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Summary: Tiller and seed number are key determinants of rice (Oryza sativa) yield. These traits are mainly affected by tiller, panicle, spikelet and stigma formation, but to date, no single gene involved in the development of all these organs has been identified. Here, we found a rice mutant defective stigma and panicle (dsp) with greatly reduced numbers of tillers and panicle branches, and ovaries lacking stigmas, due to defects in primordium initiation. We cloned DSP using sequencing‐based mapping and verified its function with the CRISPR/Cas9 system. DSP encodes a transcription factor containing an APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) domain that recognizes the GCC motif and a transcription‐activating domain at the site of 244–314 that contains an angiosperm‐related (AR) motif. Mutating the AR motif resulted in the dsp mutant phenotypes, whereas mutating the AP2/ERF domain led to seedling death. DSP directly regulated PINOID (PID) expression to determine the emergence of rice stigmas, and PID overexpression partially rescued the stigma defect in the dsp cr2‐8 and dsp mutants. Moreover, DSP indirectly affected LAX PANICLE1 (LAX1) expression to determine tiller primordium formation and synergistically regulated panicle primordium development. Our results indicated that DSP was a key regulator that modulated different genetic pathways to control the initiation of stigma primordia, the axillary meristem formation of tillers and panicle branches, which revealed their molecular mechanisms and cross‐networks, laying the vital foundation for rice yield and trait improvement. [ABSTRACT FROM AUTHOR]

Pentatricopeptide repeat (PPR) proteins function in post‐transcriptional regulation of organellar gene expression. Although several PPR proteins are known to function in chloroplast development in rice (Oryza sativa), the detailed molecular functions of many PPR proteins remain unclear. Here, we characterized a rice young leaf white stripe (ylws) mutant, which has defective chloroplast development during early seedling growth. Map‐based cloning revealed that YLWS encodes a novel P‐type chloroplast‐targeted PPR protein with 11 PPR motifs. Further expression analyses showed that many nuclear‐ and plastid‐encoded genes in the ylws mutant were significantly changed at the RNA and protein levels. The ylws mutant was impaired in chloroplast ribosome biogenesis and chloroplast development under low‐temperature conditions. The ylws mutation causes defects in the splicing of atpF, ndhA, rpl2, and rps12, and editing of ndhA, ndhB, and rps14 transcripts. YLWS directly binds to specific sites in the atpF, ndhA, and rpl2 pre‐mRNAs. Our results suggest that YLWS participates in chloroplast RNA group II intron splicing and plays an important role in chloroplast development during early leaf development. [ABSTRACT FROM AUTHOR]

Key message: Knock out OsABA8ox helps improve pre-harvest spouting resistance and do not affect rice yield. Pre-harvest sprouting(PHS) is a phenomenon that the seeds of crops germinate preharvest, which reduces the yield and quality of rice. Abscisic acid(ABA) is one of the phytohormones that promotes seed dormancy. ABA8' hydroxylase is the main enzyme that can catabolism ABA in plant. There are three genes that encode ABA8' hydroxylase in rice, named OsABA8ox1, OsABA8ox2 and OsABA8ox3. In this study, we use CRISPR/Cas9 gene editing technology to target these three genes in Ningjing6 and find that the knockout transgenic lines are all significantly strengthen in seed dormancy and have no effect on the yield. By a series of quantitative experiments, we consider that after knock out OsABA8ox, the high endogenous ABA level will influence the ABA signal which suppress the substantial and energy metabolism in the seeds, and finally led to higher dormancy. [ABSTRACT FROM AUTHOR]

Grain size is a key agronomic trait that determines the yield in plants. Regulation of grain size by brassinosteroids (BRs) in rice has been widely reported. However, the relationship between the BR signaling pathway and grain size still requires further study. Here, we isolated a rice mutant, named small grain2 (sg2), which displayed smaller grain and a semi‐dwarf phenotype. The decreased grain size was caused by repressed cell expansion in spikelet hulls of the sg2 mutant. Using map‐based cloning combined with a MutMap approach, we cloned SG2, which encodes a plant‐specific protein with a ribonuclease H‐like domain. SG2 is a positive regulator downstream of GLYCOGEN SYNTHASE KINASE2 (GSK2) in response to BR signaling, and its mutation causes insensitivity to exogenous BR treatment. Genetical and biochemical analysis showed that GSK2 interacts with and phosphorylates SG2. We further found that BRs enhance the accumulation of SG2 in the nucleus, and subcellular distribution of SG2 is regulated by GSK2 kinase activity. In addition, Oryza sativa OVATE family protein 19 (OsOFP19), a negative regulator of grain shape, interacts with SG2 and plays an antagonistic role with SG2 in controlling gene expression and grain size. Our results indicated that SG2 is a new component of GSK2‐related BR signaling response and regulates grain size by interacting with OsOFP19. [ABSTRACT FROM AUTHOR]

