Strategies for developing Green Super Rice

Identification of putative markers linked to grain plumpness in rice (Oryza sativa L.) via association mapping

BACKGROUND

Poor grain plumpness (GP) is one of the main constraints to reaching the yield potential of hybrid rice.

RESULTS

In this study, the GP of 177 rice varieties was investigated in three locations across 2 years. By combining the genotype data of 261 simple sequence repeat (SSR) markers, association mapping was conducted to identify the marker-GP association loci. Among 31 marker-GP association loci detected in two or more environments and determined using general linear model (GLM) analyses, seven association loci were also detected using mixed linear model (MLM) analyses. The seven common loci detected by the two analytical methods were located on chromosomes 2, 3 (2), 7, 8 and 12 (2) and explained 7.24~22.28% of the variance. Of these 7 association loci, five markers linked to GP were newly detected: RM5340 on Chr2, RM5480 and RM148 on Chr3, RM1235 on Chr8, and RM5479 on Chr12.

CONCLUSIONS

Five marker-GP association loci were newly detected using both the GLM and MLM analytical methods. Elite allele RM505-170 bp had the highest average phenotypic effect on increasing the GP, and the typical carrier variety was 'Maozitou'. Based on the distribution of the elite alleles among the carrier varieties, the top 10 parental combinations for improving the GP in rice via cross-breeding were predicted.

Resistance Genes in Global Crop Breeding Networks

Resistance genes are a major tool for managing crop diseases. The networks of crop breeders who exchange resistance genes and deploy them in varieties help to determine the global landscape of resistance and epidemics, an important system for maintaining food security. These networks function as a complex adaptive system, with associated strengths and vulnerabilities, and implications for policies to support resistance gene deployment strategies. Extensions of epidemic network analysis can be used to evaluate the multilayer agricultural networks that support and influence crop breeding networks. Here, we evaluate the general structure of crop breeding networks for cassava, potato, rice, and wheat. All four are clustered due to phytosanitary and intellectual property regulations, and linked through CGIAR hubs. Cassava networks primarily include public breeding groups, whereas others are more mixed. These systems must adapt to global change in climate and land use, the emergence of new diseases, and disruptive breeding technologies. Research priorities to support policy include how best to maintain both diversity and redundancy in the roles played by individual crop breeding groups (public versus private and global versus local), and how best to manage connectivity to optimize resistance gene deployment while avoiding risks to the useful life of resistance genes. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Regulation of Gene Expression in the Remobilization of Carbon Reserves in Rice Stems During Grain Filling

Carbon reserves in rice straw (stem and sheath) before flowering contribute to a significant portion of grain filling. However, the molecular mechanism of carbon reserve remobilization from straw to grains remains unclear. In this study, super rice LYP9 and conventional rice 9311 showed different carbon reserve remobilization behaviors. The transcriptomic profiles of straws of LYP9 and 9311 were analyzed at three stages of grain filling. Among the differentially expressed genes (DGs), 5,733 genes were uniquely up- or down-regulated at 30 days after anthesis (DAA) between LYP9 and 9311 in comparison with 681 at 10 DAA and 495 at 20 DAA, suggesting that the gene expression profile of LYP9 was very different from that of 9311 at the late stage of grain filling. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Gene Ontology (GO) classification of DGs both showed that the carbohydrate catabolic pathway, plant hormone signal transduction and photosynthesis pathway were enriched in DGs, suggesting their roles in carbon reserve remobilization, which explains to a certain extent the difference in non-structural carbohydrate content, photosynthesis and ABA content between the two cultivars during grain filling. Further comparative analysis and confirmation by quantitative real-time PCR and enzyme assays suggest that genes involved in trehalose synthesis (trehalose-phosphate phosphatase and trehalose 6-phosphate synthase/phosphatase), starch degradation (β-amylase) and sucrose synthesis (sucrose-phosphate synthase and sucrose synthase) were important for carbon reserve remobilization, whereas ABA content was determined by the counteraction of NCED1 and ABA8ox1 genes. The higher expression level of all these genes and ABA content in 9311 resulted in better efficiency of carbon reserve remobilization in 9311 than in LYP9.

Root Transcriptomic Analysis Revealing the Importance of Energy Metabolism to the Development of Deep Roots in Rice (Oryza sativa L.)

Drought is the most serious abiotic stress limiting rice production, and deep root is the key contributor to drought avoidance. However, the genetic mechanism regulating the development of deep roots is largely unknown. In this study, the transcriptomes of 74 root samples from 37 rice varieties, representing the extreme genotypes of shallow or deep rooting, were surveyed by RNA-seq. The 13,242 differentially expressed genes (DEGs) between deep rooting and shallow rooting varieties (H vs. L) were enriched in the pathway of genetic information processing and metabolism, while the 1,052 DEGs between the deep roots and shallow roots from each of the plants (D vs. S) were significantly enriched in metabolic pathways especially energy metabolism. Ten quantitative trait transcripts (QTTs) were identified and some were involved in energy metabolism. Forty-nine candidate DEGs were confirmed by qRT-PCR and microarray. Through weighted gene co-expression network analysis (WGCNA), we found 18 hub genes. Surprisingly, all these hub genes expressed higher in deep roots than in shallow roots, furthermore half of them functioned in energy metabolism. We also estimated that the ATP production in the deep roots was faster than shallow roots. Our results provided a lot of reliable candidate genes to improve deep rooting, and firstly highlight the importance of energy metabolism to the development of deep roots.

Accurate Digitization of the Chlorophyll Distribution of Individual Rice Leaves Using Hyperspectral Imaging and an Integrated Image Analysis Pipeline

Pigments absorb light, transform it into energy, and provide reaction sites for photosynthesis; thus, the quantification of pigment distribution is vital to plant research. Traditional methods for the quantification of pigments are time-consuming and not suitable for the high-throughput digitization of rice pigment distribution. In this study, using a hyperspectral imaging system, we developed an integrated image analysis pipeline for automatically processing enormous amounts of hyperspectral data. We also built models for accurately quantifying 4 pigments (chlorophyll a, chlorophyll b, total chlorophyll and carotenoid) from rice leaves and determined the important bands (700-760 nm) associated with these pigments. At the tillering stage, the R2 values and mean absolute percentage errors of the models were 0.827-0.928 and 6.94-12.84%, respectively. The hyperspectral data and these models can be combined for digitizing the distribution of the chlorophyll with high resolution (0.11 mm/pixel). In summary, the integrated hyperspectral image analysis pipeline and selected models can be used to quantify the chlorophyll distribution in rice leaves. The use of this technique will benefit rice functional genomics and rice breeding.

Characterizing roots and water uptake in a ground cover rice production system

Background and aims

Water-saving ground cover rice production systems (GCRPS) are gaining popularity in many parts of the world. We aimed to describe the characteristics of root growth, morphology, distribution, and water uptake for a GCRPS.

Methods

A traditional paddy rice production system (TPRPS) was compared with GCRPS in greenhouse and field experiments. In the greenhouse, GCRPS where root zone average soil water content was kept near saturation (GCRPS_sat), field capacity (GCRPS_fwc) and 80% field capacity (GCRPS_80%), were evaluated. In a two-year field experiment, GCRPS_sat and GCRPS_80% were applied.

Results

Similar results were found in greenhouse and field experiments. Before mid-tillering the upper soil temperature was higher for GCRPS, leading to enhanced root dry weight, length, surface area, specific root length, and smaller diameter of roots but lower water uptake rate per root length compared to TPRPS. In subsequent growth stages, the reduced soil water content under GCRPS caused that the preponderance of root growth under GCRPS_sat disappeared in comparison to TPRPS. Under other GCRPS treatments (GCRPS_fwc and GCRPS_80%), significant limitation on root growth, bigger root diameter and higher water uptake rate per root length were found.

