Science.gov

Sample records for rice functional genomics

  1. Ascribing Functions to Genes: Journey Towards Genetic Improvement of Rice Via Functional Genomics.

    PubMed

    Mustafiz, Ananda; Kumari, Sumita; Karan, Ratna

    2016-06-01

    Rice, one of the most important cereal crops for mankind, feeds more than half the world population. Rice has been heralded as a model cereal owing to its small genome size, amenability to easy transformation, high synteny to other cereal crops and availability of complete genome sequence. Moreover, sequence wealth in rice is getting more refined and precise due to resequencing efforts. This humungous resource of sequence data has confronted research fraternity with a herculean challenge as well as an excellent opportunity to functionally validate expressed as well as regulatory portions of the genome. This will not only help us in understanding the genetic basis of plant architecture and physiology but would also steer us towards developing improved cultivars. No single technique can achieve such a mammoth task. Functional genomics through its diverse tools viz. loss and gain of function mutants, multifarious omics strategies like transcriptomics, proteomics, metabolomics and phenomics provide us with the necessary handle. A paradigm shift in technological advances in functional genomics strategies has been instrumental in generating considerable amount of information w.r.t functionality of rice genome. We now have several databases and online resources for functionally validated genes but despite that we are far from reaching the desired milestone of functionally characterizing each and every rice gene. There is an urgent need for a common platform, for information already available in rice, and collaborative efforts between researchers in a concerted manner as well as healthy public-private partnership, for genetic improvement of rice crop better able to handle the pressures of climate change and exponentially increasing population. PMID:27252584

  2. Ascribing Functions to Genes: Journey Towards Genetic Improvement of Rice Via Functional Genomics.

    PubMed

    Mustafiz, Ananda; Kumari, Sumita; Karan, Ratna

    2016-06-01

    Rice, one of the most important cereal crops for mankind, feeds more than half the world population. Rice has been heralded as a model cereal owing to its small genome size, amenability to easy transformation, high synteny to other cereal crops and availability of complete genome sequence. Moreover, sequence wealth in rice is getting more refined and precise due to resequencing efforts. This humungous resource of sequence data has confronted research fraternity with a herculean challenge as well as an excellent opportunity to functionally validate expressed as well as regulatory portions of the genome. This will not only help us in understanding the genetic basis of plant architecture and physiology but would also steer us towards developing improved cultivars. No single technique can achieve such a mammoth task. Functional genomics through its diverse tools viz. loss and gain of function mutants, multifarious omics strategies like transcriptomics, proteomics, metabolomics and phenomics provide us with the necessary handle. A paradigm shift in technological advances in functional genomics strategies has been instrumental in generating considerable amount of information w.r.t functionality of rice genome. We now have several databases and online resources for functionally validated genes but despite that we are far from reaching the desired milestone of functionally characterizing each and every rice gene. There is an urgent need for a common platform, for information already available in rice, and collaborative efforts between researchers in a concerted manner as well as healthy public-private partnership, for genetic improvement of rice crop better able to handle the pressures of climate change and exponentially increasing population.

  3. [Genome-wide analysis and functional prediction of the Trihelix transcription factor family in rice].

    PubMed

    Jianhui, Ji; Yingjun, Zhou; Hehe, Wu; Liming, Yang

    2015-12-01

    The Trihelix transcription factor family plays an essential role in plant growth, development and stress response. However, the studies about identification and analysis of this gene family in rice on the genome-wide level have not been reported. In this study, 31 members of the Trihelix family, which contain highly conserved and characteristic trihelix domain through sequence clustering and functional domains analysis, were identified in rice genome database using bioinformatic tools. These members could be classified into 5 subfamilies (I~V) based on the evolutionary relationship and domain characteristics. Clustering analyses of the Trihelix family in rice, Arabidopsis, Brachypodium distachyom and Sorghum bicolor showed that each species contained different members of subfamily although the classification of the Trihelix family were consistent in these four species, which indicated that the differentiation of the Trihelix gene family occur earlier than that of these species. The conserved motifs in the Trihelix family of rice analyzed using the MEME program were highly consistent with the results of clustering analyses. Intraspecific and interspecific chromosomal replication in partial Trihelix family members were found to exist in rice and between rice and other species through chromosome replication analysis. Microarray data analysis revealed diverse expression patterns of Trihelix family genes in different tissues of rice or in response to six different phytohormones. Moreover, 20 members of the Trihelix transcription factor family were found to interact with other proteins in rice using RiceFRIEND online database analysis. Therefore, our results preliminarily identified the evolution, chromosome distribution and replication, expression patterns, phytohormones response of the Trihelix transcription factor family and the interaction between trihelix family proteins and other proteins in rice, which will provide a basis to further reveal the molecular evolution

  4. Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species.

    PubMed

    Singh, Sangeeta; Chand, Suresh; Singh, N K; Sharma, Tilak Raj

    2015-01-01

    The resistance (R) genes and defense response (DR) genes have become very important resources for the development of disease resistant cultivars. In the present investigation, genome-wide identification, expression, phylogenetic and synteny analysis was done for R and DR-genes across three species of rice viz: Oryza sativa ssp indica cv 93-11, Oryza sativa ssp japonica and wild rice species, Oryza brachyantha. We used the in silico approach to identify and map 786 R -genes and 167 DR-genes, 672 R-genes and 142 DR-genes, 251 R-genes and 86 DR-genes in the japonica, indica and O. brachyanth a genomes, respectively. Our analysis showed that 60.5% and 55.6% of the R-genes are tandemly repeated within clusters and distributed over all the rice chromosomes in indica and japonica genomes, respectively. The phylogenetic analysis along with motif distribution shows high degree of conservation of R- and DR-genes in clusters. In silico expression analysis of R-genes and DR-genes showed more than 85% were expressed genes showing corresponding EST matches in the databases. This study gave special emphasis on mechanisms of gene evolution and duplication for R and DR genes across species. Analysis of paralogs across rice species indicated 17% and 4.38% R-genes, 29% and 11.63% DR-genes duplication in indica and Oryza brachyantha, as compared to 20% and 26% duplication of R-genes and DR-genes in japonica respectively. We found that during the course of duplication only 9.5% of R- and DR-genes changed their function and rest of the genes have maintained their identity. Syntenic relationship across three genomes inferred that more orthology is shared between indica and japonica genomes as compared to brachyantha genome. Genome wide identification of R-genes and DR-genes in the rice genome will help in allele mining and functional validation of these genes, and to understand molecular mechanism of disease resistance and their evolution in rice and related species.

