Effects of Chalkiness on Cooking,Eating and Nutritional Qualities of Rice in Two indica Varieties

An experiment was conducted to investigate the effects of chalkiness on cooking, eating and nutrition qualities of rice using Gangyou 527 （indica hybrid rice） and Zhaiyeqing 8 （conventional indica rice） as materials. Compared with the milled rice without chalkiness, amylose content, final viscosity, setback and consistence increased significantly, while gel consistence, peak viscosity and breakdown decreased remarkably and other RVA values did not have significant changes in the chalky rice of Gangyou 527. The differences in the above indices between the chalky and non-chalky rice was not remarkable in Zhaiyeqing 8. The crude protein content of chalky rice in Zhaiyeqing 8 was significantly lower than that of non-chalky rice, but there was no remarkable change between the chalky and non-chalky rice in Gangyou 527. Glutelin content fell significantly, and albumin, globulin, prolamine and lysine contents did not change significantly in chalky rice compared with non-chalky rice in the two varieties.

Positive Regulation of Phytochrome B on Chlorophyll Biosynthesis and Chloroplast Development in Rice

Phytochromes in rice are encoded by a gene family composed of three members, PHYA, PHYB, and PHYC. Through characterizing the phytochrome mutants and wild type （WT） in terms of photomorphogenesis, roles of individual phytochromes have been preliminarily explored in regulating rice de-etiolation, flowering time and fertility. However, little information has been reported about whether or how phytochromes affect chlorophyll biosynthesis and chloroplast development in rice. In this study, we compared the chlorophyll contents of wild type and the phyA, phyB and phyAphyB mutants grown under either white light （WL） or red light （R）. The results suggest that phyB perceives R to positively regulate chlorophyll biosynthesis, while the role of phyA can be detected only in the phyB-deficient mutant. Analyses of the expression levels of genes involved in chlorophyll biosynthesis revealed that phytochromes affected the chlorophyll biosynthesis by regulating protochlorophyll oxidoreductase A （PORA） expression. The role of phyB in chloroplast development was also analyzed, and the results suggest that phyB perceives R to regulate chloroplast development by affecting the numbers of chloroplasts and grana, as well as the chloroplast membrane system.

OsSRK1,an Atypical S-Receptor-Like Kinase Positively Regulates Leaf Width and Salt Tolerance in Rice

Receptor-like kinases(RLKs)are important for plant growth,development and defense responses.The S-receptor protein kinases(SRKs),which represent an RLK subfamily,control the selfincompatibility among Brassica species.However,little information is available regarding SRK functions in rice.We identified a gene OsSRK1 encoding an atypical SRK.The transcript of OsSRK1 was induced by abscisic acid(ABA),salt and polyethylene glycol.OsSRK1 localized to the plasma membrane and cytoplasm.Leaf width was increased in OsSRK1-overexpression(OsSRK1-OX)transgenic rice plants,likely because of an increase in cell number per leaf.Furthermore,the expression levels of OsCYCA3-1 and OsCYCD2-1,which encode positive regulators of cell division,were up-regulated in leaf primordium of OsSRK1-OX rice plants relative to those in wild type.Meanwhile,the expression level of OsKRP1,which encodes cell cycle inhibitor,was down-regulated in the OsSRK1-OX plants.Therefore,it is deduced that OsSRK1 regulates leaf width by promoting cell division in the leaf primordium.Additionally,OsSRK1-OX plants exhibited enhanced ABA sensitivity and salt tolerance compared with wild type.These results suggest that OsSRK1 plays important roles in leaf development and salt responses in rice.

RNAi-mediated suppression of the abscisic acid catabolism gene Os ABA8ox1 increases abscisic acid content and tolerance to saline–alkaline stress in rice(Oryza sativa L.)

