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Many quantitative trait loci (QTLs) have been identified by molecular genetic studies which control grain size by regulating grain width, length, and/or thickness. Grain width 2 (GW2) is one such QTL that codes for a RING-type E3 ubiquitin ligase and increases grain size by regulating grain width through ubiquitin-mediated degradation of unknown substrates. A natural variation (single-nucleotide polymorphism at the 346th position) in the functional domain-coding region of OsGW2 in japonica rice genotypes has been shown to cause an increase in grain width/weight in rice. However, this variation is absent in indica rice genotypes. In this study, we report that reduced expression of OsGW2 can alter grain size, even though natural sequence variation is not responsible for increased grain size in indica rice genotypes. OsGW2 shows high expression in seed development stages and the protein localizes to the nucleus and cytoplasm. Downregulation of OsGW2 by RNAi technology results in wider and heavier grains. Microscopic observation of grain morphology suggests that OsGW2 determines grain size by influencing both cell expansion and cell proliferation in spikelet hull. Using transcriptome analysis, upregulated genes related to grain size regulation have been identified among 1,426 differentially expressed genes in an OsGW2 _RNAi transgenic line. These results reveal that OsGW2 is a negative regulator of grain size in indica rice and affects both cell number and cell size in spikelet hull. [ABSTRACT FROM AUTHOR]

Increasing the grain number is the most direct route toward enhancing the grain yield in cereals. In rice, grain number can be amplified through increasing the shoot branching (tillering), panicle branching, panicle length, and seed set percentage. Phytohormones have been conclusively shown to control the above characteristics by regulating molecular factors and their cross-interactions. The dynamic equilibrium of cytokinin levels in both shoot and inflorescence meristems, maintained by the regulation of its biosynthesis, activation, and degradation, determines the tillering and panicle branching, respectively. Auxins and gibberellins are known broadly to repress the axillary meristems, while jasmonic acid is implicated in the determination of reproductive meristem formation. The balance of auxin, gibberellin, and cytokinin determines meristematic activities in the inflorescence. Strigolactones have been shown to repress the shoot branching but seem to regulate panicle branching positively. Ethylene, brassinosteroids, and gibberellins regulate spikelet abortion and grain filling. Further studies on the optimization of endogenous hormonal levels can help in the expansion of the grain yield potential of rice. This review focuses on the molecular machinery, involving several genes and quantitative trait loci (QTL), operational in the plant that governs hormonal control and, in turn, gets governed by the hormones to regulate grain number and yield in rice. [ABSTRACT FROM AUTHOR]

Summary: Rice grain size and weight are major determinants of grain quality and yield and so have been under rigorous selection since domestication. However, the genetic basis for contrasting grain size/weight trait among Indian germplasms and their association with domestication‐driven evolution is not well understood. In this study, two long (LGG) and two short grain (SGG) genotypes were resequenced. LGG (LGR and PB 1121) differentiated from SGG (Sonasal and Bindli) by 504 439 single nucleotide polymorphisms (SNPs) and 78 166 insertion‐and‐deletion polymorphisms. The LRK gene cluster was different and a truncation mutation in the LRK8 kinase domain was associated with LGG. Phylogeny with 3000 diverse rice accessions revealed that the four sequenced genotypes belonged to the japonica group and were at the edge of the clades indicating them to be the potential source of genetic diversity available in Indian rice germplasm. Six SNPs were significantly associated with grain size/weight and the top four of these could be validated in mapping a population, suggesting this study as a valuable resource for high‐throughput genotyping. A contiguous long low‐diversity region (LDR) of approximately 6 Mb carrying a major grain weight quantitative trait loci (harbouring OsTOR gene) was identified on Chromosome 5. This LDR was identified as an evolutionary important site with significant positive selection and multiple selection sweeps, and showed association with many domestication‐related traits, including grain size/weight. The aus population retained more allelic variations in the LDR than the japonica and indica populations, suggesting it to be one of the divergence loci. All the data and analyses can be accessed from the RiceSzWtBase database. [ABSTRACT FROM AUTHOR]

Summary: Mediator, a multisubunit co‐activator complex, regulates transcription in eukaryotes and is involved in diverse processes in Arabidopsis through its different subunits. Here, we have explored developmental aspects of one of the rice Mediator subunit gene OsMED14_1. We analyzed its expression pattern through RNA in situ hybridization and pOsMED14_1:GUS transgenics that showed its expression in roots, leaves, anthers and seeds prominently at younger stages, indicating possible involvement of this subunit in multiple aspects of rice development. To understand the developmental roles of OsMED14_1 in rice, we generated and studied RNAi‐based knockdown rice plants that showed multiple effects including less height, narrower leaves and culms with reduced vasculature, lesser lateral root branching, defective microspore development, reduced panicle branching and seed set, and smaller seeds. Histological analyses showed that slender organs were caused by reduction in both cell number and cell size in OsMED14_1 knockdown plants. Flow cytometric analyses and expression analyses of cell cycle‐related genes revealed that defective cell‐cycle progression led to these defects. Expression analyses of auxin‐related genes and indole‐3‐acetic acid (IAA) immunolocalization study indicated altered auxin level in these knockdown plants. Reduction of lateral root branching in knockdown plants was corrected by exogenous IAA supplement. OsMED14_1 physically interacts with transcription factors YABBY5, TAPETUM DEGENERATION RETARDATION (TDR) and MADS29, possibly regulating auxin homeostasis and ultimately leading to lateral organ/leaf, microspore and seed development. Significance Statement: The current study addresses the mechanism of developmental control by the Mediator subunit gene OsMED14_1 in rice, thereby enhancing the understanding of subunit specific Mediator functions in plants. Spatio‐temporal expression pattern, knockdown effects, auxin‐related gene expression/immunolocalization studies and protein level interactions unravel the involvement of OsMED14_1 in various developmental processes and provide a mechanistic view of its action in regulating these processes. [ABSTRACT FROM AUTHOR]