  5. A whole-genome SNP array (RICE6K) for genomic breeding in rice.

    PubMed

    Yu, Huihui; Xie, Weibo; Li, Jing; Zhou, Fasong; Zhang, Qifa

    2014-01-01

    The advances in genotyping technology provide an opportunity to use genomic tools in crop breeding. As compared to field selections performed in conventional breeding programmes, genomics-based genotype screen can potentially reduce number of breeding cycles and more precisely integrate target genes for particular traits into an ideal genetic background. We developed a whole-genome single nucleotide polymorphism (SNP) array, RICE6K, based on Infinium technology, using representative SNPs selected from more than four million SNPs identified from resequencing data of more than 500 rice landraces. RICE6K contains 5102 SNP and insertion-deletion (InDel) markers, about 4500 of which were of high quality in the tested rice lines producing highly repeatable results. Forty-five functional markers that are located inside 28 characterized genes of important traits can be detected using RICE6K. The SNP markers are evenly distributed on the 12 chromosomes of rice with the average density of 12 SNPs per 1 Mb and can provide information for polymorphisms between indica and japonica subspecies as well as varieties within indica and japonica groups. Application tests of RICE6K showed that the array is suitable for rice germplasm fingerprinting, genotyping bulked segregating pools, seed authenticity check and genetic background selection. These results suggest that RICE6K provides an efficient and reliable genotyping tool for rice genomic breeding.

  6. Functional and genomic insights into the pathogenesis of Burkholderia species to rice.

    PubMed

    Naughton, Lynn M; An, Shi-qi; Hwang, Ingyu; Chou, Shan-Ho; He, Yong-Qiang; Tang, Ji-Liang; Ryan, Robert P; Dow, J Maxwell

    2016-03-01

    A number of species of bacteria from the genus Burkholderia have been shown to be causal agents of diseases of rice. These diseases, caused by Burkholderia glumae, B. gladioli and B. plantarii, are becoming increasingly common across the globe. This is particularly so for B. glumae, whose ability to grow at elevated temperatures suggests that it may become a prevalent problem in an era of global warming. Despite the increasing threat to rice, relatively little is known about the virulence mechanisms employed by these pathogens. Work over the last 5 years has provided an increasing insight into these factors and their control by environmental and other cues. In addition, the determination of a number of genome sequences has allowed bioinformatic predictions of further possible mechanisms, which can now be investigated experimentally. Here, we review recent advances in the understanding of virulence of Burkholderia to rice, to include discussion of the roles of toxins, type II secreted enzymes, type III secreted effectors and motility as well as their regulation by quorum sensing, two-component systems and cyclic di-GMP signalling. Finally, we consider a number of approaches for the control of bacterial virulence through the modulation of quorum sensing and toxin degradation.

  7. Harvesting rice's dispensable genome.

    PubMed

    Wing, Rod A

    2015-01-01

    A rapid and cost-effective approach has been developed to harvest and map the dispensable genome, that is, population-level natural sequence variation within a species that is not present in static genome assemblies. PMID:26429765

  8. Metabolomic and functional genomic analyses reveal varietal differences in bioactive compounds of cooked rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Emerging evidence supports that cooked brown rice (Oryza sativa L.) contains metabolites with biomedical activities, yet little is known about the genetic diversity that is responsible for metabolite variation and differences in health beneficial traits. Metabolites from cooked brown rice of ten div...

  9. Insights into genomics of salt stress response in rice.

    PubMed

    Kumar, Kundan; Kumar, Manu; Kim, Seong-Ryong; Ryu, Hojin; Cho, Yong-Gu

    2013-01-01

    Plants, as sessile organisms experience various abiotic stresses, which pose serious threat to crop production. Plants adapt to environmental stress by modulating their growth and development along with the various physiological and biochemical changes. This phenotypic plasticity is driven by the activation of specific genes encoding signal transduction, transcriptional regulation, ion transporters and metabolic pathways. Rice is an important staple food crop of nearly half of the world population and is well known to be a salt sensitive crop. The completion and enhanced annotations of rice genome sequence has provided the opportunity to study functional genomics of rice. Functional genomics aids in understanding the molecular and physiological basis to improve the salinity tolerance for sustainable rice production. Salt tolerant transgenic rice plants have been produced by incorporating various genes into rice. In this review we present the findings and investigations in the field of rice functional genomics that includes supporting genes and networks (ABA dependent and independent), osmoprotectants (proline, glycine betaine, trehalose, myo-inositol, and fructans), signaling molecules (Ca2+, abscisic acid, jasmonic acid, brassinosteroids) and transporters, regulating salt stress response in rice. PMID:24280112

  10. Identification and functional characterization of silicon transporters in soybean using comparative genomics of major intrinsic proteins in Arabidopsis and rice.

    PubMed

    Deshmukh, Rupesh K; Vivancos, Julien; Guérin, Valérie; Sonah, Humira; Labbé, Caroline; Belzile, François; Bélanger, Richard R

    2013-11-01

    Silicon (Si) confers several benefits to many plant species when absorbed as silicic acid through nodulin 26-like intrinsic proteins (NIPs). The NIPs belong to major intrinsic protein (MIP) family, members of which form channels with high selectivity to control transport of water and different solutes. Here, comparative genomic analysis of the MIPs was performed to investigate the presence of Si transporter MIPs in soybean. Thorough analysis of phylogeny, gene organization, transcriptome profiling and protein modeling was performed to characterize MIPs in rice, Arabidopsis and soybean. Based on several attributes, two putative Si transporter genes, GmNIP2-1 and GmNIP2-2, were identified, characterized and cloned from soybean. Expression of both genes was detected in shoot and root tissues, and decreased as Si increased. The protein encoded by GmNIP2-2 showed functionality for Si transport when expressed in Xenopus oocytes, thus confirming the genetic capability of soybean to absorb the element. Comparative analysis of MIPs in plants provides opportunities to decipher gene evolution, functionality and selectivity of nutrient uptake mechanisms. Exploitation of this strategy has helped to uncover unique features of MIPs in soybean. The identification and functional characterization of Si transporters can be exploited to optimize the benefits that plants can derive from Si absorption. PMID:23771580

  11. Genome-wide identification and expression analysis of rice pectin methylesterases: Implication of functional roles of pectin modification in rice physiology.

