and root development, the development of the embryo shoot-root axis was suppressed in the rgb1 mutants. RGB1 was expressed mainly in the root epidermal and vascular tissues of the embryo. Moreover, transcript profiling analysis revealed that the expression of a large number of auxin-, cytokinin-, and brassinosteroid-inducible genes was upregulated or downregulated in the rgb1 mutant compared to the wild type during seedling development. Conclusions Overall, the rgb1 mutants provide an ideal material for exploring the molecular mechanism underlying rice seedling formation during early postgermination development by G proteins. Significance statement The heterotrimeric G protein β subunit RGB1 acts as a crucial factor in promoting early postgermination seedling development in rice. Electronic supplementary material The online version of this article (10.1186/s12284-019-0313-y) contains supplementary material, which is available to authorized users.

Table S1. Oligonucleotide primers and probe sequences used. (DOC 113 kb)

Figure S5. Comparison of gene expression determined by qRT-PCR and RNA-seq and relative expression of auxin signaling-related genes in the embryos of the WT and rgb1–2 mutants at 2 and 3 days after germination. (a) Comparison of relative gene expression levels determined by RNA-seq and qRT-PCR. Pearson’s test indicated a strong correlation between the two techniques (r = 0.85; p

Figure S3. Induction of RGB1 expression by NAA and measurements of the concentrations of endogenous hormones in the rgb1 mutant and WT. (a) Relative expression of RGB1 in 7-day-old wild-type seedlings grown in mock medium and in medium supplemented with 10 ÎźM NAA. (b-f) Mass spectrometric measurements of different endogenous hormones in the embryos of 3-day-old seedlings. (b) IAA, (c) BRs, (d) IPA, (e) ABA, (f) GA3. (DOCX 2663 kb)

Figure S4. Stages of seed germination and early postgermination seedlings of rice. (DOCX 4775 kb)

Table S3. Number of differentially expressed genes identified in the transcriptome analysis. (DOCX 13 kb)

Figure S2. Phenotypes and genotypes of the rgb1 mutants; relative expression of G protein genes in the embryos of the WT and rgb1 mutants. (a-d) DNA sequences and phenotypes of the WT and rgb1 mutants. (a) WT, (b) rgb1–1, (c) rgb1–2, (d) rgb1–3. Mutations are shown in red. (e) Relative expression of RGB1 in the embryos of the WT and the rgb1–1 and rgb1–2 mutant lines, as determined by qRT-PCR. The forward primer used in the qRT-PCR assays was the RGB1-Cas9 target sequence. (f-h) Relative expression of G protein family genes in the embryos of the WT and the rgb1–1 and rgb1–2 mutant lines from (f) 1-day-old seedlings, (g) 2-day-old seedlings, and (h) 3-day-old seedlings. (DOCX 2619 kb)

Figure S1. Pollen viability and embryo structures in the RGB1/rgb1 heterozygous mutant lines. (a) Pollen viability in the WT and RGB1/rgb1 heterozygous mutants (Bar = 200 μm). The pollen grains were stained with 1% I2–KI and imaged with a Leica DM 1000 light microscope. (b) Median longitudinal sections of WT and RGB1/rgb1 heterozygous mutant seeds (18 days after flowering); a plumule, b radicle. (DOCX 3952 kb)

Rice (Oryza sativa) grain shape, which is controlled by quantitative trait loci (QTL), has a strong effect on yield production and quality. However, the molecular basis for grain development remains largely unknown. In this study, we identified a novel QTL, Slender grain on chromosome 7 (SLG7), that is responsible for grain shape, using backcross introgression lines derived from 9311 and Azucena. The SLG7 allele from Azucena produces longer and thinner grains, although it has no influence on grain weight and yield production. SLG7 encodes a protein homologous to LONGIFOLIA 1 and LONGIFOLIA 2, both of which increase organ length in Arabidopsis. SLG7 is constitutively expressed in various tissues in rice, and the SLG7 protein is located in plasma membrane. Morphological and cellular analyses suggested that SLG7 produces slender grains by longitudinally increasing cell length, while transversely decreasing cell width, which is independent from cell division. Our findings show that the functions of SLG7 family members are conserved across monocots and dicots and that the SLG7 allele could be applied in breeding to modify rice grain appearance.

We constructed 128 chromosome segment substitution lines (CSSLs), derived from a cross between indica rice (Oryza sativa L.) 9311 and japonica rice Nipponbare, to investigate the genetic mechanism of heterosis. Three photo-thermo-sensitive-genic male sterile lines (Guangzhan63-4s, 036s, and Lian99s) were selected to cross with each CSSL to produce testcross populations (TCs). Field experiments were carried out in 2009, 2011, and 2015 to evaluate yield and yield-related traits in the CSSLs and TCs. Four traits (plant height, spikelet per panicle, thousand-grain weight, and grain yield per plant) were significantly related between CSSLs and TCs. In the TCs, plant height, panicle length, seed setting rate, thousand-grain weight, and grain yield per plant showed partial dominance, indicating that dominance largely contributes to heterosis of these five traits. While overdominance may be more important for heterosis of panicles per plant and spikelet per panicle. Based on the bin-maps of CSSLs and TCs, we detected 62 quantitative trait loci (QTLs) and 97 heterotic loci (HLs) using multiple linear regression analyses. Some of these loci were clustered together. The identification of QTLs and HLs for yield and yield-related traits provide useful information for hybrid rice breeding, and help to uncover the genetic basis of rice heterosis.