Conclusions

Discrepancies in soil water and temperature between TPRPS and GCRPS caused adjustments to root growth, morphology, distribution and function. Even though drought stress was inevitable after mid-tillering under GCRPS, especially GCRPS_80%, similar or even enhanced root water uptake capacity in comparison to TPRPS might promote allocation of photosynthetic products to shoots and increase water productivity.

SesameFG: an integrated database for the functional genomics of sesame

Sesame (Sesamum indicum L.) has high oil content, a small diploid genome and a short growth period, making it an attractive species for genetic studies on oilseed crops. With the advancement of next-generation sequencing technology, genomics and functional genomics research of sesame has developed quickly in the last few years, and large amounts of data have been generated. However, these results are distributed in many different publications, and there is a lack of integration. To promote functional genomics research of sesame, we collected genetic information combined with comprehensive phenotypic information and integrated them in the web-based database named SesameFG. The current version of SesameFG contains phenotypic information on agronomic traits of 705 sesame accessions, de novo assembled genomes of three sesame varieties, massive numbers of identified SNPs, gene expression profiles of five tissues, gene families, candidate genes for the important agronomic traits and genomic-SSR markers. All phenotypic and genotypic information in SesameFG is available for online queries and can be downloaded freely. SesameFG provides useful search functions and data mining tools, including Genome Browser and local BLAST services. SesameFG is freely accessible at http://ncgr.ac.cn/SesameFG/. SesameFG provides valuable resources and tools for functional genomics research and the molecular breeding of sesame.

Advances in understanding broad-spectrum resistance to pathogens in rice

Rice diseases caused by multiple pathogen species are a major obstacle to achieving optimal yield. Using host pathogen species-non-specific broad-spectrum resistance (BSR) for rice improvement is an efficient way to control diseases. Recent advances in rice genomics and improved understanding of the mechanisms of rice-pathogen interactions have shown that using a single gene to improve rice BSR to multiple pathogen species is technically possible and the necessary resources exist. A variety of rice genes, including major disease resistance genes and defense-responsive genes, which function in pattern-triggered immunity signaling, effector-triggered immunity signaling or quantitative resistance, can mediate BSR to two or more pathogen species independently. These genes encode diverse proteins and function differently in promoting disease resistance, thus providing a relatively broad choice for different breeding programs. This updated knowledge will facilitate rice improvement with pathogen species-non-specific BSR via gene marker-assisted selection or biotechnological approaches.

Overexpression of the 16-kDa α-amylase/trypsin inhibitor RAG2 improves grain yield and quality of rice

Increasing grain yield and improving grain quality are two important goals for rice breeding. A better understanding of the factors that contribute to the overall grain quantity and nutritional quality of rice will lay the foundation for developing new breeding strategies. RAG2 is a member of 14-to-16-kDa α-amylase/trypsin inhibitors in rice, which belong to the albumin of seed storage proteins. We found that RAG2 was specifically expressed in ripening seed and its transcription peak was between 14 and 21 days after flowering. Grain size and 1000-grain weight were obviously increased in RAG2-overexpressed lines compared with wild type, and grain size was reduced in RAG2-suppressed lines. In addition, the major storage substances of the seeds differed significantly in RAG2-overexpressed and RAG2-suppressed lines compared to wild type. The protein content and amount of total lipids were increased and decreased, respectively, in the seeds of RAG2-overexpressed and RAG2-suppressed lines. Overexpression of RAG2 significantly increased grain size and improved grain quality and yield simultaneously. These results imply that RAG2 might play an important role in regulating grain weight and seed quality of rice. The functional characterization of rice RAG2 facilitates a further understanding of the mechanisms involved in grain size and seed quality and may be helpful in improving grain yield and quantity in cereal crops.

Functional Roles of microRNAs in Agronomically Important Plants-Potential as Targets for Crop Improvement and Protection

MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses toward environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic-or abiotic origin.

Rational design of high-yield and superior-quality rice

Rice (Oryza sativa L.) is a staple food for more than half of the world's population. To meet the ever-increasing demand for food, because of population growth and improved living standards, world rice production needs to double by 2030¹. The development of new elite rice varieties with high yield and superior quality is challenging for traditional breeding approaches, and new strategies need to be developed. Here, we report the successful development of new elite varieties by pyramiding major genes that significantly contribute to grain quality and yield from three parents over five years. The new varieties exhibit higher yield potential and better grain quality than their parental varieties and the China's leading super-hybrid rice, Liang-you-pai-jiu (LYP9 or Pei-ai 64S/93-11). Our results demonstrate that rational design is a powerful strategy for meeting the challenges of future crop breeding, particularly in pyramiding multiple complex traits.

Complementary Proteome and Transcriptome Profiling in Developing Grains of a Notched-Belly Rice Mutant Reveals Key Pathways Involved in Chalkiness Formation

Rice grain chalkiness is a highly complex trait involved in multiple metabolic pathways and controlled by polygenes and growth conditions. To uncover novel aspects of chalkiness formation, we performed an integrated profiling of gene activity in the developing grains of a notched-belly rice mutant. Using exhaustive tandem mass spectrometry-based shotgun proteomics and whole-genome RNA sequencing to generate a nearly complete catalog of expressed mRNAs and proteins, we reliably identified 38,476 transcripts and 3,840 proteins. Comparison between the translucent part and chalky part of the notched-belly grains resulted in only a few differently express genes (240) and differently express proteins (363), thus making it possible to focus on 'core' genes or common pathways. Several novel key pathways were identified as of relevance to chalkiness formation, in particular the shift of C and N metabolism, the down-regulation of ribosomal proteins and the resulting low abundance of storage proteins especially the 13 kDa prolamin subunit, and the suppressed photosynthetic capacity in the pericarp of the chalky part. Further, genes and proteins as transporters for carbohydrates, amino acid/peptides, proteins, lipids and inorganic ions showed an increasing expression pattern in the chalky part of the notched-belly grains. Similarly, transcripts and proteins of receptors for auxin, ABA, ethylene and brassinosteroid were also up-regulated. In summary, this joint analysis of transcript and protein profiles provides a comprehensive reference map of gene activity regarding the physiological state in the chalky endosperm.

Constitutive expression of a plant ferredoxin-like protein (pflp) enhances capacity of photosynthetic carbon assimilation in rice (Oryza sativa)

The plant ferredoxin-like protein (PFLP) gene, cloned from sweet peppers predicted as an electron carrier in photosynthesis, shows high homology to the Fd-I sequence of Arabidopsis thaliana, Lycopersicon esculentum, Oryza sativa and Spinacia oleracea. Most of pflp related studies focused on anti-pathogenic effects, while less understanding for the effects in photosynthesis with physiological aspects, such as photosynthesis rate, and levels of carbohydrate metabolites. This project focuses on the effects of pflp overexpression on photosynthesis by physiological evaluations of carbon assimilation with significant higher levels of carbohydrates with higher photosynthesis efficiency. In this report, two independent transgenic lines of rice plants (designated as pflp-1 and pflp-2) were generated from non-transgenic TNG67 rice plant (WT). Both transgenic pflp rice plants exhibited enhanced photosynthesis efficiency, and gas exchange rates of photosynthesis were 1.3- and 1.2-fold higher for pflp-1 and pflp-2 than WT respectively. Significantly higher electron transport rates of pflp rice plants were observed. Moreover, photosynthetic products, such as fructose, glucose, sucrose and starch contents of pflp transgenic lines were increased accordingly. Molecular evidences of carbohydrate metabolism related genes activities (osHXK5, osHXK6, osAGPL3, osAGPS2α, osSPS, ospFBPase, oscFBPase, and osSBPase) in transgenic lines were higher than those of WT. For performance of crop production, 1000-grain weight for pflp-1 and pflp-2 rice plants were 52.9 and 41.1 g that were both significantly higher than 31.6 g for WT, and panicles weights were 1.4- and 1.2-fold higher than WT. Panicle number, tiller number per plants for pflp rice plants were all significantly higher compared with those of WT where there was no significant difference observed between two pflp rice plants. Taken altogether; this study demonstrated that constitutive pflp expression can improve rice production by enhancing the capacity of photosynthetic carbon assimilation.