    PubMed

    Jeong, Ho Young; Nguyen, Hong Phuong; Lee, Chanhui

    2015-07-01

    Pectin, which is enriched in primary cell walls and middle lamellae, is an essential polysaccharide in all higher plants. Homogalacturonans (HGA), a major form of pectin, are synthesized and methylesterified by enzymes localized in the Golgi apparatus and transported into the cell wall. Depending on cell type, the degree and pattern of pectin methylesterification are strictly regulated by cell wall-localized pectin methylesterases (PMEs). Despite its importance in plant development and growth, little is known about the physiological functions of pectin in rice, which contains 43 different types of PME. The presence of pectin in rice cell walls has been substantiated by uronic acid quantification and immunodetection of JIM7 monoclonal antibodies. We performed PME activity assays with cell wall proteins isolated from different rice tissues. In accordance with data from Arabidopsis, the highest activity was observed in germinating tissues, young culm, and spikelets, where cells are actively elongating. Transcriptional profiling of OsPMEs by real-time PCR and meta-analysis indicates that PMEs exhibit spatial- and stress-specific expression patterns during rice development. Based on in silico analysis, we identified subcellular compartments, isoelectric point, and cleavage sites of OsPMEs. Our findings provide an important tool for further studies seeking to unravel the functional importance of pectin modification during plant growth and abiotic and biotic responses of grass plants.

  12. Extensive de Novo genomic variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.).

    PubMed

    Wang, Yong-Ming; Dong, Zhen-Ying; Zhang, Zhong-Juan; Lin, Xiu-Yun; Shen, Ye; Zhou, Daowei; Liu, Bao

    2005-08-01

    To study the possible impact of alien introgression on a recipient plant genome, we examined >6000 unbiased genomic loci of three stable rice recombinant inbred lines (RILs) derived from intergeneric hybridization between rice (cv. Matsumae) and a wild relative (Zizania latifolia Griseb.) followed by successive selfing. Results from amplified fragment length polymorphism (AFLP) analysis showed that, whereas the introgressed Zizania DNA comprised <0.1% of the genome content in the RILs, extensive and genome-wide de novo variations occurred in up to 30% of the analyzed loci for all three lines studied. The AFLP-detected changes were validated by DNA gel-blot hybridization and/or sequence analysis of genomic loci corresponding to a subset of the differentiating AFLP fragments. A BLAST analysis revealed that the genomic variations occurred in diverse sequences, including protein-coding genes, transposable elements, and sequences of unknown functions. Pairwise sequence comparison of selected loci between a RIL and its rice parent showed that the variations represented either base substitutions or small insertion/deletions. Genome variations were detected in all 12 rice chromosomes, although their distribution was uneven both among and within chromosomes. Taken together, our results imply that even cryptic alien introgression can be highly mutagenic to a recipient plant genome. PMID:15937131

  13. The rice mitochondrial genomes and their variations.

    PubMed

    Tian, Xiangjun; Zheng, Jing; Hu, Songnian; Yu, Jun

    2006-02-01

    Based on highly redundant and high-quality sequences, we assembled rice (Oryza sativa) mitochondrial genomes for two cultivars, 93-11 (an indica variety) and PA64S (an indica-like variety with maternal origin of japonica), which are paternal and maternal strains of an elite superhybrid rice Liang-You-Pei-Jiu (LYP-9), respectively. Following up with a previous analysis on rice chloroplast genomes, we divided mitochondrial sequence variations into two basic categories, intravarietal and intersubspecific. Intravarietal polymorphisms are variations within mitochondrial genomes of an individual variety. Intersubspecific polymorphisms are variations between subspecies among their major genotypes. In this study, we identified 96 single nucleotide polymorphisms (SNPs), 25 indels, and three segmental sequence variations as intersubspecific polymorphisms. A signature sequence fragment unique to indica varieties was confirmed experimentally and found in two wild rice samples, but absent in japonica varieties. The intersubspecific polymorphism rate for mitochondrial genomes is 0.02% for SNPs and 0.006% for indels, nearly 2.5 and 3 times lower than that of their chloroplast counterparts and 21 and 38 times lower than corresponding rates of the rice nuclear genome, respectively. The intravarietal polymorphism rates among analyzed mitochondrial genomes, such as 93-11 and PA64S, are 1.26% and 1.38% for SNPs and 1.13% and 1.09% for indels, respectively. Based on the total number of SNPs between the two mitochondrial genomes, we estimate that the divergence of indica and japonica mitochondrial genomes occurred approximately 45,000 to 250,000 years ago. PMID:16384910

  14. Plant functional genomics.

    PubMed

    Holtorf, Hauke; Guitton, Marie-Christine; Reski, Ralf

    2002-06-01

    Functional genome analysis of plants has entered the high-throughput stage. The complete genome information from key species such as Arabidopsis thaliana and rice is now available and will further boost the application of a range of new technologies to functional plant gene analysis. To broadly assign functions to unknown genes, different fast and multiparallel approaches are currently used and developed. These new technologies are based on known methods but are adapted and improved to accommodate for comprehensive, large-scale gene analysis, i.e. such techniques are novel in the sense that their design allows researchers to analyse many genes at the same time and at an unprecedented pace. Such methods allow analysis of the different constituents of the cell that help to deduce gene function, namely the transcripts, proteins and metabolites. Similarly the phenotypic variations of entire mutant collections can now be analysed in a much faster and more efficient way than before. The different methodologies have developed to form their own fields within the functional genomics technological platform and are termed transcriptomics, proteomics, metabolomics and phenomics. Gene function, however, cannot solely be inferred by using only one such approach. Rather, it is only by bringing together all the information collected by different functional genomic tools that one will be able to unequivocally assign functions to unknown plant genes. This review focuses on current technical developments and their impact on the field of plant functional genomics. The lower plant Physcomitrella is introduced as a new model system for gene function analysis, owing to its high rate of homologous recombination.