A biological experiment was conducted to evaluate the effect of feeding rice based distillers dried grains with solubles (rDDGS) as soybean replacement without or with different enzymes on carcass characteristics in broiler chickens. The experiment was conducted as per 3x4 factorial completely randomized design. A total of 384 broiler chicks of same hatch with uniform weight were used. There were twelve different treatments with 4 replicates for each treatment and each replicate consisted of 8 chicks. Two levels of rice DDGS were taken (12.5 and 15%). Protease, xylanase and multienzymes supplementation under different treatments were done. The results revealed that no significant (p>0.05) difference was observed due to different levels of rice DDGS and their interaction with different enzymes in carcass traits, cut up parts, visceral organ and immune organ weight except abdomen fat and giblet weight. Abdomen fat was significantly (p<0.05) higher in 15% rDDGS level with or without xylanase supplementation. Xylanase supplementation increased significantly (p<0.05) giblet weight as compared to multienzymes and without enzyme groups. The study concludes that the feeding of rDDGS levels of 12.5% and 15%, respectively with or without enzyme supplementation do not have any adverse effects on the carcass traits, but xylanase supplementation improved abdomen fat and giblet weight of broiler chicken at 42 days. [ABSTRACT FROM AUTHOR]

A biological experiment was undertaken with (4x2) factorial CRD in 26 wk old CARI Sonali layers (n=120) assigned to eight treatments (i.e. 2 control + 6 test diets) having 15 replicates with one layer in each replicate for ten weeks (26th-35th week of age). Eight experimental diets (D1 to D8) were prepared by incorporating rice dry distiller grain with soluble (DDGS) without and with enzyme at 0, 5, 7.5 and 10% level. Weighed amount of respective diet was offered to individual birds daily. All diets had been kept isocaloric and isonitrogenous in nature. Findings through experiment I revealed that rice DDGS employed in this study contained CP 45.0% which is almost at par of fish meal protein and slightly lower to SBM. However, the gross energy is higher than FM and SBM but lower than maize. In vitro pepsin-pancreatin digestibility and available carbohydrate contents (ACHO) of rice DDGS was found 78.05 and 23.25% respectively. Phytate phosphorus content in rice DDGS was 0.44%. However non-phytate phosphorus was 0.33% which is 57.14% of total phosphorus. Different levels of rice DDGS either sole or in combination with enzyme did not have any significant (P>0.05) effect on egg cholesterol, sensory attributes except appearance and colour of boiled egg, however significantly (P<0.01) increased the haematological, serum protein profile and have lowering effect on serum lipid profile, which was found better effect after dietary addition of enzyme during II experiment. [ABSTRACT FROM AUTHOR]

Molecular mapping studies which aim to identify genetic basis of diverse agronomic traits are vital for marker-assisted crop improvement. Numerous Quantitative Trait Loci (QTLs) mapped in rice span long genomic intervals with hundreds to thousands of genes, which limits their utilization for marker-assisted genetic enhancement of rice. Although potent, fine mapping of QTLs is challenging task as it requires screening of large number of segregants to identify suitable recombination events. Association mapping offers much higher resolution as compared to QTL mapping, but detects considerable number of spurious QTLs. Therefore, combined use of QTL and association mapping strategies can provide advantages associated with both these methods. In the current study, we utilized meta-analysis approach to identify metaQTLs associated with grain size/weight in diverse Indian indica and aromatic rice accessions. Subsequently, attempt has been made to narrow-down identified grain size/weight metaQTLs through individual SNP- as well as haplotype-based regional association analysis. The study identified six different metaQTL regions, three of which were successfully revalidated, and substantially scaled-down along with GS3 QTL interval (positive control) by regional association analysis. Consequently, two potential candidate genes within two reduced metaQTLs were identified based on their differential expression profiles in different tissues/stages of rice accessions during seed development. The developed strategy has broader practical utility for rapid delineation of candidate genes and natural alleles underlying QTLs associated with complex agronomic traits in rice as well as major crop plants enriched with useful genetic and genomic information. [ABSTRACT FROM AUTHOR]

Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus, and wild rice accessions. These markers were mapped on diverse coding and noncoding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16-74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 x Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7-8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region (OsqGW5.1) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis-regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse cultivar groups) and integrated genomic strategy can efficiently scan functionally relevant potential molecular tags (markers, candidate genes and alleles) regulating complex agronomic traits (grain weight) and expedite marker-assisted genetic enhancement in rice. [ABSTRACT FROM AUTHOR]