Saline–alkaline(SA) stress is characterized by high salinity and high alkalinity(high p H), which severely inhibit plant growth and cause huge losses in crop yields worldwide. Here we show that a moderate elevation of endogenous abscisic acid(ABA) levels by RNAi-mediated suppression of Os ABA8 ox1(Os ABA8 ox1-kd), a key ABA catabolic gene, significantly increased tolerance to SA stress in rice plants. We produced Os ABA8 ox1-kd lines in two different japonica cultivars, Dongdao 4 and Nipponbare. Compared with nontransgenic control plants(WT), the Os ABA8 ox1-kd seedlings accumulated 25.9%–55.7% higher levels of endogenous ABA and exhibited reduced plasmalemma injury, ROS accumulation and Na;/K;ratio, and higher survival rates, under hydroponic alkaline conditions simulated by 10, 15, and 20 mmol L-1 of Na;CO;. In pot trials using SA field soils of different alkali levels(p H 7.59, 8.86, and 9.29), Os ABA8 ox1–kd plants showed markedly higher seedling survival rates and more vigorous plant growth, resulting in significantly higher yield components including panicle number(85.7%–128.6%), spikelets per panicle(36.9%–61.9%), branches(153.9%–236.7%), 1000–kernel weight(20.0%–28.6%), and percentage of filled spikelets(96.6%–1340.8%) at harvest time. Under severe SA soil conditions(p H = 9.29, EC = 834.4 μS cm-1),Os ABA8 ox1-kd lines showed an 194.5%–1090.8% increase in grain yield per plant relative to WT plants.These results suggest that suppression of Os ABA8 ox1 to increase endogenous ABA levels provides a new molecular approach for improving rice yield in SA paddies.

Phenotypic analysis and molecular characterization of an allelic mutant of the D61 gene in rice

Brassinosteroids(BRs) are a class of plant-specific steroidal hormones that play important roles in multiple biological processes. In this paper, a classic rice mutant gsor300084,showing erect leaves and semi-dwarf stature, was characterized. Morphological analysis in darkness showed that the mesocotyl of the gsor300084 mutant did not elongate when grown in darkness. Coleoptile elongation and root growth were less affected by the exogenous application of brassinolide(BL), the most active form of BR, in gsor300084 than in the wild-type rice variety Matsumae. Lamina joint bending analysis also showed that gsor300084 was less sensitive to exogenous BL than Matsumae. These results suggested that the gsor300084 mutant is defective in BR sensitivity. Map-based cloning indicated that gsor300084 is a novel allelic mutant of the DWARF61(D61) gene, which encodes the putative BR receptor OsBRI1. A single-base mutation appears in the LRR domain of OsBRI1, changing the 444 th amino acid from tryptophan(W) to arginine(R). Subcellular localization analysis suggested that both the wild-type and mutant OsBRI1 protein are localized at the cytoplasmic membrane. Structure modeling revealed that the W444 R substitution may affect the perception of BRs by the LRR domain.

Cloning and Expression of Gene Responsible for High-Tillering Dwarf Phenotype in Indica Rice Mutant gsor23

High-tillering dwarf mutant gsor23 was generated from an indica rice variety Indica9 radiatied by y-ray. Genetic analysis showed that this phenotype was controlled by one single recessive gene, which was mapped within a physical distance of 386 kb between two insertion-deletion （InDel） markers CI-WT2 and C1-WT4 on the long arm of chromosome 1. There is a known gene DIO within this region, the mutation of which causes high-tillering in rice. Sequence analysis of the DIO allele in gsor23 revealed that the base cytosine （C） at the 404th position in the coding region was deleted, which would cause frameshift mutation after the 134th amino acids. The mutation site and indica background of gsor23 were different from the previously reported japonica mutants d10-1 and d10-2. Therefore, gsor23 is a novel allelic mutant of D10 which encodes the carotenoid-cleaving dioxygenase 8 （CCD8）, a key enzyme involved in the biosynthesis of the new plant hormone strigolactones （SLs）. After treatment with GR24, a synthetic analogue of SLs, the high-tillering phenotype of gsor23 was restored to normal. Real-time RT-PCR analysis showed that D10 expression was high in roots, but low in leaves. Compared with the wild type Indica9, the expression of the SL biosynthesis gene DIO was upregulated, while genes likely involved in the SL signal transduction pathway such as D3 and D14 were down-regulated in the gsor23 mutant.

QTL Detection and Epistasis Analysis for Heading Date Using Single Segment Substitution Lines in Rice(Oryza sativa L.)

Heading date of rice is a key agronomic trait determining cultivated areas and seasons and affecting yield. In the present study, ifve primary single segment substitution lines with the same genetic background were used to detect quantitative trait loci （QTLs） for heading date in rice. Two QTLs, qHD3 and qHD6 on the short arm of chromosome 3 and the short arm of chromosome 6, respectively, were identiifed under natural long-day （NLD）. Nineteen secondary single segment substitution lines （SSSLs） and seven double segments pyramiding lines were designed to map the two QTLs and to evaluate their epistatic interaction between them. By overlapping mapping, qHD3 was mapped in a 791-kb interval between SSR markers RM3894 and RM569 and qHD6 in a 1 125-kb interval between RM587 and RM225. Results revealed the existence of epistatic interaction between qHD3 and qHD6 under natural long-day （NLD）. It was also found that qHD3 and qHD6 had signiifcant effects on plant height and yield traits, indicating that both of the QTLs have pleiotropic effects.