  15. Detection of genomic deletions in rice using oligonucleotide microarrays

    PubMed Central

    Bruce, Myron; Hess, Ann; Bai, Jianfa; Mauleon, Ramil; Diaz, M Genaleen; Sugiyama, Nobuko; Bordeos, Alicia; Wang, Guo-Liang; Leung, Hei; Leach, Jan E

    2009-01-01

    Background The induction of genomic deletions by physical- or chemical- agents is an easy and inexpensive means to generate a genome-saturating collection of mutations. Different mutagens can be selected to ensure a mutant collection with a range of deletion sizes. This would allow identification of mutations in single genes or, alternatively, a deleted group of genes that might collectively govern a trait (e.g., quantitative trait loci, QTL). However, deletion mutants have not been widely used in functional genomics, because the mutated genes are not tagged and therefore, difficult to identify. Here, we present a microarray-based approach to identify deleted genomic regions in rice mutants selected from a large collection generated by gamma ray or fast neutron treatment. Our study focuses not only on the utility of this method for forward genetics, but also its potential as a reverse genetics tool through accumulation of hybridization data for a collection of deletion mutants harboring multiple genetic lesions. Results We demonstrate that hybridization of labeled genomic DNA directly onto the Affymetrix Rice GeneChip® allows rapid localization of deleted regions in rice mutants. Deletions ranged in size from one gene model to ~500 kb and were predicted on all 12 rice chromosomes. The utility of the technique as a tool in forward genetics was demonstrated in combination with an allelic series of mutants to rapidly narrow the genomic region, and eventually identify a candidate gene responsible for a lesion mimic phenotype. Finally, the positions of mutations in 14 mutants were aligned onto the rice pseudomolecules in a user-friendly genome browser to allow for rapid identification of untagged mutations . Conclusion We demonstrate the utility of oligonucleotide arrays to discover deleted genes in rice. The density and distribution of deletions suggests the feasibility of a database saturated with deletions across the rice genome. This community resource can continue

  16. Understanding of evolutionary genomics of invasive species of rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Red rice is an aggressive, weedy form of cultivated rice (Oryza sativa) that infests crop fields and is a primary factor limiting rice productivity in the U.S. and worldwide. As the weedy relative of a genomic model species, red rice is a model for understanding the genetic and evolutionary mechani...

  17. Genome-wide analysis of chitinase genes and their varied functions in larval moult, pupation and eclosion in the rice striped stem borer, Chilo suppressalis.

    PubMed

    Su, C; Tu, G; Huang, S; Yang, Q; Shahzad, M F; Li, F

    2016-08-01

    Some insect chitinases are required to degrade chitin and ensure successful metamorphosis. Although chitinase genes have been well characterized in several model insects, no reports exist for the rice striped stem borer, Chilo suppressalis, a highly destructive pest that causes huge yield losses in rice production. Here, we conducted a genome-level analysis of chitinase genes in C. suppressalis. After amplification of full-length transcripts with rapid amplification of cDNA ends, we identified 12 chitinase genes in C. suppressalis. All these genes had the conserved domains and motifs of glycoside hydrolase family 18 and grouped phylogenetically into five subgroups. C. suppressalis chitinase 1 (CsCht1) was highly expressed in late pupae, whereas CsCht3 was abundant in early pupae. Both CsCht2 and CsCht4 were highly expressed in larvae. CsCht2 was abundant specifically in the third-instar larvae and CsCht4 showed periodic high expression in 2- to 5-day-old larvae in each instar. Tissue specific expression analysis indicated that CsCht1 and CsCht3 were highly expressed in epidermis whereas CsCht2 and CsCht4 were specifically abundant in the midgut. Knockdown of CsCht1 resulted in adults with curled wings, indicating that CsCht1 might have an important role in wing expansion. Silencing of CsCht2 or CsCht4 arrested moulting, suggesting essential roles in larval development. When the expression of CsCht3 was interfered, defects in pupation occurred. Overall, we provide here the first catalogue of chitinase genes in the rice striped stem borer and have elucidated the functions of four chitinases in metamorphosis. PMID:27080989

  18. Structure, Function, and Evolution of Rice Centromeres

    SciTech Connect

    Jiang, Jiming

    2010-02-04

    The centromere is the most characteristic landmark of eukaryotic chromosomes. Centromeres function as the site for kinetochore assembly and spindle attachment, allowing for the faithful pairing and segregation of sister chromatids during cell division. Characterization of centromeric DNA is not only essential to understand the structure and organization of plant genomes, but it is also a critical step in the development of plant artificial chromosomes. The centromeres of most model eukaryotic species, consist predominantly of long arrays of satellite DNA. Determining the precise DNA boundary of a centromere has proven to be a difficult task in multicellular eukaryotes. We have successfully cloned and sequenced the centromere of rice chromosome 8 (Cen8), representing the first fully sequenced centromere from any multicellular eukaryotes. The functional core of Cen8 spans ~800 kb of DNA, which was determined by chromatin immunoprecipitation (ChIP) using an antibody against the rice centromere-specific H3 histone. We discovered 16 actively transcribed genes distributed throughout the Cen8 region. In addition to Cen8, we have characterized eight additional rice centromeres using the next generation sequencing technology. We discovered four subfamilies of the CRR retrotransposon that is highly enriched in rice centromeres. CRR elements are constitutively transcribed and different CRR subfamilies are differentially processed by RNAi. These results suggest that different CRR subfamilies may play different roles in the RNAi-mediated pathway for formation and maintenance of centromeric chromatin.

  19. Rice genomes recorded ancient pararetrovirus activities: Virus genealogy and multiple origins of endogenization during rice speciation.

    PubMed

    Chen, Sunlu; Liu, Ruifang; Koyanagi, Kanako O; Kishima, Yuji

    2014-12-01

    Viral fossils in rice genomes are a best entity to understand ancient pararetrovirus activities through host plant history because of our advanced knowledge of the genomes and evolutionary history with rice and its related species. Here, we explored organization, geographic origins and genealogy of rice pararetroviruses, which were turned into endogenous rice tungro bacilliform virus-like (eRTBVL) sequences. About 300 eRTBVL sequences from three representative rice genomes were clearly classified into six families. Most of the endogenization events of the eRTBVLs were initiated before differentiation of the rice progenitor (> 160,000 years ago). We successfully followed the genealogy of old relic viruses during rice speciation, and inferred the geographical origins for these viruses. Possible virus genomic sequences were explained mostly by recombinations between different virus families. Interestingly, we discovered that only a few recombination events among the numerous occasions had determined the virus genealogy. PMID:25461539

  20. Draft Genome Sequence of Rice Isolate Pseudomonas chlororaphis EA105

    PubMed Central

    McCully, Lucy M.; Bitzer, Adam S.; Spence, Carla A.; Bais, Harsh P.

    2014-01-01

    Pseudomonas chlororaphis EA105, a strain isolated from rice rhizosphere, has shown antagonistic activities against a rice fungal pathogen, and could be important in defense against rice blast. We report the draft genome sequence of EA105, which is an estimated size of 6.6 Mb. PMID:25540352

  1. Genome-wide study of KNOX regulatory network reveals brassinosteroid catabolic genes important for shoot meristem function in rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In flowering plants, knotted1-like homeobox (KNOX) transcription factors play crucial roles in establishment and maintenance of the shoot apical meristem (SAM), from which aerial organs such as leaves, stems, and flowers initiate. We report that a rice (Oryza sativa) KNOX gene Oryza sativa homeobox1...