Changes in Rice Grain Quality of Indica and Japonica Type Varieties Released in China from 2000 to 2014

China is the first country to use heterosis successfully for commercial rice production. This study compared the main quality characteristics (head rice rate, chalky rice rate, chalkiness degree, gel consistency, amylose content, and length-to-width ratio) of 635 rice varieties (not including upland and glutinous rice) released from 2000 to 2014 to establish the quality status and offer suggestions for future rice breeding for grain quality in China. In the past 15 years, grain quality in japonica rice and indica hybrid rice has improved. In japonica rice, inbred varieties have increased head rice rates and decreased chalkiness degree over time, while hybrid rice varieties have decreased chalky rice rates and chalkiness degree. In indica hybrid rice, the chalkiness degree and amylose contents have decreased and gel consistency has increased. Improvements in grain quality in indica inbred rice have been limited, with some increases in head rice rate and decreases in chalky rice rate and amylose content. From 2010 to 2014, the percentage of indica varieties meeting the Grade III national standard of rice quality for different quality traits was low, especially for chalky rice rate and chalkiness degree. Japonica varieties have more superior grain quality than indica rice in terms of higher head rice rates and gel consistency, lower chalky rice rates and chalkiness degree, and lower amylose contents, which may explain why the Chinese prefer japonica rice. The japonica rice varieties, both hybrid and inbred, had similar grain qualities, but this varied in indica rice with the hybrid varieties having higher grain quality than inbred varieties due to significantly better head rice rates and lower chalkiness degree. For better quality rice in future, the chalky rice rate and chalkiness degree should be improved in japonica rice along with most of the quality traits in indica rice.

OsSAPK2 Confers Abscisic Acid Sensitivity and Tolerance to Drought Stress in Rice

SNF 1-RELATED PROTEIN KINASE 2 (SnRK2) is a family of plant-specific protein kinases which is the key regulator of hyper-osmotic stress signaling and abscisic acid (ABA)-dependent development in various plants. Among the rice subclass-I and -II SnRK2s, osmotic stress/ABA-activated protein kinase 2 (SAPK2) may be the primary mediator of ABA signaling. However, SAPK2 has not been comprehensively characterized. In this study, we elucidated the functional properties of SAPK2 using loss-of-function mutants produced with the CRISPR/Cas9 system. The SAPK2 expression level was strongly upregulated by drought, high-salinity, and polyethylene glycol (PEG) treatments. The sapk2 mutants exhibited an ABA-insensitive phenotype during the germination and post-germination stages, suggesting that SAPK2 had a pivotal role related to ABA-mediated seed dormancy. The sapk2 mutants were more sensitive to drought stress and reactive oxygen species (ROS) than the wild-type plants, indicating that SAPK2 was important for responses to drought conditions in rice. An additional investigation revealed that SAPK2 increased drought tolerance in the following two ways: (i) by reducing water loss via the accumulation of compatible solutes, promoting stomatal closure, and upregulating the expression levels of stress-response genes such as OsRab16b, OsRab21, OsbZIP23, OsLEA3, OsOREB1 and slow anion channel (SLAC)-associated genes such as OsSLAC1 and OsSLAC7; (ii) by inducing the expression of antioxidant enzyme genes to promote ROS-scavenging abilities that will ultimately decrease ROS damages. Moreover, we also observed that SAPK2 significantly increased the tolerance of rice plants to salt and PEG stresses. These findings imply that SAPK2 is a potential candidate gene for future crop improvement studies.

OsSGL, a Novel DUF1645 Domain-Containing Protein, Confers Enhanced Drought Tolerance in Transgenic Rice and Arabidopsis

Drought is a major environmental factor that limits plant growth and crop productivity. Genetic engineering is an effective approach to improve drought tolerance in various crops, including rice (Oryza sativa). Functional characterization of relevant genes is a prerequisite when identifying candidates for such improvements. We investigated OsSGL (Oryza sativa Stress tolerance and Grain Length), a novel DUF1645 domain-containing protein from rice. OsSGL was up-regulated by multiple stresses and localized to the nucleus. Transgenic plants over-expressing or hetero-expressing OsSGL conferred significantly improved drought tolerance in transgenic rice and Arabidopsis thaliana, respectively. The overexpressing plants accumulated higher levels of proline and soluble sugars but lower malondialdehyde (MDA) contents under osmotic stress. Our RNA-sequencing data demonstrated that several stress-responsive genes were significantly altered in transgenic rice plants. We unexpectedly observed that those overexpressing rice plants also had extensive root systems, perhaps due to the altered transcript levels of auxin- and cytokinin-associated genes. These results suggest that the mechanism by which OsSGL confers enhanced drought tolerance is due to the modulated expression of stress-responsive genes, higher accumulations of osmolytes, and enlarged root systems.

Emergence of a Novel Chimeric Gene Underlying Grain Number in Rice

Grain number is an important factor in determining grain production of rice (Oryza sativa L.). The molecular genetic basis for grain number is complex. Discovering new genes involved in regulating rice grain number increases our knowledge regarding its molecular mechanisms and aids breeding programs. Here, we identified GRAINS NUMBER 2 (GN2), a novel gene that is responsible for rice grain number, from "Yuanjiang" common wild rice (O. rufipogon Griff.). Transgenic plants overexpressing GN2 showed less grain number, reduced plant height, and later heading date than control plants. Interestingly, GN2 arose through the insertion of a 1094-bp sequence from LOC_Os02g45150 into the third exon of LOC_Os02g56630, and the inserted sequence recruited its nearby sequence to generate the chimeric GN2 The gene structure and expression pattern of GN2 were distinct from those of LOC_Os02g45150 and LOC_Os02g56630 Sequence analysis showed that GN2 may be generated in the natural population of Yuanjiang common wild rice. In this study, we identified a novel functional chimeric gene and also provided information regarding the molecular mechanisms regulating rice grain number.

OsSGL, a novel pleiotropic stress-related gene enhances grain length and yield in rice

Abiotic stress seriously affects the yield of rice (Oryza sativa L.). Grain yield in rice is multiplicatively determined by the number of panicles, number of grains per panicle, and grain weight. Here, we describe the molecular and functional characterization of STRESS_tolerance and GRAIN_LENGTH (OsSGL), a rice gene strongly up-regulated by a wide spectrum of abiotic stresses. OsSGL encodes a putative member of the DUF1645 protein family of unknown function. Overexpression of OsSGL significantly altered certain development processes greatly and positively affecting an array of traits in transgenic rice plants, including increased grain length, grain weight and grain number per panicle, resulting in a significant increase in yield. Microscopical analysis showed that the enhanced OsSGL expression promoted cell division and grain filling. Microarray and quantitative real-time PCR (qRT-PCR) analyses revealed that a large number of genes involved in stress-response, cell cycle and cytokinin signaling processes were induced or suppressed in OsSGL-overexpressing plants. Together, our results suggest that OsSGL may regulate stress-tolerance and cell growth by acting via a cytokinin signaling pathway. This study not only contributes to our understanding of the underlying mechanism regulating rice stress-tolerance and grain length, but also provides a strategy for tailor-made crop yield improvement.

Rice: The First Crop Genome

Rice was the first sequenced crop genome, paving the way for the sequencing of additional and more complicated crop genomes. The impact that the genome sequence made on rice genetics and breeding research was immediate, as evidence by citations and DNA marker use. The impact on other crop genomes was evident too, particularly for those within the grass family. As we celebrate 10 years since the completion of the rice genome sequence, we look forward to new empowering tool sets that will further revolutionize research in rice genetics and breeding and result in varieties that will continue to feed a growing population.