Background: The knowledge of the extent and pattern of diversity in the crop species is a prerequisite for any crop improvement as it helps breeders in deciding suitable breeding strategies for their future improvement. Rice is the main staple crop in India with the large number of varieties released every year. Studies based on the small set of rice genotypes have reported a loss in genetic diversity especially after green revolution. However, a detailed study of the trend of diversity in Indian rice varieties is lacking. SSR markers have proven to be a marker of choice for studying the genetic diversity. Therefore, the present study was undertaken with the aim to characterize and assess trends of genetic diversity in a large set of Indian rice varieties (released between 1940-2013), conserved in the National Gene Bank of India using SSR markers. Result: A set of 729 Indian rice varieties were genotyped using 36 HvSSR markers to assess the genetic diversity and genetic relationship. A total of 112 alleles was amplified with an average of 3.11 alleles per locus with mean Polymorphic Information Content (PIC) value of 0.29. Cluster analysis grouped these varieties into two clusters whereas the model based population structure divided them into three populations. AMOVA study based on hierarchical cluster and model based approach showed 3% and 11% variation between the populations, respectively. Decadal analysis for gene diversity and PIC showed increasing trend from 1940 to 2005, thereafter values for both the parameters showed decreasing trend between years 2006-2013. In contrast to this, allele number demonstrated increasing trend in these varieties released and notified between1940 to 1985, it remained nearly constant during 1986 to 2005 and again showed an increasing trend. Conclusion: Our results demonstrated that the Indian rice varieties harbors huge amount of genetic diversity. However, the trait based improvement program in the last decades forced breeders to rely on few parents, which resulted in loss of gene diversity during 2006 to 2013. The present study indicates the need for broadening the genetic base of Indian rice varieties through the use of diverse parents in the current breeding program. [ABSTRACT FROM AUTHOR]

Plants have developed intricate mechanisms to overcome abiotic stresses. The process of signal perception and activation of signaling cascades involves a large number of factors and molecules belonging to diverse classes of gene families. In comparison to animals, plants harbor larger multigene families along with the occurrence of plant-specific ones. Gene families with abiotic-stress-responsive members were analyzed and categorized into classes such as transcription factors, signal transduction components, transporters, epigenetic regulators, and other regulatory components. The number of members, phylogeny, family expansion, domain composition, subcellular localization, and expression profiling during varied abiotic stresses have been summarized. Candidate genes from families, functionally characterized for abiotic stress responses, have been described. Based on our compilation, the expansion of abiotic-stress-responsive gene families in rice has occurred via segmental and tandem duplication events to accommodate sub-functionalization needed for regulating diverse abiotic stress responses at expression, localization, and functional levels. The information documented here can be further utilized as a primer for selecting candidate genes for improvement of rice yield under abiotic stresses. [ABSTRACT FROM PUBLISHER]

Ca2+ homeostasis is required to maintain a delicate balance of cytosolic Ca2+ during normal and adverse growth conditions. Various Ca2+ transporters actively participate to maintain this delicate balance especially during abiotic stresses and developmental events in plants. In this study, we present a genome-wide account, detailing expression profiles, subcellular localization and functional analysis of rice Ca2+ transport elements. Exhaustive in silico data mining and analysis resulted in the identification of 81 Ca2+ transport element genes, which belong to various groups such as Ca2+- ATPases (pumps), exchangers, channels, glutamate receptor homologs and annexins. Phylogenetic analysis revealed that different Ca2+ transporters are evolutionarily conserved across different plant species. Comprehensive expression analysis by gene chip microarray and quantitative RT- PCR revealed that a substantial proportion of Ca2+ transporter genes were expressed differentially under abiotic stresses (salt, cold and drought) and reproductive developmental stages (panicle and seed) in rice. These findings suggest a possible role of rice Ca2+ transporters in abiotic stress and development triggered signaling pathways. Subcellular localization of Ca2+ transporters from different groups in Nicotiana benthamiana revealed their variable localization to different compartments, which could be their possible sites of action. Complementation of Ca2+ transport activity of K616 yeast mutant by Ca2+- ATPase Os ACA7 and involvement in salt tolerance verified its functional behavior. This study will encourage detailed characterization of potential candidate Ca2+ transporters for their functional role in planta. [ABSTRACT FROM AUTHOR]