  2. Comparative DNA Sequence Analysis of Wheat and Rice Genomes

    PubMed Central

    Sorrells, Mark E.; La Rota, Mauricio; Bermudez-Kandianis, Catherine E.; Greene, Robert A.; Kantety, Ramesh; Munkvold, Jesse D.; Miftahudin; Mahmoud, Ahmed; Ma, Xuefeng; Gustafson, Perry J.; Qi, Lili L.; Echalier, Benjamin; Gill, Bikram S.; Matthews, David E.; Lazo, Gerard R.; Chao, Shiaoman; Anderson, Olin D.; Edwards, Hugh; Linkiewicz, Anna M.; Dubcovsky, Jorge; Akhunov, Eduard D.; Dvorak, Jan; Zhang, Deshui; Nguyen, Henry T.; Peng, Junhua; Lapitan, Nora L.V.; Gonzalez-Hernandez, Jose L.; Anderson, James A.; Hossain, Khwaja; Kalavacharla, Venu; Kianian, Shahryar F.; Choi, Dong-Woog; Close, Timothy J.; Dilbirligi, Muharrem; Gill, Kulvinder S.; Steber, Camille; Walker-Simmons, Mary K.; McGuire, Patrick E.; Qualset, Calvin O.

    2003-01-01

    The use of DNA sequence-based comparative genomics for evolutionary studies and for transferring information from model species to crop species has revolutionized molecular genetics and crop improvement strategies. This study compared 4485 expressed sequence tags (ESTs) that were physically mapped in wheat chromosome bins, to the public rice genome sequence data from 2251 ordered BAC/PAC clones using BLAST. A rice genome view of homologous wheat genome locations based on comparative sequence analysis revealed numerous chromosomal rearrangements that will significantly complicate the use of rice as a model for cross-species transfer of information in nonconserved regions. PMID:12902377

  3. Rice breeding in the post-genomics era: from concept to practice.

    PubMed

    Li, Zhi-Kang; Zhang, Fan

    2013-05-01

    Future world food security requires continued and sustainable increase in rice production. Much of this increase has to come from new high yielding cultivars with resistances to multiple stresses. While future rice breeding in the post-genomics era has to build upon the progress in rice functional genomics research, great challenges remain in understanding the genetic/molecular systems underlying complex traits and linking the tremendous genome sequence diversity in the rice germplasm collections to the phenotypic variation of important traits. To meet the challenges in future rice improvement, a molecular breeding (MB) strategy has been practiced in China with significant progress in establishing the MB material and information platforms in the process of breeding, and in developing new varieties through two novel MB schemes. However, full implementation of this strategy requires tremendous investment to build capacities in high-throughput genotyping, reliable/precision phenotyping and in developing and adopting new genomics/genetic information-based analytic/application breeding tools, which are not in place in most of the public rice breeding institutions. Nevertheless, future advances and developments in these areas are expected to generate enormous knowledge of rice traits and application tools that enable breeders to deploy more efficient and effective breeding strategies to maximize rice productivity and resource use efficiencies in various ecosystems. PMID:23571011

  4. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.

    PubMed

    Duitama, Jorge; Silva, Alexander; Sanabria, Yamid; Cruz, Daniel Felipe; Quintero, Constanza; Ballen, Carolina; Lorieux, Mathias; Scheffler, Brian; Farmer, Andrew; Torres, Edgar; Oard, James; Tohme, Joe

    2015-01-01

    Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops. PMID:25923345

  5. Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection

    PubMed Central

    Duitama, Jorge; Silva, Alexander; Sanabria, Yamid; Cruz, Daniel Felipe; Quintero, Constanza; Ballen, Carolina; Lorieux, Mathias; Scheffler, Brian; Farmer, Andrew; Torres, Edgar; Oard, James; Tohme, Joe

    2015-01-01

    Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops. PMID:25923345

  6. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.

    PubMed

    Duitama, Jorge; Silva, Alexander; Sanabria, Yamid; Cruz, Daniel Felipe; Quintero, Constanza; Ballen, Carolina; Lorieux, Mathias; Scheffler, Brian; Farmer, Andrew; Torres, Edgar; Oard, James; Tohme, Joe

    2015-01-01

    Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.

  7. Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.

    PubMed

    Sakai, Hiroaki; Lee, Sung Shin; Tanaka, Tsuyoshi; Numa, Hisataka; Kim, Jungsok; Kawahara, Yoshihiro; Wakimoto, Hironobu; Yang, Ching-chia; Iwamoto, Masao; Abe, Takashi; Yamada, Yuko; Muto, Akira; Inokuchi, Hachiro; Ikemura, Toshimichi; Matsumoto, Takashi; Sasaki, Takuji; Itoh, Takeshi

    2013-02-01

    The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics.

  8. Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis.

    PubMed

    Narsai, Reena; Devenish, James; Castleden, Ian; Narsai, Kabir; Xu, Lin; Shou, Huixia; Whelan, James

    2013-12-01

    Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or 'expressology', thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au).

  9. Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis

    PubMed Central

    Narsai, Reena; Devenish, James; Castleden, Ian; Narsai, Kabir; Xu, Lin; Shou, Huixia; Whelan, James

    2013-01-01

    Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or ‘expressology’, thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au). PMID:24147765

  10. Genome duplication improves rice root resistance to salt stress

    PubMed Central

    2014-01-01

    Background Salinity is a stressful environmental factor that limits the productivity of crop plants, and roots form the major interface between plants and various abiotic stresses. Rice is a salt-sensitive crop and its polyploid shows advantages in terms of stress resistance. The objective of this study was to investigate the effects of genome duplication on rice root resistance to salt stress. Results Both diploid rice (HN2026-2x and Nipponbare-2x) and their corresponding tetraploid rice (HN2026-4x and Nipponbare-4x) were cultured in half-strength Murashige and Skoog medium with 150 mM NaCl for 3 and 5 days. Accumulations of proline, soluble sugar, malondialdehyde (MDA), Na+ content, H+ (proton) flux at root tips, and the microstructure and ultrastructure in rice roots were examined. We found that tetraploid rice showed less root growth inhibition, accumulated higher proline content and lower MDA content, and exhibited a higher frequency of normal epidermal cells than diploid rice. In addition, a protective gap appeared between the cortex and pericycle cells in tetraploid rice. Next, ultrastructural analysis showed that genome duplication improved membrane, organelle, and nuclei stability. Furthermore, Na+ in tetraploid rice roots significantly decreased while root tip H+ efflux in tetraploid rice significantly increased. Conclusions Our results suggest that genome duplication improves root resistance to salt stress, and that enhanced proton transport to the root surface may play a role in reducing Na+ entrance into the roots. PMID:25184027