Marker-assisted breeding of the rice restorer line Wanhui 6725 for disease resistance, submergence tolerance and aromatic fragrance

BACKGROUND

Rice is a staple food crop in the world. With the increase in world population and economic development, farmers need to produce more rice in limited field. However, the rice production is frequently affected by biotic and abiotic stresses. The use of natural disease resistance and stress tolerance through genetic breeding is the most efficient and economical way to combat or acclimate to these stresses. In addition, rice with aromatic fragrance can significantly increase market value for its good grain quality. Mianhui 725 (MH725) is an elite restorer line that has been widely used to produce three-line hybrid rice in China. We previously introduced rice bacterial blight resistance genes Xa4 and Xa21 into MH725 and obtained an introgression rice line Wanhui 421 (WH421), which theoretically possesses 96.9% genetic background of MH725.

RESULTS

Here we report the introduction and pyramiding of disease resistance genes Xa27 and Pi9, submergence tolerance gene Sub1A and aromatic fragrance gene badh2.1 in WH421 through backcrossing and marker-assisted selection. The newly developed introgression rice line was designated as Wanhui 6725 (WH6725), which theoretically possesses 95.0% genetic background of MH725. WH6725 and its hybrid rice conferred disease resistance to both blast and bacterial blight diseases and showed tolerance to submergence for over 14 days without significant loss of viability. Compared with non-aromatic rice MH725, WH6725 has strong aromatic fragrance. The major important agronomic traits and grain quality of WH6725 and its hybrid rice obtained in field trials were similar to those of MH725 and the control hybrid rice, indicating that WH6725 is as good as MH725 when it is used as a restorer line for three-line hybrid rice production.

CONCLUSION

We have successfully developed a new restorer line WH6725 with disease resistance to rice blast and bacterial blight, tolerance to submergence and aromatic fragrance, which can be used to replace MH725 for hybrid rice production.

Potential Yield Increase of Hybrid Rice at Five Locations in Southern China

BACKGROUND

A number of field studies have demonstrated that the yield potential of hybrid rice cultivars is higher than that of inbred cultivars, although the magnitude of difference between hybrid and inbred cultivars at different yield levels has not been described. The objective of this study is to compare the yield increase potential at different yield levels between hybrid and conventional rice. Ten field experiments were conducted at five locations in southern China in 2012 and 2013. At each location, two hybrid and two inbred cultivars were grown at three N levels: high (225 kg/hm(2)), moderate (161-191 kg/hm(2)) and the control, zero N (0 kg/hm(2)).

RESULTS

Hybrid rice yielded approximately 8 % more grain than did inbred cultivars in Huaiji, Binyang and Haikou; approximately 7 % more in Changsha; and approximately 19 % more in Xingyi. The high grain yields observed for hybrid rice cultivars were attributed to high grain weight and biomass accumulation at maturity. On average, rice yields were approximately 6.0-7.5 t ha(-1) (medium yield) in Huaiji, Binyang and Haikou; approximately 9.0 t ha(-1) in Changsha (high yield); and approximately 12.0 t ha(-1) (super high yield) in Xingyi. The yield gaps among Huaiji, Binyang and Haikou and Changsha were attributed to the differences in spikelets m(-2) and biomass production, whereas the yield gap between Changsha and Xingyi was caused by the differences in grain-filling percentage, grain weight and harvest index. The differences in biomass production among sites were primarily due to variation in crop growth rate induced by varied temperatures and accumulative solar radiation.

CONCLUSIONS

The yield superiority of hybrid rice was relatively small in comparison with that of inbred cultivars at medium and high yield levels, but the difference was large at super high yield levels. Improving rice yields from medium to high should focus on spikelets m(-2) and biomass, whereas further improvement to super high level should emphasize on grain-filling percentage, grain weight and harvest index. Favorable environmental conditions are essential for high yields in hybrid rice.

Identification of QTLs for yield-related traits in RILs derived from the cross between pLIA-1 carrying Oryza longistaminata chromosome segments and Norin 18 in rice

To improve rice yield, a wide genetic pool is necessary. It is therefore important to explore wild rice relatives. Oryza longistaminata is a distantly related wild rice relative that carries the AA genome. Its potential for improving agronomic traits is not well studied. Introgression line (pLIA-1) that carries Oryza longistaminata's chromosome segments, showed high performance in yield-related traits under non-fertilized conditions. Therefore, to illustrate Oryza longistaminata's potential for improving yield-related traits, RILs from the F₁ of a cross between pLIA-1 and Norin 18 were developed and QTL analysis was done using the RAD-Seq method. In total, 36 QTLs for yield-related traits were identified on chromosomes 1, 2, 3, 5, 6, 7, 8, 10, and 11. Clusters of QTLs for strongly correlated traits were also identified on chromosomes 1, 3, 6, and 8. Phenotypic data from recombinant plants for chromosomes 1 and 8 QTL clusters revealed that the pLIA-1 genotype on chromosome 1 region was more important for panicle-related traits and a combination of pLIA-1 genotypes on chromosomes 1 and 8 showed a favorable phenotype under non-fertilized conditions. These results suggest that Oryza longistaminata's chromosome segments carry important alleles that can be used to improve yield-related traits of rice.

Rice Yield and the Fate of Fertilizer Nitrogen as Affected by Addition of Earthworm Casts Collected from Oilseed Rape Fields: A Pot Experiment

The mechanism associated with improvement of soil nutritional status by oilseed rape crop, leading to better performance of rice crop, in rice-oilseed rape cropping systems is little known. The present study was aimed to test the hypothesis that earthworm casts produced during oilseed rape-growing season have positive effects on grain yield and fertilizer nitrogen (N) utilization in the subsequent flooded rice crop. A ¹⁵N-tracing pot experiment was conducted to determine the effects of earthworm casts collected from oilseed rape fields on yield attributes in rice and the fate of fertilizer N. Soil treated with earthworm casts (soil: earthworm casts = 4: 1, w/w) (EC₁) produced 39% higher grain yield than soil only (EC₀). EC₁ had 18% more panicle number and 10% higher spikelet filling percentage than EC₀. Aboveground biomass and harvest index were higher in EC₁ than in EC₀ by 20% and 15%, respectively. SPAD values in flag leaves were 10% and 22% higher under EC₁ than EC₀ at 15 and 20 days after heading, respectively. EC₁ had 19% higher total N uptake and 18% higher physiological N-use efficiency than EC₀. These positive effects of earthworm casts on yield attributes offset negative effects of decreasing N rate from 0.74 g pot^–1 (equivalent to the recommended field rate of 150 kg ha^–1) to 0.44 g pot^–1 (equivalent to 60% of the recommended rate). Fertilizer N retention rate was 7% higher while fertilizer N loss rate was 6% lower in EC₁ than in EC₀. Our study suggests that earthworm casts produced during oilseed rape-growing season are expected to have the following benefits on the subsequent flooded rice system: (1) improving growth and physiological processes in rice plants and consequently increasing rice grain yield, and (2) increasing fertilizer N retention rate and hence decreasing fertilizer N loss rate and reducing environmental risk.

Allelic diversity in an NLR gene BPH9 enables rice to combat planthopper variation

Brown planthopper (BPH), Nilaparvata lugens Stål, is one of the most devastating insect pests of rice (Oryza sativa L.). Currently, 30 BPH-resistance genes have been genetically defined, most of which are clustered on specific chromosome regions. Here, we describe molecular cloning and characterization of a BPH-resistance gene, BPH9, mapped on the long arm of rice chromosome 12 (12L). BPH9 encodes a rare type of nucleotide-binding and leucine-rich repeat (NLR)-containing protein that localizes to the endomembrane system and causes a cell death phenotype. BPH9 activates salicylic acid- and jasmonic acid-signaling pathways in rice plants and confers both antixenosis and antibiosis to BPH. We further demonstrated that the eight BPH-resistance genes that are clustered on chromosome 12L, including the widely used BPH1, are allelic with each other. To honor the priority in the literature, we thus designated this locus as BPH1/9 These eight genes can be classified into four allelotypes, BPH1/9-1, -2, -7, and -9 These allelotypes confer varying levels of resistance to different biotypes of BPH. The coding region of BPH1/9 shows a high level of diversity in rice germplasm. Homologous fragments of the nucleotide-binding (NB) and leucine-rich repeat (LRR) domains exist, which might have served as a repository for generating allele diversity. Our findings reveal a rice plant strategy for modifying the genetic information to gain the upper hand in the struggle against insect herbivores. Further exploration of natural allelic variation and artificial shuffling within this gene may allow breeding to be tailored to control emerging biotypes of BPH.