Background: Phospholipase C (PLC) is one of the major lipid hydrolysing enzymes, implicated in lipid mediated signaling. PLCs have been found to play a significant role in abiotic stress triggered signaling and developmental processes in various plant species. Genome wide identification and expression analysis have been carried out for this gene family in Arabidopsis, yet not much has been accomplished in crop plant rice. Methodology/Principal Findings: An exhaustive in-silico exploration of rice genome using various online databases and tools resulted in the identification of nine PLC encoding genes. Based on sequence, motif and phylogenetic analysis rice PLC gene family could be divided into phosphatidylinositol-specific PLCs (PI-PLCs) and phosphatidylcholine- PLCs (PC-PLC or NPC) classes with four and five members, respectively. A comparative analysis revealed that PLCs are conserved in Arabidopsis (dicots) and rice (monocot) at gene structure and protein level but they might have evolved through a separate evolutionary path. Transcript profiling using gene chip microarray and quantitative RT-PCR showed that most of the PLC members expressed significantly and differentially under abiotic stresses (salt, cold and drought) and during various developmental stages with condition/stage specific and overlapping expression. This finding suggested an important role of different rice PLC members in abiotic stress triggered signaling and plant development, which was also supported by the presence of relevant cis-regulatory elements in their promoters. Sub-cellular localization of few selected PLC members in Nicotiana benthamiana and onion epidermal cells has provided a clue about their site of action and functional behaviour. Conclusion/Significance: The genome wide identification, structural and expression analysis and knowledge of sub-cellular localization of PLC gene family envisage the functional characterization of these genes in crop plants in near future. [ABSTRACT FROM AUTHOR]

Pollen, regarded as the gold dust carrying the male germ line of flowering plants, is generated in the male reproductive organ called stamen. During the last few years, molecular biology and genetics have been integrated to enhance our knowledge regarding the structural and functional aspects of anther and pollen development. The promoters of several anther-/pollen-specific genes have been characterized to help understand the development of anther that involves the expression of a large number of genes temporally as well as spatially. The cis-acting regulatory elements of promoters necessary for interaction with transcription factors and their activity have been delineated. Many transcription factor genes having distinct anther-specific expression pattern have been identified with the help of transcriptome studies in Oryza sativa as well as Arabidopsis thaliana. The nature of complex interactions between genes and regulatory hierarchy involving developmental signal cascades have been investigated to design a working model for anther development. The immediate challenge ahead is to isolate and functionally characterize missing links and terminal ends of regulatory components for enhancing our knowledge about the male gametophyte development. The information generated on this aspect would help design suitable strategies to develop traits such as male sterility in crop plants. [ABSTRACT FROM AUTHOR]

Summary [ABSTRACT FROM AUTHOR]

Glutaredoxins (GRXs) are glutathione-dependent oxidoreductase enzymes involved in a variety of cellular processes. In this study, our analysis revealed the presence of 48 genes encoding GRX proteins in the rice genome. GRX proteins could be classified into four classes, namely CC-, CGFS-, CPYC- and GRL-type, based on phylogenetic analysis. The classification was supported with organization of predicted conserved putative motifs in GRX proteins. We found that expansion of this gene family has occurred largely via whole genome duplication events in a species-specific manner. We explored rice oligonucleotide array data to gain insights into the function of GRX gene family members during various stages of development and in response to environmental stimuli. The comprehensive expression analysis suggested diverse roles of GRX genes during growth and development in rice. Some of the GRX genes were expressed in specific organs/developmental stages only. The expression of many of rice GRX genes was influenced by various phytohormones, abiotic and biotic stress conditions, suggesting an important role of GRX proteins in response to these stimuli. The identification of GRX genes showing differential expression in specific tissues or in response to environmental stimuli provide a new avenue for in-depth characterization of selected genes of importance. [ABSTRACT FROM PUBLISHER]

Background: Protein phosphatases are the key components of a number of signaling pathways where they modulate various cellular responses. In plants, protein phosphatases constitute a large gene family and are reportedly involved in the regulation of abiotic stress responses and plant development. Recently, the whole complement of protein phosphatases has been identified in Arabidopsis genome. While PP2C class of serine/threonine phosphatases has been explored in rice, the whole complement of this gene family is yet to be reported. Results: In silico investigation revealed the presence of 132-protein phosphatase-coding genes in rice genome. Domain analysis and phylogenetic studies of evolutionary relationship categorized these genes into PP2A, PP2C, PTP, DSP and LMWP classes. PP2C class represents a major proportion of this gene family with 90 members. Chromosomal localization revealed their distribution on all the 12 chromosomes, with 42 genes being present on segmentally duplicated regions and 10 genes on tandemly duplicated regions of chromosomes. The expression profiles of 128 genes under salinity, cold and drought stress conditions, 11 reproductive developmental (panicle and seed) stages along with three stages of vegetative development were analyzed using microarray expression data. 46 genes were found to be differentially expressing in 3 abiotic stresses out of which 31 were up-regulated and 15 exhibited downregulation. A total of 82 genes were found to be differentially expressing in different developmental stages. An overlapping expression pattern was found for abiotic stresses and reproductive development, wherein 8 genes were up-regulated and 7 down-regulated. Expression pattern of the 13 selected genes was validated employing real time PCR, and it was found to be in accordance with the microarray expression data for most of the genes. Conclusions: Exploration of protein phosphatase gene family in rice has resulted in the identification of 132 members, which can be further divided into different classes phylogenetically. Expression profiling and analysis indicate the involvement of this large gene family in a number of signaling pathways triggered by abiotic stresses and their possible role in plant development. Our study will provide the platform from where; the expression pattern information can be transformed into molecular, cellular and biochemical characterization of members belonging to this gene family. [ABSTRACT FROM AUTHOR]