Effects of Different Planting Densities on the Yield of Rice Developed from Seedlings Dry Raised in Plug Trays

[Objectives]This study was conducted to investigate the effects of different planting densities on rice tillering dynamics and yield. [Methods]The effects of different planting densities on rice yield were studied based on seedlings dry raised in plug trays. [Results]Planting density had obvious effects on tillering dynamics,number of panicles per unit area,number of grains per panicle and rice yield under the condition of seedlings dry raised in plug trays. Comprehensive analysis showed that the row spacing × hill spacing = 25 cm × 14 cm,that is,the planting density of 2. 85 × 10~5 hills/hm^2,achieved the highest yield,at 9 960 kg/hm^2. [Conclusions]This study provides a scientific basis for optimizing rice cultivation techniques and achieving high yield and high efficiency in rice production.

Comparative transcriptome analysis of abalone Haliotis discus hannai with green and gray egg colors

Haliotis discus hannai is an important marine economic species in China.Its egg color was found to be associated with economic traits,which provides a new idea for breeding.However,the molecular mechanism of the egg-color formation has not been reported.Thus,the pigment composition and comparative transcriptome analyses of H.discus hannai with green and gray egg color were conducted using high-performance liquid chromatography(HPLC)and RNA-Seq methods.Results show that individuals with green and gray eggs both possess the fucoxanthin.Lutein existed in gray-egged individuals,but not in green-egged individuals.In transcriptome analysis,272310 unigenes were received from 461162 transcripts with a mean length of 985 bp and N50 of 1524 bp,respectively.A total of 185 unigenes were identifi ed as diff erentially expressed genes(DEGs).The DEGs involved in“fl avin-containing compound metabolic process”,“melanosome”,“glutathione metabolism”,and“cytochrome b6f complex”were likely related to the formation of the egg color.Our results provide foundational information for the functional analysis of egg-color related genes and are benefi cial to the selective breeding of H.discus hannai.

Hydrogen Peroxide-Mediated Growth of the Root System Occurs via Auxin Signaling Modification and Variations in the Expression of Cell-Cycle Genes in Rice Seedlings Exposed to Cadmium Stress

The link between root growth, H2O2, auxin signaling, and the ceil cycle in cadmium （Cd）-stressed rice （Oryza sativa L. cv. Zhonghua No. 11） was analyzed in this study. Exposure to Cd induced a significant accumulation of Cd, but caused a decrease in zinc （Zn） content which resulted from the decreased expression of OsHMA9 and OsZIP. Analysis using a Cd-specific probe showed that Cd was mainly localized in the meristematic zone and vascular tissues. Formation and elongation of the root system were significantly promoted by 3-amino-l,2,4-triazole （AT）, but were markedly inhibited by N,N＇. dimethylthiourea （DMTU） under Cd stress. The effect of H2O2 on Cd-stressed root growth was further confirmed by examining a gain-of-function rice mutant （carrying catalasel and glutathione-S-transferase） in the presence or absence of diphenylene iodonium. DR5-GUS staining revealed close associations between H2O2 and the concentration and distribution of auxin. H2O2 affected the expression of key genes, including OsYUCCA, OsPIN, OsARF, and OslAA, in the auxin signaling pathway in Cd-treated plants. These results suggest that H2O2 functions upstream of the auxin signaling pathway. Furthermore, H2O2 modified the expression of cell-cycle genes in Cd-treated roots. The effects of H2O2 on root system growth are therefore linked to auxin signal modification and to variations in the expression of cell-cycle genes in Cd-stressed rice. A working model for the effects of H2O2 on Cd-stressed root system growth is thus proposed and discussed in this paper.

Phenotypic Characterization, Genetic Analysis and Gene-mapping for a Brittle Mutant in Rice

Plant mechanical strength is an important agronomic trait of rice. An ethyl methane sulfonate （EMS）-induced rice mutant, fragile plant 2 （fp2）, showed morphological changes and reduced mechanical strength. Genetic analysis indicated that the brittle of fp2 was controlled by a recessive gene. The fp2 gene was mapped on chromosome 10. Anatomical analyses showed that the fp2 mutation caused the reduction of cell length and cell wall thickness, increasing of cell width, and the alteration of cell wall structure as well as the vessel elements. The consequence was a global alteration in plant morphology. Chemical analyses indicated that the contents of cellulose and lignin decreased, and hemicelluloses and silicon increased in fp2. These results were different from the other mutants reported in rice. Thus, fp2 might affect the deposition and patterning of microflbrils, the biosynthesis and deposition of cell wall components, which influences the formation of primary and secondary cell walls, the thickness of cell walls, cell elongation and expansion, plant morphology and plant strength in rice.