Drought-Responsive Mechanisms in Plant Leaves Revealed by Proteomics

Plant drought tolerance is a complex trait that requires a global view to understand its underlying mechanism. The proteomic aspects of plant drought response have been extensively investigated in model plants, crops and wood plants. In this review, we summarize recent proteomic studies on drought response in leaves to reveal the common and specialized drought-responsive mechanisms in different plants. Although drought-responsive proteins exhibit various patterns depending on plant species, genotypes and stress intensity, proteomic analyses show that dominant changes occurred in sensing and signal transduction, reactive oxygen species scavenging, osmotic regulation, gene expression, protein synthesis/turnover, cell structure modulation, as well as carbohydrate and energy metabolism. In combination with physiological and molecular results, proteomic studies in leaves have helped to discover some potential proteins and/or metabolic pathways for drought tolerance. These findings provide new clues for understanding the molecular basis of plant drought tolerance.

Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)-Based Comparative Proteome Analysis of the Response of Ramie under Drought Stress

In this study, we conducted the first isobaric tags for relative and absolute quantitation (isobaric tags for relative and absolute quantitation (iTRAQ))-based comparative proteomic analysis of ramie plantlets after 0 (minor drought stress), 24 (moderate drought stress), and 72 h (severe drought stress) of treatment with 15% (w/v) poly (ethylene glycol)6000 (PEG6000) to simulate drought stress. In our study, the association analysis of proteins and transcript expression revealed 1244 and 968 associated proteins identified in leaves and roots, respectively. L1, L2, and L3 are leaf samples which were harvested at 0, 24, and 72 h after being treated with 15% PEG6000, respectively. Among those treatment groups, a total of 118, 216, and 433 unique proteins were identified as differentially expressed during L1 vs. L2, L2 vs. L3, and L1 vs. L3, respectively. R1, R2, and R3 are root samples which were harvested at 0, 24, and 72 h after being treated with 15% PEG6000, respectively. Among those treatment groups，a total of 124, 27, and 240 unique proteins were identified as differentially expressed during R1 vs. R2, R2 vs. R3, and R1 vs. R3, respectively. Bioinformatics analysis indicated that glycolysis/gluconeogenesis was significantly upregulated in roots in response to drought stress. This enhancement may result in more glycolytically generated adenosine triphosphate (ATP) in roots to adapt to adverse environmental conditions. To obtain complementary information related to iTRAQ data, the mRNA levels of 12 proteins related to glycolysis/gluconeogenesis in leaves and 7 in roots were further analyzed by qPCR. Most of their expression levels were higher in R3 than R1 and R2, suggesting that these compounds may promote drought tolerance by modulating the production of available energy.

The Systemic Acquired Resistance Regulator OsNPR1 Attenuates Growth by Repressing Auxin Signaling through Promoting IAA-Amido Synthase Expression

Systemic acquired resistance is a long-lasting and broad-spectrum disease resistance to pathogens. Our previous study demonstrated that overexpression of NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (OsNPR1), a master gene for systemic acquired resistance in rice (Oryza sativa), greatly enhanced resistance to bacterial blight caused by Xanthomonas oryzae pv oryzae However, the growth and development of the OsNPR1 overexpression (OsNPR1-OX) plants were restrained, and the mechanism remained elusive. In this study, we dissected the OsNPR1-induced growth inhibition. We found that the OsNPR1-OX lines displayed phenotypes mimicking auxin-defective mutants, with decreases in root system, seed number and weight, internode elongation, and tiller number. Whole-genome expression analysis revealed that genes related to the auxin metabolism and signaling pathway were differentially expressed between the OsNPR1-OX and wild-type plants. Consistently, the indole-3-acetic acid (IAA) content was decreased and the auxin distribution pattern was altered in OsNPR1-OX plants. Importantly, we found that some GH3 family members, in particular OsGH3.8 coding IAA-amido synthetase, were constitutively up-regulated in OsNPR1-OX plants. Decreased OsGH3.8 expression by RNA interference could partially restore IAA level and largely rescue the restrained growth and development phenotypes but did not affect the disease resistance of OsNPR1-OX plants. Taken together, we revealed that OsNPR1 affects rice growth and development by disrupting the auxin pathway at least partially through indirectly up-regulating OsGH3.8 expression.

A two-year field measurement of methane and nitrous oxide fluxes from rice paddies under contrasting climate conditions

The effects of three irrigation levels (traditional normal amount of irrigation [NA100%], 70%, and 30% of the normal amount [NA70% and NA30%]) and two rice varieties (Oryza sativa L. Huayou14 and Hanyou8) on CH₄ and N₂O emissions were investigated over two years under contrasting climate conditions (a ‘warm and dry’ season in 2013 and a normal season in 2014). Hanyou8 was developed as a drought-resistant variety. The mean seasonal air temperature in 2013 was 2.3 °C higher than in 2014, while the amount of precipitation from transplanting to the grain-filling stage in 2013 was only 36% of that in 2014. CH₄ emission rose by 93–161%, but rice grain yield fell by 7–13% in 2013, compared to 2014 under the NA100% conditions. Surface standing water depths (SSWD) were higher in Hanyou8 than in Huayou14 due to the lower water demand by Hanyou8. A reduction in the amount of irrigation water applied can effectively reduce the CH₄ emissions regardless of the rice variety and climate condition. However, less irrigation during the ‘warm and dry’ season greatly decreased Huayou14 grain yield, but had little impact on Hanyou8. In contrast, N₂O emission depended more on fertilization and SSWD than on rice variety.

Over-Expression of the Pikh Gene with a CaMV 35S Promoter Leads to Improved Blast Disease (Magnaporthe oryzae) Tolerance in Rice

Magnaporthe oryzae is a rice blast fungus and plant pathogen that causes a serious rice disease and, therefore, poses a threat to the world's second most important food security crop. Plant transformation technology has become an adaptable system for cultivar improvement and to functionally analyze genes in plants. The objective of this study was to determine the effects (through over-expressing and using the CaMV 35S promoter) of Pikh on MR219 resistance because it is a rice variety that is susceptible to the blast fungus pathotype P7.2. Thus, a full DNA and coding DNA sequence (CDS) of the Pikh gene, 3172 bp, and 1206 bp in length, were obtained through amplifying the gDNA and cDNA template from a PH9-resistant rice variety using a specific primer. Agrobacterium-mediated transformation technology was also used to introduce the Pikh gene into the MR219 callus. Subsequently, transgenic plants were evaluated from the DNA to protein stages using polymerase chain reaction (PCR), semi-quantitative RT-PCR, real-time quantitative PCR and high performance liquid chromatography (HPLC). Transgenic plants were also compared with a control using a real-time quantification technique (to quantify the pathogen population), and transgenic and control plants were challenged with the local most virulent M. oryzae pathotype, P7.2. Based on the results, the Pikh gene encodes a hydrophilic protein with 18 sheets, 4 helixes, and 21 coils. This protein contains 401 amino acids, among which the amino acid sequence from 1 to 376 is a non-cytoplasmic region, that from 377 to 397 is a transmembrane region, and that from 398 to 401 is a cytoplasmic region with no identified disordered regions. The Pikh gene was up-regulated in the transgenic plants compared with the control plants. The quantity of the amino acid leucine in the transgenic rice plants increased significantly from 17.131 in the wild-type to 47.865 mg g(-1) in transgenic plants. The M. oryzae population was constant at 31, 48, and 72 h after inoculation in transgenic plants, while it was increased in the inoculated control plants. This study successfully clarified that over-expression of the Pikh gene in transgenic plants can improve their blast resistance against the M. oryzae pathotype P7.2.