Microorganisms are the most abundant and diverse organisms in soils and have important effects on soil fertility. In this study, effects of the long-term fertilization treatments no fertilizer (CK), chemical fertilizer (nitrogen–phosphorus–potassium (NPK)), and organic–inorganic fertilizer (NPK and organic fertilizer (NPKM)) on rice yield and soil bacterial and fungal community diversity, structure, composition, and interaction networks were evaluated. Of the three treatments, the highest rice yield was in NPKM. Bacterial richness was significantly higher in NPKM than in NPK. Fertilization treatment significantly altered β diversity of communities, species composition of bacterial and fungal communities, and structure of soil microbial networks. The most complex bacterial and fungal interaction co-occurrence network with the highest average degree and numbers of edges and nodes was in NPKM. Relative abundance of the plant growth-promoting fungus Trichoderma increased significantly in NPKM compared with CK and NPK. The results of the study indicate that bacterial richness and microbial community member interactions (network complexity) might be suitable indicators of soil biological fertility. This research provides new insights on the effects of different fertilization regimes on responses of soil bacterial and fungal communities and their contributions to crop yield. New indicators such as bacterial richness and complexity of microbial interaction networks are also identified that can be used to evaluate soil biological fertility. [ABSTRACT FROM AUTHOR]

Polar auxin transport, mediated by influx and efflux transporters, controls many aspects of plant growth and development. The auxin influx carriers in A rabidopsis have been shown to control lateral root development and gravitropism, but little is known about these proteins in rice. This paper reports on the functional characterization of OsAUX 1. Three OsAUX 1 T- DNA insertion mutants and RNAi knockdown transgenic plants reduced lateral root initiation compared with wild-type ( WT) plants. OsAUX 1 overexpression plants exhibited increased lateral root initiation and OsAUX 1 was highly expressed in lateral roots and lateral root primordia. Similarly, the auxin reporter, DR5- GUS, was expressed at lower levels in osaux 1 than in the WT plants, which indicated that the auxin levels in the mutant roots had decreased. Exogenous 1-naphthylacetic acid ( NAA) treatment rescued the defective phenotype in osaux 1-1 plants, whereas indole-3-acetic acid ( IAA) and 2,4- D could not, which suggested that OsAUX 1 was a putative auxin influx carrier. The transcript levels of several auxin signalling genes and cell cycle genes significantly declined in osaux 1, hinting that the regulatory role of OsAUX 1 may be mediated by auxin signalling and cell cycle genes. Overall, our results indicated that OsAUX 1 was involved in polar auxin transport and functioned to control auxin-mediated lateral root initiation in rice. [ABSTRACT FROM AUTHOR]

Lack of seed dormancy, a major cause of pre-harvest sprouting in rice and other cereal crops, causes significant reductions in grain yield and quality. Weedy rice is often strongly dormant; therefore, quantitative trait loci (QTLs) related to seed dormancy in weedy rice "Ludao" could be useful for improving pre-harvest sprouting resistance in the important japonica variety "Ninggeng 4." To identify SD QTLs in variety Ludao, we constructed an advanced backcross population (BC6F2) of Ninggeng 4 with Ludao as the donor parent by marker-assisted backcrossing followed by SD phenotyping. The consistently detected QTL qSdr9 on chromosome 9L explained 18.09% of the phenotypic variance, and the Ludao allele decreased germination percentage by 10.78%. qSdr9 was fine-mapped to a 586.60 kb region between markers QNU9–10 and RM5777. Based on the closest linked marker for locus qSdr9, we developed near-isogenic lines with the qSdr9 allele from Ludao in Ninggeng 4 background. The qSdr9 near-isogenic lines with strong SD will be useful as parents in breeding for pre-harvest sprouting resistance. [ABSTRACT FROM AUTHOR]