Rice ( Oryza sativa L.), a non-accumulator of glycinebetaine (GB), is highly susceptible to abiotic stress. Transgenic rice with chloroplast-targeted choline oxidase encoded by the codA gene from Arthrobacter globiformis has been evaluated for inheritance of transgene up to R5 generation and water-stress tolerance. During seedling, vegetative and reproductive stages, transgenic plants could maintain higher activity of photosystem II and they show better physiological performance, for example, enhanced detoxification of reactive oxygen species compared to wild-type plants under water-stress. Survival rate and agronomic performance of transgenic plants is also better than wild-type following prolonged water-stress. Choline oxidase converts choline into GB and H2O2 in a single step. It is possible that H2O2/GB might activate stress response pathways and prepare transgenic plants to mitigate stress. To check this possibility, microarray-based transcriptome analysis of transgenic rice has been done. It unravelled altered expression of many genes involved in stress responses, signal transduction, gene regulation, hormone signalling and cellular metabolism. Overall, 165 genes show more than two-fold up-regulation at P-value < 0.01 in transgenic rice. Out of these, at least 50 genes are known to be involved in plant stress response. Exogenous application of H2O2 or GB to wild-type plants also induces such genes. Our data show that metabolic engineering for GB is a promising strategy for introducing stress tolerance in crop plants and which could be imparted, in part, by H2O2- and/or GB-induced stress response genes. [ABSTRACT FROM AUTHOR]

Receptor-like cytoplasmic kinases (RLCKs) in plants belong to the super family of receptor-like kinases (RLKs). These proteins show homology to RLKs in kinase domain but lack the transmembrane domain. Some of the functionally characterized RLCKs from plants have been shown to play roles in development and stress responses. Previously, 149 and 187 RLCK encoding genes were identified from Arabidopsis and rice, respectively. By using HMM-based domain structure and phylogenetic relationships, we have identified 379 OsRLCKs from rice. OsRLCKs are distributed on all 12 chromosomes of rice and some members are located on duplicated chromosomal segments. Several OsRLCKs probably also undergo alternative splicing, some having evidence only in the form of gene models. To understand their possible functions, expression patterns during landmark stages of vegetative and reproductive development as well as abiotic and biotic stress using microarray and MPSS-based data were analyzed. Real-time PCR-based expression profiling for a selected few genes confirmed the outcome of microarray analysis. Differential expression patterns observed for majority of OsRLCKs during development and stress suggest their involvement in diverse functions in rice. Majority of the stress-responsive OsRLCKs were also found to be localized within mapped regions of abiotic stress QTLs. Outcome of this study would help in selecting organ/development stage specific OsRLCK genes/targets for functional validation studies. [ABSTRACT FROM PUBLISHER]

F-box proteins constitute a large family in eukaryotes and are characterized by a conserved F-box motif (approximately 40 amino acids). As components of the Skp1p-cullin-F-box complex, F-box proteins are critical for the controlled degradation of cellular proteins. We have identified 687 potential F-box proteins in rice (Oryza sativa), the model monocotyledonous plant, by a reiterative database search. Computational analysis revealed the presence of several other functional domains, including leucine-rich repeats, kelch repeats, F-box associated domain, domain of unknown function, and tubby domain in F-box proteins. Based upon their domain composition, they have been classified into 10 subfamilies. Several putative novel conserved motifs have been identified in F-box proteins, which do not contain any other known functional domain. An analysis of a complete set of F-box proteins in rice is presented, including classification, chromosomal location, conserved motifs, and phylogenetic relationship. It appears that the expansion of F-box family in rice, in large part, might have occurred due to localized gene duplications. Furthermore, comprehensive digital expression analysis of F-box protein-encoding genes has been complemented with microarray analysis. The results reveal specific and/or overlapping expression of rice F-box protein- encoding genes during floral transition as well as panicle and seed development. At least 43 F-box protein-encoding genes have been found to be differentially expressed in rice seedlings subjected to different abiotic stress conditions. The expression of several F-box protein-encoding genes is also influenced by light. The structure and function of F-box proteins in plants is discussed in light of these results and the published information. These data will be useful for prioritization of F-box proteins for functional validation in rice. [ABSTRACT FROM AUTHOR]

Rice is the most amenable crop plant for genetic manipulation amongst monocots due to its small genome size, enriched genetic map, availability of entire genome sequence, and relative ease of transformation. Improvement in agronomic traits of rice is bound to affect a sizeable population since it is a primary source of sustenance. Recent advances like use of 'clean gene' technology or matrix attachment regions would help improve rice transformation. Function of several novel genes and their promoters has been analyzed in transgenic rice. Significant progress has been made in introducing traits like herbicide, biotic stress and abiotic stress tolerance. Attempts also have been made to enhance nutritional characteristics of the grain and yield. Identification of genes controlling growth and development can be used to modify plant architecture and heading period. Transgenic rice can serve as a biofactory for the production of molecules of pharmaceutical and industrial utility. The drive to apply transgenic rice for public good as well as commercial gains has fueled research to an all time high. Successful field trials and biosafety of transgenic rice have been reported. This would act as a catalyst for greater acceptance of genetically modified food crops. The lessons learnt from rice can be extended to other cereals thereby opening new opportunities and possibilities. [ABSTRACT FROM AUTHOR]