Mapping quantitative trait loci for heat tolerance at anthesis in rice using chromosomal segment substitution lines

To study the genetic basis of heat tolerance at anthesis, a set of chromosome segment substitution lines (CSSLs) derived from Sasanishiki (japonica ssp. heat susceptible) and Habataki (indica spp. heat tolerant) were used for analysis across three high temperature environments. Spikelet fertility (SF), daily flowering time (DFT) and pollen shedding level (PSL) under high temperature (HT) were assessed. Eleven related QTLs were detected, of which, two QTLs qSF (ht) 2 and qSF (ht) 4.2 for spikelet fertility were identified on chromosomes 2 and 4. Four QTLs qDFT3, qDFT8, qDFT10.1 and qDFT11 for daily flowering time were detected on chromosomes 3, 8, 10 and 11. The other five QTLs qPSL (ht) 1, qPSL (ht) 4.1, qPSL (ht) 5, qPSL (ht) 7 and qPSL (ht) 10.2 on chromosomes 1, 4, 5, 7 and 10, respectively, were found had effects both on spikelet fertility and pollen shedding level. Of the 11 QTLs, 8 were overlapped with QTLs reported by others, 3 QTLs qPSL (ht) 4.1, qPSL (ht) 7 and qPSL (ht) 10.2 identified in this study were novel. The stability of qPSL (ht) 4.1 was further verified at different temperatures, which could be used to improve the pollen shedding and pollen growth on stigma for rice heat-tolerance breeding.

Mapping quantitative trait loci for heat tolerance at anthesis in rice using chromosomal segment substitution lines

To study the genetic basis of heat tolerance at anthesis, a set of chromosome segment substitution lines (CSSLs) derived from Sasanishiki (japonica ssp. heat susceptible) and Habataki (indica spp. heat tolerant) were used for analysis across three high temperature environments. Spikelet fertility (SF), daily flowering time (DFT) and pollen shedding level (PSL) under high temperature (HT) were assessed. Eleven related QTLs were detected, of which, two QTLs qSF (ht) 2 and qSF (ht) 4.2 for spikelet fertility were identified on chromosomes 2 and 4. Four QTLs qDFT3, qDFT8, qDFT10.1 and qDFT11 for daily flowering time were detected on chromosomes 3, 8, 10 and 11. The other five QTLs qPSL (ht) 1, qPSL (ht) 4.1, qPSL (ht) 5, qPSL (ht) 7 and qPSL (ht) 10.2 on chromosomes 1, 4, 5, 7 and 10, respectively, were found had effects both on spikelet fertility and pollen shedding level. Of the 11 QTLs, 8 were overlapped with QTLs reported by others, 3 QTLs qPSL (ht) 4.1, qPSL (ht) 7 and qPSL (ht) 10.2 identified in this study were novel. The stability of qPSL (ht) 4.1 was further verified at different temperatures, which could be used to improve the pollen shedding and pollen growth on stigma for rice heat-tolerance breeding.

Hemipteran and dipteran pests: Effectors and plant host immune regulators

Hemipteran and dipteran insects have behavioral, cellular and chemical strategies for evading or coping with the host plant defenses making these insects particularly destructive pests worldwide. A critical component of a host plant's defense to herbivory is innate immunity. Here we review the status of our understanding of the receptors that contribute to perception of hemipteran and dipteran pests and highlight the gaps in our knowledge in these early events in immune signaling. We also highlight recent advances in identification of the effectors that activate pattern-triggered immunity and those involved in effector-triggered immunity.

Flowering-Related RING Protein 1 (FRRP1) Regulates Flowering Time and Yield Potential by Affecting Histone H2B Monoubiquitination in Rice (Oryza Sativa)

Flowering time is a critical trait for crops cultivated under various temperature/photoperiod conditions around the world. To understand better the flowering time of rice, we used the vector pTCK303 to produce several lines of RNAi knockdown transgenic rice and investigated their flowering times and other agronomic traits. Among them, the heading date of FRRP1-RNAi knockdown transgenic rice was 23-26 days earlier than that of wild-type plants. FRRP1 is a novel rice gene that encodes a C3HC4-type Really Interesting Novel Gene (RING) finger domain protein. In addition to the early flowering time, FRRP1-RNAi knockdown transgenic rice caused changes on an array of agronomic traits, including plant height, panicle length and grain length. We analyzed the expression of some key genes associated with the flowering time and other agronomic traits in the FRRP1-RNAi knockdown lines and compared with that in wild-type lines. The expression of Hd3a increased significantly, which was the key factor in the early flowering time. Further experiments showed that the level of histone H2B monoubiquitination (H2Bub1) was noticeably reduced in the FRRP1-RNAi knockdown transgenic rice lines compared with wild-type plants and MBP-FRRP1-F1 was capable of self-ubiquitination. The results indicate that Flowering Related RING Protein 1 (FRRP1) is involved in histone H2B monoubiquitination and suggest that FRRP1 functions as an E3 ligase in vivo and in vitro. In conclusion, FRRP1 probably regulates flowering time and yield potential in rice by affecting histone H2B monoubiquitination, which leads to changes in gene expression in multiple processes.

Breeding high-yield superior quality hybrid super rice by rational design

The challenge of meeting the increasing demand for worldwide rice production has driven a sustained quest for advances in rice breeding for yield. Two breakthroughs that led to quantum leaps in productivity last century were the introduction of semidwarf varieties and of hybrid rice. Subsequent gains in yield have been incremental. The next major leap in rice breeding is now upon us through the application of rational design to create defined ideotypes. The exploitation of wide-cross compatibility and intersubspecific heterosis, combined with rapid genome sequencing and the molecular identification of genes for major yield and quality traits have now unlocked the potential for rational design.

The phenome analysis of mutant alleles in Leucine-Rich Repeat Receptor-Like Kinase genes in rice reveals new potential targets for stress tolerant cereals

Plants are constantly exposed to a variety of biotic and abiotic stresses that reduce their fitness and performance. At the molecular level, the perception of extracellular stimuli and the subsequent activation of defense responses require a complex interplay of signaling cascades, in which protein phosphorylation plays a central role. Several studies have shown that some members of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) family are involved in stress and developmental pathways. We report here a systematic analysis of the role of the members of this gene family by mutant phenotyping in the monocotyledon model plant rice, Oryza sativa. We have then targeted 176 of the ∼320 LRR-RLK genes (55.7%) and genotyped 288 mutant lines. Position of the insertion was confirmed in 128 lines corresponding to 100 LRR-RLK genes (31.6% of the entire family). All mutant lines harboring homozygous insertions have been screened for phenotypes under normal conditions and under various abiotic stresses. Mutant plants have been observed at several stages of growth, from seedlings in Petri dishes to flowering and grain filling under greenhouse conditions. Our results show that 37 of the LRR-RLK rice genes are potential targets for improvement especially in the generation of abiotic stress tolerant cereals.