  11. Validation of rice genome sequence by optical mapping

    PubMed Central

    Zhou, Shiguo; Bechner, Michael C; Place, Michael; Churas, Chris P; Pape, Louise; Leong, Sally A; Runnheim, Rod; Forrest, Dan K; Goldstein, Steve; Livny, Miron; Schwartz, David C

    2007-01-01

    Background Rice feeds much of the world, and possesses the simplest genome analyzed to date within the grass family, making it an economically relevant model system for other cereal crops. Although the rice genome is sequenced, validation and gap closing efforts require purely independent means for accurate finishing of sequence build data. Results To facilitate ongoing sequencing finishing and validation efforts, we have constructed a whole-genome SwaI optical restriction map of the rice genome. The physical map consists of 14 contigs, covering 12 chromosomes, with a total genome size of 382.17 Mb; this value is about 11% smaller than original estimates. 9 of the 14 optical map contigs are without gaps, covering chromosomes 1, 2, 3, 4, 5, 7, 8 10, and 12 in their entirety – including centromeres and telomeres. Alignments between optical and in silico restriction maps constructed from IRGSP (International Rice Genome Sequencing Project) and TIGR (The Institute for Genomic Research) genome sequence sources are comprehensive and informative, evidenced by map coverage across virtually all published gaps, discovery of new ones, and characterization of sequence misassemblies; all totalling ~14 Mb. Furthermore, since optical maps are ordered restriction maps, identified discordances are pinpointed on a reliable physical scaffold providing an independent resource for closure of gaps and rectification of misassemblies. Conclusion Analysis of sequence and optical mapping data effectively validates genome sequence assemblies constructed from large, repeat-rich genomes. Given this conclusion we envision new applications of such single molecule analysis that will merge advantages offered by high-resolution optical maps with inexpensive, but short sequence reads generated by emerging sequencing platforms. Lastly, map construction techniques presented here points the way to new types of comparative genome analysis that would focus on discernment of structural differences

  12. Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot.

    PubMed

    Quibod, Ian Lorenzo; Grande, Genelou; Oreiro, Eula Gems; Borja, Frances Nikki; Dossa, Gerbert Sylvestre; Mauleon, Ramil; Cruz, Casiana Vera; Oliva, Ricardo

    2015-01-01

    Sheath rot complex and seed discoloration in rice involve a number of pathogenic bacteria that cannot be associated with distinctive symptoms. These pathogens can easily travel on asymptomatic seeds and therefore represent a threat to rice cropping systems. Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world. The appearance of a similar Pseudomonas population, which here we named P. fuscovaginae-like, represents a perfect opportunity to understand common genomic features that can explain the infection mechanism in rice. We showed that the novel population is indeed closely related to P. fuscovaginae. A comparative genomics approach on eight rice-infecting Pseudomonas revealed heterogeneous genomes and a high number of strain-specific genes. The genomes of P. fuscovaginae-like harbor four secretion systems (Type I, II, III, and VI) and other important pathogenicity machinery that could probably facilitate rice colonization. We identified 123 core secreted proteins, most of which have strong signatures of positive selection suggesting functional adaptation. Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism. The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments. PMID:26422147

  13. Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot.

    PubMed

    Quibod, Ian Lorenzo; Grande, Genelou; Oreiro, Eula Gems; Borja, Frances Nikki; Dossa, Gerbert Sylvestre; Mauleon, Ramil; Cruz, Casiana Vera; Oliva, Ricardo

    2015-01-01

    Sheath rot complex and seed discoloration in rice involve a number of pathogenic bacteria that cannot be associated with distinctive symptoms. These pathogens can easily travel on asymptomatic seeds and therefore represent a threat to rice cropping systems. Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world. The appearance of a similar Pseudomonas population, which here we named P. fuscovaginae-like, represents a perfect opportunity to understand common genomic features that can explain the infection mechanism in rice. We showed that the novel population is indeed closely related to P. fuscovaginae. A comparative genomics approach on eight rice-infecting Pseudomonas revealed heterogeneous genomes and a high number of strain-specific genes. The genomes of P. fuscovaginae-like harbor four secretion systems (Type I, II, III, and VI) and other important pathogenicity machinery that could probably facilitate rice colonization. We identified 123 core secreted proteins, most of which have strong signatures of positive selection suggesting functional adaptation. Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism. The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.

  14. Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot

    PubMed Central

    Quibod, Ian Lorenzo; Grande, Genelou; Oreiro, Eula Gems; Borja, Frances Nikki; Dossa, Gerbert Sylvestre; Mauleon, Ramil; Cruz, Casiana Vera; Oliva, Ricardo

    2015-01-01

    Sheath rot complex and seed discoloration in rice involve a number of pathogenic bacteria that cannot be associated with distinctive symptoms. These pathogens can easily travel on asymptomatic seeds and therefore represent a threat to rice cropping systems. Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world. The appearance of a similar Pseudomonas population, which here we named P. fuscovaginae-like, represents a perfect opportunity to understand common genomic features that can explain the infection mechanism in rice. We showed that the novel population is indeed closely related to P. fuscovaginae. A comparative genomics approach on eight rice-infecting Pseudomonas revealed heterogeneous genomes and a high number of strain-specific genes. The genomes of P. fuscovaginae-like harbor four secretion systems (Type I, II, III, and VI) and other important pathogenicity machinery that could probably facilitate rice colonization. We identified 123 core secreted proteins, most of which have strong signatures of positive selection suggesting functional adaptation. Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism. The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments. PMID:26422147

  15. Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice

    PubMed Central

    Hernandez, Ryan D; Boyko, Adam; Fledel-Alon, Adi; York, Thomas L; Polato, Nicholas R; Olsen, Kenneth M; Nielsen, Rasmus; McCouch, Susan R; Bustamante, Carlos D; Purugganan, Michael D

    2007-01-01

    Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns of polymorphisms in rice, including a (i) selectively neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and (iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been the dominant demographic model for domesticated species, cannot explain the derived nucleotide polymorphism site frequency spectrum in rice. Instead, a bottleneck model that incorporates selective sweeps, or a more complex demographic model that includes subdivision and gene flow, are more plausible explanations for patterns of variation in domesticated rice varieties. If selective sweeps are indeed the explanation for the observed nucleotide data of domesticated rice, it suggests that strong selection can leave its imprint on genome-wide polymorphism patterns, contrary to expectations that selection results only in a local signature of variation. PMID:17907810