Overexpression of OsPIL15, a phytochrome-interacting factor-like protein gene, represses etiolated seedling growth in rice

Phytochrome-interacting factors （PIFs） regulate an array of developmental responses ranging from seed germi- nation to vegetational architecture in Arabidopsis. However, information regarding the functions of the PIF family in monocots has not been widely reported. Here, we investigate the roles of OsPIL15, a member of the rice （Oryza sativa L. cv. Nipponbare） PIF family, in regulating seedling growth. OsPIL15 encodes a basic helix-loop-helix factor localized in the nucleus. OsPIL15-OX seedlings exhibit an exaggerated shorter above- ground part and undeveloped root system relative to wild-type seedlings, suggesting that OsPIL15 represses seedling growth in the dark. Microarray analysis combined with gene ontology analysis revealed that OsPIL15 represses a set of genes involved in auxin pathways and cell wall organization or biogenesis. Given the important roles of the auxin pathway and cell wall properties in controlling plant growth, we speculate that OsPIL15 represses seedling growth likely by regulating the auxin pathway and suppressing cell wall organization in etiolated rice seedlings. Additionally, exposure to red light or far-red light relieved growth retardation and promoted seedling elongation in the OsPIL15-OX lines, despite higher levels of OsPIL15 transcripts under red light and far-red light than in the dark. These results suggest that light regulation of OsPIL15 expres- sion is probably involved in photomorphogenesis in rice.

The Ghd7 transcription factor represses ARE1 expression to enhance nitrogen utilization and grain yield in rice

The genetic improvement of nitrogen use efficiency(NUE)of crops is vital for grain productivity and sustainable agriculture.However,the regulatory mechanism of NUE remains largely elusive.Here,we report that the rice Grain number,plant height,and heading date7(Ghd7)gene genetically acts upstream of ABC1 REPRESSOR1(ARE1),a negative regulator of NUE,to positively regulate nitrogen utilization.As a transcriptional repressor,Ghd7 directly binds to two Evening Element-like motifs in the promoter and intron 1 of ARE1,likely in a cooperative manner,to repress its expression.Ghd7 and ARE1 display diurnal expression patterns in an inverse oscillation manner,mirroring a regulatory scheme based on these two loci.Analysis of a panel of 2656 rice varieties suggests that the elite alleles of Ghd7 and ARE1 have undergone diversifying selection during breeding.Moreover,the allelic distribution of Ghd7 and ARE1 is associated with the soil nitrogen deposition rate in East Asia and South Asia.Remarkably,the combination of the Ghd7 and ARE1 elite alleles substantially improves NUE and yield performance under nitrogen-limiting conditions.Collectively,these results define a Ghd7–ARE1-based regulatory mechanism of nitrogen utilization,providing useful targets for genetic improvement of rice NUE.

MIT1, encoding a 15-cis-ζ-carotene isomerase, regulates tiller number and stature in rice

Lateral branching is an important determinant of shoot architecture and crop yield. The plant hormone strigolactone (SL) inhibits lateral bud outgrowth in various plant species. Deficiencies in SL biosynthesis and signal transduction result in excessive outgrowth of lateral buds (Stirnberg et al., 2002;Sorefan et al., 2003).

The rice histone methylation regulates hub species of the root microbiota

Plants have a close relationship with their root microbiota,which comprises a complex microbial network.Histone methylation is an important epigenetic modification influencing multiple plant traits;however,little is known about the role of plant histone methylation in the assembly and network structure of the root microbiota.In this study,we established that the rice(Oryza sativa)histone methylation regulates the structure and composition of the root microbiota,especially the hub species in the microbial network.DJjmj703(defective in histone H3K4 demethylation)and ZH11-sdg714(defective in H3K9 methylation)showed significant different root microbiota compared with the corresponding wild types at the phylum and family levels,with a consistent increase in the abundance of Betaproteobacteria and a decrease in the Firmicutes.In the root microbial network,35 of 44 hub species in the top 10 modules in the tested field were regulated by at least one histone methylation-related gene.These observations establish that the rice histone methylation plays a pivotal role in regulating the assembly of the root microbiota,providing insights into the links between plant epigenetic regulation and root microbiota.