Genome-Wide Association Study for Plant Height and Grain Yield in Rice under Contrasting Moisture Regimes

Drought is one of the vitally critical environmental stresses affecting both growth and yield potential in rice. Drought resistance is a complicated quantitative trait that is regulated by numerous small effect loci and hundreds of genes controlling various morphological and physiological responses to drought. For this study, 270 rice landraces and cultivars were analyzed for their drought resistance. This was done via determination of changes in plant height and grain yield under contrasting water regimes, followed by detailed identification of the underlying genetic architecture via genome-wide association study (GWAS). We controlled population structure by setting top two eigenvectors and combining kinship matrix for GWAS in this study. Eighteen, five, and six associated loci were identified for plant height, grain yield per plant, and drought resistant coefficient, respectively. Nine known functional genes were identified, including five for plant height (OsGA2ox3, OsGH3-2, sd-1, OsGNA1, and OsSAP11/OsDOG), two for grain yield per plant (OsCYP51G3 and OsRRMh) and two for drought resistant coefficient (OsPYL2 and OsGA2ox9), implying very reliable results. A previous study reported OsGNA1 to regulate root development, but this study reports additional controlling of both plant height and root length. Moreover, OsRLK5 is a new drought resistant candidate gene discovered in this study. OsRLK5 mutants showed faster water loss rates in detached leaves. This gene plays an important role in the positive regulation of yield-related traits under drought conditions. We furthermore discovered several new loci contributing to the three investigated traits (plant height, grain yield, and drought resistance). These associated loci and candidate genes significantly improve our knowledge of the genetic control of these traits in rice. In addition, many drought resistant cultivars screened in this study can be used as parental genotypes to improve drought resistance of rice by molecular breeding.

Transcriptomic and Metabolomic Studies Disclose Key Metabolism Pathways Contributing to Well-maintained Photosynthesis under the Drought and the Consequent Drought-Tolerance in Rice

In contrast to wild species, drought-tolerance in crops requires a fully functional metabolism during drought (particularly photosynthetic processes). However, the link between drought-tolerance, photosynthetic regulation during drought, and the associated transcript and metabolic foundation, remains largely unknown. For this study, we used two rice cultivars with contrasting drought-tolerance (the drought-intolerant cultivar IRAT109 and the drought-tolerant cultivar IAC1246) to explore transcript and metabolic responses to long-term drought. The drought-tolerant cultivar represented higher osmotic adjustment and antioxidant capacity, as well as higher relative photosynthesis rate under a progressive drought stress occurred in a modified field with shallow soil-layers. A total of 4059 and 2677 differentially expressed genes (DEGs) were identified in IRAT109 and IAC1246 between the drought and well-watered conditions, respectively. A total of 69 and 47 differential metabolites (DMs) were identified between the two treatments in IRAT109 and IAC1246, respectively. Compared to IRAT109, the DEGs of IAC1246 displayed enhanced regulatory amplitude during drought. We found significant correlations between DEGs and the osmolality and total antioxidant capacity (AOC) of both cultivars. During the early stages of drought, we detected up-regulation of DEGs in IAC1246 related to photosynthesis, in accordance with its higher relative photosynthesis rate. The contents of six differential metabolites were correlated with the osmotic potential and AOC. Moreover, they were differently regulated between the two cultivars. Particularly, up-regulations of 4-hydroxycinnamic acid and ferulic acid were consistent with the performance of photosynthesis-related DEGs at the early stages of drought in IAC1246. Therefore, 4-hydroxycinnamic acid and ferulic acid were considered as key metabolites for rice drought-tolerance. DEGs involved in pathways of these metabolites are expected to be good candidate genes to improve drought-tolerance. In conclusion, well-maintained photosynthesis under drought should contribute to improved drought-tolerance in rice. Metabolites play vital roles in protecting photosynthesis under dehydration via osmotic adjustments and/or antioxidant mechanisms. A metabolite-based method was thus an effective way to explore drought candidate genes. Metabolic accompanied by transcript responses to drought stress should be further studied to find more useful metabolites, pathways, and genes.

Physiological Mechanisms Underlying the High-Grain Yield and High-Nitrogen Use Efficiency of Elite Rice Varieties under a Low Rate of Nitrogen Application in China

Selecting rice varieties with a high nitrogen (N) use efficiency (NUE) is the best approach to reduce N fertilizer application in rice production and is one of the objectives of the Green Super Rice (GSR) Project in China. However, the performance of elite candidate GSR varieties under low N supply remains unclear. In the present study, differences in the grain yield and NUE of 13 and 14 candidate varieties with two controls were determined at a N rate of 100 kg ha(-1) in field experiments in 2014 and 2015, respectively. The grain yield for all of the rice varieties ranged from 8.67 to 11.09 t ha(-1), except for a japonica rice variety YG29, which had a grain yield of 6.42 t ha(-1). HY549 and YY4949 produced the highest grain yield, reflecting a higher biomass production and harvest index in 2014 and 2015, respectively. Total N uptake at maturity (TNPM) ranged from 144 to 210 kg ha(-1), while the nitrogen use efficiency for grain production (NUEg) ranged from 35.2 to 62.0 kg kg(-1). Both TNPM and NUEg showed a significant quadratic correlation with grain yield, indicating that it is possible to obtain high grain yield and NUEg with the reduction of TNPM. The correlation between N-related parameters and yield-related traits suggests that promoting pre-heading growth could increase TNPM, while high biomass accumulation during the grain filling period and large panicles are important for a higher NUEg. In addition, there were significant and negative correlations between the NUEg and N concentrations in leaf, stem, and grain tissues at maturity. Further improvements in NUEg require a reduction in the stem N concentration but not the leaf N concentration. The daily grain yield was the only parameter that significantly and positively correlated with both TNPMand NUEg. This study determined variations in the grain yield and NUE of elite candidate GSR rice varieties and provided plant traits that could be used as selection criteria in breeding N-efficient rice varieties.

Comprehensive Analysis and Expression Profiling of the OsLAX and OsABCB Auxin Transporter Gene Families in Rice (Oryza sativa) under Phytohormone Stimuli and Abiotic Stresses

The plant hormone auxin regulates many aspects of plant growth and developmental processes. Auxin gradient is formed in plant as a result of polar auxin transportation by three types of auxin transporters such as OsLAX, OsPIN, and OsABCB. We report here the analysis of two rice auxin transporter gene families, OsLAX and OsABCB, using bioinformatics tools, publicly accessible microarray data, and quantitative RT-PCR. There are 5 putative OsLAXs and 22 putative OsABCBs in rice genome, which were mapped on 8 chromosomes. The exon-intron structure of OsLAX genes and properties of deduced proteins were relatively conserved within grass family, while that of OsABCB genes varied greatly. Both constitutive and organ/tissue specific expression patterns were observed in OsLAXs and OsABCBs. Analysis of evolutionarily closely related "gene pairs" together with organ/tissue specific expression revealed possible "function gaining" and "function losing" events during rice evolution. Most OsLAX and OsABCB genes were regulated by drought and salt stress, as well as hormonal stimuli [auxin and Abscisic Acid (ABA)], which suggests extensive crosstalk between abiotic stresses and hormone signaling pathways. The existence of large number of auxin and stress related cis-regulatory elements in promoter regions might account for their massive responsiveness of these genes to these environmental stimuli, indicating complexity of regulatory networks involved in various developmental and physiological processes. The comprehensive analysis of OsLAX and OsABCB auxin transporter genes in this study would be helpful for understanding the biological significance of these gene families in hormone signaling and adaptation of rice plants to unfavorable environments.

Isolation and Functional Characterization of Bidirectional Promoters in Rice

Bidirectional promoters, which show great application potential in genetic improvement of plants, have aroused great research interest recently. However, most bidirectional promoters were cloned individually in the studies of single genes. Here, we initiatively combined RNA-seq data and cDNA microarray data to discover the potential bidirectional promoters in rice genome. Based on the expression level and correlation of each adjacent and oppositely transcribed gene pair, we selected four candidate gene pairs. Then, the intergenic region between each pair was isolated and cloned into a dual reporter vector pDX2181 for functional identification. GUS and GFP assays of the transgenic plants indicated that all the intergenic regions showed bidirectional expression activity in various tissues. Through 5' and 3' deletion analysis on one of the above bidirectional promoters, we identified the enhancing region which sharply increased its bidirectional expression efficiency and the essential regions respectively responsible for its 5' and 3' basic expression activity. The bidirectional arrangement of the four gene pairs in six gramineous plants was also analyzed, showing the conserved characteristics of the four bidirectional promoters identified in our study. In addition, two novel cis-sequences conserved in the four bidirectional promoters were discovered by bioinformatic identification. Our study proposes a feasible method for selecting, cloning, and functionally identifying bidirectional promoters as well as for discovering their bidirectional regulatory regions and conserved sequences in rice.