  16. Genomic evolution of Saccharomyces cerevisiae under Chinese rice wine fermentation.

    PubMed

    Li, Yudong; Zhang, Weiping; Zheng, Daoqiong; Zhou, Zhan; Yu, Wenwen; Zhang, Lei; Feng, Lifang; Liang, Xinle; Guan, Wenjun; Zhou, Jingwen; Chen, Jian; Lin, Zhenguo

    2014-09-10

    Rice wine fermentation represents a unique environment for the evolution of the budding yeast, Saccharomyces cerevisiae. To understand how the selection pressure shaped the yeast genome and gene regulation, we determined the genome sequence and transcriptome of a S. cerevisiae strain YHJ7 isolated from Chinese rice wine (Huangjiu), a popular traditional alcoholic beverage in China. By comparing the genome of YHJ7 to the lab strain S288c, a Japanese sake strain K7, and a Chinese industrial bioethanol strain YJSH1, we identified many genomic sequence and structural variations in YHJ7, which are mainly located in subtelomeric regions, suggesting that these regions play an important role in genomic evolution between strains. In addition, our comparative transcriptome analysis between YHJ7 and S288c revealed a set of differentially expressed genes, including those involved in glucose transport (e.g., HXT2, HXT7) and oxidoredutase activity (e.g., AAD10, ADH7). Interestingly, many of these genomic and transcriptional variations are directly or indirectly associated with the adaptation of YHJ7 strain to its specific niches. Our molecular evolution analysis suggested that Japanese sake strains (K7/UC5) were derived from Chinese rice wine strains (YHJ7) at least approximately 2,300 years ago, providing the first molecular evidence elucidating the origin of Japanese sake strains. Our results depict interesting insights regarding the evolution of yeast during rice wine fermentation, and provided a valuable resource for genetic engineering to improve industrial wine-making strains.

  17. RiceVarMap: a comprehensive database of rice genomic variations

    PubMed Central

    Zhao, Hu; Yao, Wen; Ouyang, Yidan; Yang, Wanneng; Wang, Gongwei; Lian, Xingming; Xing, Yongzhong; Chen, Lingling; Xie, Weibo

    2015-01-01

    Rice Variation Map (RiceVarMap, http:/ricevarmap.ncpgr.cn) is a database of rice genomic variations. The database provides comprehensive information of 6 551 358 single nucleotide polymorphisms (SNPs) and 1 214 627 insertions/deletions (INDELs) identified from sequencing data of 1479 rice accessions. The SNP genotypes of all accessions were imputed and evaluated, resulting in an overall missing data rate of 0.42% and an estimated accuracy greater than 99%. The SNP/INDEL genotypes of all accessions are available for online query and download. Users can search SNPs/INDELs by identifiers of the SNPs/INDELs, genomic regions, gene identifiers and keywords of gene annotation. Allele frequencies within various subpopulations and the effects of the variation that may alter the protein sequence of a gene are also listed for each SNP/INDEL. The database also provides geographical details and phenotype images for various rice accessions. In particular, the database provides tools to construct haplotype networks and design PCR-primers by taking into account surrounding known genomic variations. These data and tools are highly useful for exploring genetic variations and evolution studies of rice and other species. PMID:25274737

  18. Development of genomics-based genotyping platforms and their applications in rice breeding.

    PubMed

    Chen, Haodong; He, Hang; Zhou, Fasong; Yu, Huihui; Deng, Xing Wang

    2013-05-01

    Breeding by design has been an aspiration of researchers in the plant sciences for a decade. With the rapid development of genomics-based genotyping platforms and available of hundreds of functional genes/alleles in related to important traits, however, it may now be possible to turn this enduring ambition into a practical reality. Rice has a relatively simple genome comparing to other crops, and its genome composition and genetic behavior have been extensively investigated. Recently, rice has been taken as a model crop to perform breeding by design. The essential process of breeding by design is to integrate functional genes/alleles in an ideal genetic background, which requires high throughput genotyping platforms to screen for expected genotypes. With large amount of genome resequencing data and high-throughput genotyping technologies available, quite a number of genomics-based genotyping platforms have been developed. These platforms are widely used in genetic mapping, integration of target traits via marker-assisted backcrossing (MABC), pyramiding, recurrent selection (MARS) or genomic selection (GS). Here, we summarize and discuss recent exciting development of rice genomics-based genotyping platforms and their applications in molecular breeding.

  19. Development of genomics-based genotyping platforms and their applications in rice breeding.

    PubMed

    Chen, Haodong; He, Hang; Zhou, Fasong; Yu, Huihui; Deng, Xing Wang

    2013-05-01

    Breeding by design has been an aspiration of researchers in the plant sciences for a decade. With the rapid development of genomics-based genotyping platforms and available of hundreds of functional genes/alleles in related to important traits, however, it may now be possible to turn this enduring ambition into a practical reality. Rice has a relatively simple genome comparing to other crops, and its genome composition and genetic behavior have been extensively investigated. Recently, rice has been taken as a model crop to perform breeding by design. The essential process of breeding by design is to integrate functional genes/alleles in an ideal genetic background, which requires high throughput genotyping platforms to screen for expected genotypes. With large amount of genome resequencing data and high-throughput genotyping technologies available, quite a number of genomics-based genotyping platforms have been developed. These platforms are widely used in genetic mapping, integration of target traits via marker-assisted backcrossing (MABC), pyramiding, recurrent selection (MARS) or genomic selection (GS). Here, we summarize and discuss recent exciting development of rice genomics-based genotyping platforms and their applications in molecular breeding. PMID:23706659

  20. Physical mapping of the rice genome with BACs.

    PubMed

    Zhang, H B; Wing, R A

    1997-09-01

    The development of genetics in this century has been catapulted forward by several milestones: rediscovery of Mendel's laws, determination of DNA as the genetic material, discovery of the double-helix structure of DNA and its implications for genetic behavior, and most recently, analysis of restriction fragment length polymorphisms (RFLPs). Each of these milestones has generated a huge wave of progress in genetics. Consequently, our understanding of organismal genetics now extends from phenotypes to their molecular genetic basis. It is now clear that the next wave of progress in genetics will hinge on genome molecular physical mapping, since a genome physical map will provide an invaluable, readily accessible system for many detailed genetic studies and isolation of many genes of economic or biological importance. Recent development of large-DNA fragment (> 100 kb) manipulation and cloning technologies, such as pulsed-field gel electrophoresis (PFGE), and yeast artificial chromosome (YAC) and bacterial artificial chromosome (BAC) cloning, has provided the powerful tools needed to generate molecular physical maps for higher-organism genomes. This chapter will discuss (1) an ideal physical map of plant genome and its applications in plant genetic and biological studies, (2) reviews on physical mapping of the genomes of Caenorhabditis elegans, Arabidopsis thaliana, and man, (3) large-insert DNA libraries: cosmid, YAC and BAC, and genome physical mapping, (4) physical mapping of the rice genome with BACs, and (5) perspectives on the physical mapping of the rice genome with BACs.