Background: MADS-box transcription factors, besides being involved in floral organ specification, have also been implicated in several aspects of plant growth and development. In recent years, there have been reports on genomic localization, protein motif structure, phylogenetic relationships, gene structure and expression of the entire MADS-box family in the model plant system, Arabidopsis. Though there have been some studies in rice as well, an analysis of the complete MADS-box family along with a comprehensive expression profiling was still awaited after the completion of rice genome sequencing. Furthermore, owing to the role of MADS-box family in flower development, an analysis involving structure, expression and functional aspects of MADS-box genes in rice and Arabidopsis was required to understand the role of this gene family in reproductive development. Results: A genome-wide molecular characterization and microarray-based expression profiling of the genes encoding MADS-box transcription factor family in rice is presented. Using a thorough annotation exercise, 75 MADS-box genes have been identified in rice and categorized into MIKCc, MIKC*, Mα, Mβ and Mγ groups based on phylogeny. Chromosomal localization of these genes reveals that 16 MADS-box genes, mostly MIKCc-type, are located within the duplicated segments of the rice genome, whereas most of the M-type genes, 20 in all, seem to have resulted from tandem duplications. Nine members belonging to the Mβ group, which was considered absent in monocots, have also been identified. The expression profiles of all the MADS-box genes have been analyzed under 11 temporal stages of panicle and seed development, three abiotic stress conditions, along with three stages of vegetative development. Transcripts for 31 genes accumulate preferentially in the reproductive phase, of which, 12 genes are specifically expressed in seeds, and six genes show expression specific to panicle development. Differential expression of seven genes under stress conditions is also evident. An attempt has been made to gain insight into plausible functions of rice MADS-box genes by collating the expression data of functionally validated genes in rice and Arabidopsis. Conclusion: Only a limited number of MADS genes have been functionally validated in rice. A comprehensive annotation and transcriptome profiling undertaken in this investigation adds to our understanding of the involvement of MADS-box family genes during reproductive development and stress in rice and also provides the basis for selection of candidate genes for functional validation studies. [ABSTRACT FROM AUTHOR]

DNA topoisomerase 6 (TOP6) belongs to a novel family of type II DNA topoisomerases present, other than in archaebacteria, only in plants. Here we report the isolation of full-length cDNAs encoding putative TOP6 subunits A and B from rice ( Oryza sativa ssp. indica), preserving all the structural domains conserved among archaebacterial TOP6 homologs and eukaryotic meiotic recombination factor SPO11. OsTOP6A1 was predominantly expressed in prepollinated flowers. The transcript abundance of OsTOP6A2, OsTOP6A3 and OsTOP6B was also higher in prepollinated flowers and callus. The expression of OsTOP6A2, OsTOP6A3 and OsTOP6B was differentially regulated by the plant hormones, auxin, cytokinin, and abscisic acid. Yeast two-hybrid analysis revealed that the full-length OsTOP6B protein interacts with both OsTOP6A2 and OsTOP6A3, but not with OsTOP6A1. The nuclear localization of OsTOP6A3 and OsTOP6B was established by the transient expression of their β-glucuronidase fusion proteins in onion epidermal cells. Overexpression of OsTOP6A3 and OsTOP6B in transgenic Arabidopsis plants conferred reduced sensitivity to the stress hormone, abscisic acid, and tolerance to high salinity and dehydration. Moreover, the stress tolerance coincided with enhanced induction of many stress-responsive genes in transgenic Arabidopsis plants. In addition, microarray analysis revealed that a large number of genes are expressed differentially in transgenic plants. Taken together, our results demonstrate that TOP6 genes play a crucial role in stress adaptation of plants by altering gene expression. [ABSTRACT FROM AUTHOR]

Abstract: Small auxin-up RNAs (SAURs) are the early auxin-responsive genes represented by a large multigene family in plants. Here, we report the identification of 58 OsSAUR gene family members from rice (Oryza sativa japonica cv Nipponbare), the model monocot plant, by a reiterative database search and manual reannotation; 2 of these are pseudogenes. The coding sequences of OsSAURs do not possess any intron. Most of the predicted OsSAUR protein sequences harbor a putative nuclear localization signal at their N-terminus. Localized gene duplications appear to be the primary genetic event responsible for SAUR gene family expansion in rice. Interestingly, the duplication of OsSAURs was found to be associated with the chromosomal block duplication as well. The phylogenetic analysis revealed that the SAUR gene family expanded in rice and Arabidopsis due to species-specific expansion of the family in monocots and dicots. The auxin-responsive elements and downstream element are conserved in the upstream and downstream sequences, respectively, of OsSAURs. In addition to the 21 OsSAURs with full-length cDNA sequences and 20 with expressed sequence tags, gene expression analyses of at least 7 OsSAURs by RT-qPCR indicated that the majority of identified OsSAURs most likely are expressed in rice. The transcript abundance of the OsSAURs examined increased within a few minutes of exogenous auxin application with varying kinetics. The present study provides basic genomic information for the rice SAUR gene family and will pave the way for deciphering the precise role of SAURs in plant growth and development. [Copyright &y& Elsevier]