Novel green tissue-specific synthetic promoters and cis-regulatory elements in rice

As an important part of synthetic biology, synthetic promoter has gradually become a hotspot in current biology. The purposes of the present study were to synthesize green tissue-specific promoters and to discover green tissue-specific cis-elements. We first assembled several regulatory sequences related to tissue-specific expression in different combinations, aiming to obtain novel green tissue-specific synthetic promoters. GUS assays of the transgenic plants indicated 5 synthetic promoters showed green tissue-specific expression patterns and different expression efficiencies in various tissues. Subsequently, we scanned and counted the cis-elements in different tissue-specific promoters based on the plant cis-elements database PLACE and the rice cDNA microarray database CREP for green tissue-specific cis-element discovery, resulting in 10 potential cis-elements. The flanking sequence of one potential core element (GEAT) was predicted by bioinformatics. Then, the combination of GEAT and its flanking sequence was functionally identified with synthetic promoter. GUS assays of the transgenic plants proved its green tissue-specificity. Furthermore, the function of GEAT flanking sequence was analyzed in detail with site-directed mutagenesis. Our study provides an example for the synthesis of rice tissue-specific promoters and develops a feasible method for screening and functional identification of tissue-specific cis-elements with their flanking sequences at the genome-wide level in rice.

Root Morphology Was Improved in a Late-Stage Vigor Super Rice Cultivar

This study aimed to test the hypothesis that root morphology might be improved and consequently contributing to superior post-heading shoot growth and grain yield in late-stage vigor super rice. A pot experiment was carried out to compare yield attributes, shoot growth and physiological properties and root morphological traits between a late-stage vigor super rice cultivar (Y-liangyou 087) and an elite rice cultivar (Teyou 838). Grain yield and total shoot biomass were 7–9% higher in Y-liangyou 087 than in Teyou 838. Y-liangyou 087 had 60–64% higher post-heading shoot growth rate and biomass production than Teyou 838. Average relative chlorophyll concentration and net photosynthetic rate in flag leaves were 7–11% higher in Y-liangyou 087 than in Teyou 838 during heading to 25 days after heading. Y-liangyou 087 had 41% higher post-heading shoot N uptake but 17–25% lower root biomass and root-shoot ratio at heading and maturity than Teyou 838. Specific root length and length and surface area of fine roots were higher in Y-liangyou 087 than in Teyou 838 at heading and maturity by more than 15%. These results indicated that root-shoot relationships were well balanced during post-heading phase in the late-stage vigor super rice cultivar Y-liangyou 087 by improving root morphology including avoiding a too great root biomass and developing a large fine root system.

Ensifer-mediated transformation: an efficient non-Agrobacterium protocol for the genetic modification of rice

While Agrobacterium-mediated transformation (AMT) remains the most widely used technique for gene transfer in plants, interest exists for the use of non-Agrobacterium gene delivery systems due to freedom-to-operate issues that remain with AMT across several jurisdictions. In addition, the plant pathogenic mode of action of Agrobacterium tumefaciens significantly increases the costs to passage engineered cultivars through the regulatory process. Ensifer adhaerens (OV14) is a soil-related bacterium with the proven ability to genetically modify the model plant A. thaliana and the staple crop S. tuberosum (Wendt et al., Trans Res 21:567-578, 2012). While previous work was relevant for dicotyledonous species, in this study, the efficacy of Ensifer adhaerens (OV14)-mediated transformation (EMT) was determined on two japonica rice varieties, Curinga and Nipponbare, and the recalcitrant indica variety, IR64. The results indicated that E. adhaerens (OV14) exhibits infection efficiencies ranging between 50-70 %, 90-100 % and 90-95 % for Curinga, Nipponbare and IR64 respectively. Curinga and Nipponbare plants transformed with E. adhaerens (OV14) and A. tumefaciens (LBA4404 and EHA105) were regenerated achieving transformation efficiencies of 16 % and 26-32 % for Curinga and 7 and 4 % for Nipponbare respectively. Separately, the transformation of IR64 was only recorded via EMT (transformation efficiency ~1 %). Integration analyses conducted on 24 transgenic rice lines illustrated that T-DNA insertion occurred randomly throughout the rice genome for EMT (and AMT), with similar integration patterns in the rice genomic DNA observed for both bacterial species.

Excavating abiotic stress-related gene resources of terrestrial macroscopic cyanobacteria for crop genetic engineering: dawn and challenge

Genetically engineered (GE) crops with resistance to environmental stresses are one of the most important solutions for future food security. Numerous genes associated to plant stress resistance have been identified and characterized. However, the current reality is that only a few transgenic crops expressing prokaryotic genes are successfully applied in field conditions. These few prokaryotic genes include Agrobacterium strain CP4 EPSPS gene, Bacillus thuringiensis Cry1Ab gene and a bacterial chaperonin gene. Thus, the excavation of potentially critical genes still remains an arduous task for crop engineering. Terrestrial macroscopic cyanobacteria, Nostoc commune and Nostoc flagelliforme, which exhibit extreme resistance to desiccation stress, may serve as new prokaryotic bioresources for excavating critical genes. Recently, their marker gene wspA was heterologously expressed in Arabidopsis plant and the transgenics exhibited more flourishing root systems than wild-type plants under osmotic stress condition. In addition, some new genes associated with drought response and adaptation in N. flagelliforme are being uncovered by our ongoing RNA-seq analysis. Although the relevant work about the terrestrial macroscopic cyanobacteria is still underway, we believe that the prospect of excavating their critical genes for application in GE crops is quite optimistic.

Small RNAs and Gene Network in a Durable Disease Resistance Gene--Mediated Defense Responses in Rice

Accumulating data have suggested that small RNAs (sRNAs) have important functions in plant responses to pathogen invasion. However, it is largely unknown whether and how sRNAs are involved in the regulation of rice responses to the invasion of Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial blight, the most devastating bacterial disease of rice worldwide. We performed simultaneous genome-wide analyses of the expression of sRNAs and genes during early defense responses of rice to Xoo mediated by a major disease resistance gene, Xa3/Xa26, which confers durable and race-specific qualitative resistance. A large number of sRNAs and genes showed differential expression in Xa3/Xa26-mediated resistance. These differentially expressed sRNAs include known microRNAs (miRNAs), unreported miRNAs, and small interfering RNAs. The candidate genes, with expression that was negatively correlated with the expression of sRNAs, were identified, indicating that these genes may be regulated by sRNAs in disease resistance in rice. These results provide a new perspective regarding the putative roles of sRNA candidates and their putative target genes in durable disease resistance in rice.

OsPIN5b modulates rice (Oryza sativa) plant architecture and yield by changing auxin homeostasis, transport and distribution

Plant architecture attributes such as tillering, plant height and panicle size are important agronomic traits that determine rice (Oryza sativa) productivity. Here, we report that altered auxin content, transport and distribution affect these traits, and hence rice yield. Overexpression of the auxin efflux carrier-like gene OsPIN5b causes pleiotropic effects, mainly reducing plant height, leaf and tiller number, shoot and root biomass, seed-setting rate, panicle length and yield parameters. Conversely, reduced expression of OsPIN5b results in higher tiller number, more vigorous root system, longer panicles and increased yield. We show that OsPIN5b is an endoplasmic reticulum (ER) -localized protein that participates in auxin homeostasis, transport and distribution in vivo. This work describes an example of an auxin-related gene where modulating its expression can simultaneously improve plant architecture and yield potential in rice, and reveals an important effect of hormonal signaling on these traits.