Auxin exerts pleiotropic effects on plant growth and development by regulating the expression of early auxin-responsive genes of auxin/indoleacetic acid ( Aux/IAA), small auxin-up RNA, and GH3 classes. These genes have been studied extensively in dicots like soybean and Arabidopsis. We had earlier characterized a cDNA of the first monocot member of Aux/IAA family from rice. The achievement of the large scale rice genome sequencing combined with the availability of full-length cDNA sequences from Knowledge-based Oryza Molecular Biological Encyclopedia provided us the opportunity to draw up the first comprehensive list of Aux/IAA genes in a monocot. By screening the available databases, we have identified 31 Aux/IAA genes having high sequence identity within the conserved domains I, II, III, and IV. The genomic organization as well as chromosomal location of all the Oryza sativa indoleacetic acid ( OsIAA) genes is reported. The rice Aux/IAA proteins can be classified in two groups (A and B) on the basis of their phylogenetic relationship with Arabidopsis Aux/IAA proteins. An evolutionary pattern of the rice Aux/IAA genes has been discussed by analyzing their structure (exon/intron organization) and duplications. Interestingly, the duplication of rice Aux/IAA genes was found to be associated with chromosomal block duplication events in rice. The in-silico analysis has been complemented with real-time polymerase chain reaction analysis to quantify transcript levels of all Aux/IAA family members. OsIAA genes showed differential and overlapping organ-specific expression patterns in light- and dark-grown seedlings/plants. Although auxin enhanced the transcript abundance of most of the OsIAA genes, the effect was more pronounced on OsIAA9, 14, 19, 20, 24, and 31. These results provide a foundation for future studies on elucidating the precise role of rice Aux/IAA genes in early steps of auxin signal transduction. [ABSTRACT FROM AUTHOR]

The COP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1) gene has been identified earlier from dicot species namely Arabidopsis, tomato and pea. The protein encoded by this gene acts as a molecular switch that negatively regulates the transition from the skotomorphogenic to the photomorphogenic mode of plant development. We have isolated and characterized the COP1 homolog from a monocot species, i.e. rice (var. Pusa Basmati 1). All the functional domains (Zn-binding RING finger motif, coiled-coil region, WD-40 repeats, cytoplasmic/nuclear localization sequences and protein-protein interaction domains) that are known in the COP1 proteins from dicots are conserved in COP1 from rice as well. The transcript levels of COP1 vary in various tissues of the rice plant. These variations were found to be development-dependent and do not solely depend on the light conditions. [ABSTRACT FROM PUBLISHER]

Transcriptional regulation includes both activation and repression of downstream genes. In plants, a well-established class of repressors are proteins with an ERF-associated amphiphilic repression/EAR domain. They contain either DLNxxP or LxLxL as the identifying hexapeptide motif. In rice (Oryza sativa), we have identified a total of 266 DLN repressor proteins, with the former motif and its modifications thereof comprising 227 transcription factors and 39 transcriptional regulators. Apart from DLNxxP motif conservation, DLNxP and DLNxxxP motifs with variable numbers/positions of proline and those without any proline conservation have been identified. Most of the DLN repressome proteins have a single DLN motif, with higher relative percentage in the C-terminal region. We have designed a simple yeast-based experiment wherein a DLN motif can successfully cause strong repression of downstream reporter genes, when fused to a transcriptional activator of rice or yeast. The DLN hexapeptide motif is essential for repression, and at least two "DLN" residues cause maximal repression. Comparatively, rice has more DLN repressor encoding genes than Arabidopsis, and DLNSPP motif from rice is 40% stronger than the known Arabidopsis SRDX motif. The study reports a straightforward assay to analyze repressor activity, along with the identification of a strong DLN repressor from rice. [ABSTRACT FROM AUTHOR]

For accurate and reliable gene expression results, normalization of real-time PCR data is required against a control gene, which displays highly uniform expression in living organisms during various phases of development and under different environmental conditions. We assessed the gene expression of 10 frequently used housekeeping genes, including 18S rRNA, 25S rRNA, UBC, UBQ5, UBQ10, ACT11, GAPDH, eEF-1α, eIF-4a, and β-TUB, in a diverse set of 25 rice samples. Their expression varied considerably in different tissue samples analyzed. The expression of UBQ5 and eEF-1α was most stable across all the tissue samples examined. However, 18S and 25S rRNA exhibited most stable expression in plants grown under various environmental conditions. Also, a set of two genes was found to be better as control for normalization of the data. The expression of these genes (with more uniform expression) can be used for normalization of real-time PCR results for gene expression studies in a wide variety of samples in rice. [Copyright &y& Elsevier]

Pollen development and its germination are obligatory for the reproductive success of flowering plants. Calcium-dependent protein kinases (CPKs, also known as CDPKs) regulate diverse signaling pathways controlling plant growth and development. Here, we report the functional characterization of a novel OsCPK29 from rice, which is mainly expressed during pollen maturation stages of the anther. OsCPK29 exclusively localizes in the nucleus, and its N-terminal variable domain is responsible for retaining it in the nucleus. OsCPK29 knockdown rice plants exhibit reduced fertility, set fewer seeds, and produce collapsed non-viable pollen grains that do not germinate. Cytological analysis of anther semi-thin sections during different developmental stages suggested that pollen abnormalities appear after the vacuolated pollen stage. Detailed microscopic study of pollen grains further revealed that they were lacking the functional intine layer although exine layer was present. Consistent with that, downregulation of known intine development-related rice genes was also observed in OsCPK29 silenced anthers. Furthermore, it has been demonstrated that OsCPK29 interacts in vitro as well as in vivo with the MADS68 transcription factor which is a known regulator of pollen development. Therefore, phenotypic observations and molecular studies suggest that OsCPK29 is an important regulator of pollen development in rice. • OsCPK29 is a nuclear-localized protein kinase expressed during late pollen development. • Silencing of OsCPK29 severely affects fertility and seed set in rice owing to the failure of pollen maturation. • OsCPK29 silenced pollen grains lack an intine layer and fail to germinate. • OsCPK29 physically interacts with MADS68 in vitro and in vivo and possibly controls the expression of its target genes. [ABSTRACT FROM AUTHOR]

Eukaryotic A20/AN1 zinc-finger proteins (ZFPs) play an important role in the regulation of immune and stress response. After elucidation of the role of first such protein, OsSAP1, in abiotic stress tolerance, 18 rice stress associated protein (SAP) genes have been shown to be regulated by multiple abiotic stresses. In the present study, expression pattern of all the 18 OsSAP genes have been analysed in response to different biotic stress simulators, in order to get insights into their possible involvement in biotic stress tolerance. Our results showed the upregulation of OsSAP1 and OsSAP11 by all biotic stress simulator treatments. Furthermore, the functional role of OsSAP1 in plant defence responses has been explored through overexpression in transgenic plants. Constitutive expression of OsSAP1 in transgenic tobacco resulted into enhanced disease resistance against virulent bacterial pathogen, together with the upregulation of known defence-related genes. Present investigation suggests that rice SAPs are responsive to multiple biotic stresses and OsSAP1 plays a key role in basal resistance against pathogen infection. This strongly supports the involvement of rice SAPs in cross-talk between biotic and abiotic stress signalling pathways, which makes them ideal candidate to design strategies for protecting crop plants against multiple stresses. [ABSTRACT FROM AUTHOR]

Abstract: Isolation and characterization of rice (Oryza sativa L. ssp. indica) OsPHOT1 cDNA, encoding a blue light photoreceptor phototropin 1, is reported. The predicted amino acid sequence of OsPHOT1 corresponds to a protein of 103.6kDa harboring two LOV domains (LOV1 and LOV2) and a C-terminal protein kinase domain conserved in other phototropins. The structural part of the gene is interrupted by 22 introns. The OsPHOT1 gene is represented by two copies in the rice genome (designated as OsPHOT1a and OsPHOT1b), one each on the duplicated segments of chromosomes 11 and 12. BLASTN and TBLASTN searches also led to the identification of another phototropin homologue, OsPHOT2, present on chromosome 4. The real-time PCR analysis showed that both the OsPHOT1 and OsPHOT2 are expressed at significantly higher levels in mature leaves. The mRNA levels of OsPHOT1 were higher in the coleoptiles and that too in the apical portion, whereas OsPHOT2 was strongly expressed in leaves of etiolated rice seedlings. The transcript levels of OsPHOT1 and OsPHOT2 were differentially regulated by a broad spectrum of light, including white, blue, red, and far-red light; the transcript levels of OsPHOT1 declined, whereas those of OsPHOT2 were upregulated. These results indicate the participation of red/far-red sensing phytochromes and blue light (perceived through either cryptochromes or phototropins) in differential regulation of transcript abundance of phototropins, OsPHOT1 and OsPHOT2. [Copyright &y& Elsevier]

Rice (Oryza sativa L. subsp. indica) cDNA for the gene OsiBBC1, encoding homologue of the breast basic conserved protein 1 (BBC1), similar to ribosomal protein L13, has been identified and characterized. OsiBBC1 codes for a 24 kDa highly basic protein with two potential bipartite nuclear localization signals (NLS) and a transcriptional activation domain (TAD). The structural part of the gene is interrupted by four introns. The OsiBBC1 gene is represented by two copies in the rice genome and both of them are expressed. Northern analysis showed that OsiBBC1 is expressed more in the young root, post-fertilized inflorescence, leaf base and callus tissue, which are comprised of actively dividing cells, indicating its role in cell division. The OsiBBC1 transcript accumulated more in the root of light-grown seedlings as compared to the shoot while its levels were higher in the shoot as compared to root of the etiolated seedlings, indicating its down-regulation by light. The western analysis, carried out using antibodies raised against a recombinant fusion protein, 6xHis–OsiBBC1, corroborated its tissue-specific expression profile observed by northern analysis. In addition, OsiBBC1/RPL13 protein could be targetted to the nucleus by particle bombardment of OsiBBC1::GUS fusion construct in the onion epidermal cells. [Copyright &y& Elsevier]