  1. Genome-Wide Transcriptome Analysis of Cadmium Stress in Rice

    PubMed Central

    Oono, Youko; Yazawa, Takayuki; Kanamori, Hiroyuki; Sasaki, Harumi; Mori, Satomi; Handa, Hirokazu; Matsumoto, Takashi

    2016-01-01

    Rice growth is severely affected by toxic concentrations of the nonessential heavy metal cadmium (Cd). To elucidate the molecular basis of the response to Cd stress, we performed mRNA sequencing of rice following our previous study on exposure to high concentrations of Cd (Oono et al., 2014). In this study, rice plants were hydroponically treated with low concentrations of Cd and approximately 211 million sequence reads were mapped onto the IRGSP-1.0 reference rice genome sequence. Many genes, including some identified under high Cd concentration exposure in our previous study, were found to be responsive to low Cd exposure, with an average of about 11,000 transcripts from each condition. However, genes expressed constitutively across the developmental course responded only slightly to low Cd concentrations, in contrast to their clear response to high Cd concentration, which causes fatal damage to rice seedlings according to phenotypic changes. The expression of metal ion transporter genes tended to correlate with Cd concentration, suggesting the potential of the RNA-Seq strategy to reveal novel Cd-responsive transporters by analyzing gene expression under different Cd concentrations. This study could help to develop novel strategies for improving tolerance to Cd exposure in rice and other cereal crops. PMID:27034955

  2. The Nipponbare genome and the next-generation of rice genomics research in Japan.

    PubMed

    Matsumoto, Takashi; Wu, Jianzhong; Itoh, Takeshi; Numa, Hisataka; Antonio, Baltazar; Sasaki, Takuji

    2016-12-01

    The map-based genome sequence of the japonica rice cultivar Nipponbare remains to date as the only monocot genome that has been sequenced to a high-quality level. It has become the reference sequence for understanding the diversity among thousands of rice cultivars and its wild relatives as well as the major cereal crops that comprised the food source for the entire human race. This review focuses on the accomplishments in rice genomics in Japan encompassing the last 10 years which have led into deeper understanding of the genome, characterization of many agronomic traits, comprehensive analysis of the transcriptome, and the map-based cloning of many genes associated with agronomic traits.

  3. The Nipponbare genome and the next-generation of rice genomics research in Japan.

    PubMed

    Matsumoto, Takashi; Wu, Jianzhong; Itoh, Takeshi; Numa, Hisataka; Antonio, Baltazar; Sasaki, Takuji

    2016-12-01

    The map-based genome sequence of the japonica rice cultivar Nipponbare remains to date as the only monocot genome that has been sequenced to a high-quality level. It has become the reference sequence for understanding the diversity among thousands of rice cultivars and its wild relatives as well as the major cereal crops that comprised the food source for the entire human race. This review focuses on the accomplishments in rice genomics in Japan encompassing the last 10 years which have led into deeper understanding of the genome, characterization of many agronomic traits, comprehensive analysis of the transcriptome, and the map-based cloning of many genes associated with agronomic traits. PMID:27447712

  4. Enabling functional genomics with genome engineering.

    PubMed

    Hilton, Isaac B; Gersbach, Charles A

    2015-10-01

    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances.

  5. Enabling functional genomics with genome engineering.

    PubMed

    Hilton, Isaac B; Gersbach, Charles A

    2015-10-01

    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances. PMID:26430154

  6. Genome-Wide Analysis of Basic/Helix-Loop-Helix Transcription Factor Family in Rice and Arabidopsis1[W

    PubMed Central

    Li, Xiaoxing; Duan, Xuepeng; Jiang, Haixiong; Sun, Yujin; Tang, Yuanping; Yuan, Zheng; Guo, Jingkang; Liang, Wanqi; Chen, Liang; Yin, Jingyuan; Ma, Hong; Wang, Jian; Zhang, Dabing

    2006-01-01

    The basic/helix-loop-helix (bHLH) transcription factors and their homologs form a large family in plant and animal genomes. They are known to play important roles in the specification of tissue types in animals. On the other hand, few plant bHLH proteins have been studied functionally. Recent completion of whole genome sequences of model plants Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) allows genome-wide analysis and comparison of the bHLH family in flowering plants. We have identified 167 bHLH genes in the rice genome, and their phylogenetic analysis indicates that they form well-supported clades, which are defined as subfamilies. In addition, sequence analysis of potential DNA-binding activity, the sequence motifs outside the bHLH domain, and the conservation of intron/exon structural patterns further support the evolutionary relationships among these proteins. The genome distribution of rice bHLH genes strongly supports the hypothesis that genome-wide and tandem duplication contributed to the expansion of the bHLH gene family, consistent with the birth-and-death theory of gene family evolution. Bioinformatics analysis suggests that rice bHLH proteins can potentially participate in a variety of combinatorial interactions, endowing them with the capacity to regulate a multitude of transcriptional programs. In addition, similar expression patterns suggest functional conservation between some rice bHLH genes and their close Arabidopsis homologs. PMID:16896230

  7. Review of functional markers for improving cooking, eating, and the nutritional qualities of rice.

    PubMed

    Lau, Wendy C P; Rafii, Mohd Y; Ismail, Mohd R; Puteh, Adam; Latif, Mohammad A; Ramli, Asfaliza

    2015-01-01

    After yield, quality is one of the most important aspects of rice breeding. Preference for rice quality varies among cultures and regions; therefore, rice breeders have to tailor the quality according to the preferences of local consumers. Rice quality assessment requires routine chemical analysis procedures. The advancement of molecular marker technology has revolutionized the strategy in breeding programs. The availability of rice genome sequences and the use of forward and reverse genetics approaches facilitate gene discovery and the deciphering of gene functions. A well-characterized gene is the basis for the development of functional markers, which play an important role in plant genotyping and, in particular, marker-assisted breeding. In addition, functional markers offer advantages that counteract the limitations of random DNA markers. Some functional markers have been applied in marker-assisted breeding programs and have successfully improved rice quality to meet local consumers' preferences. Although functional markers offer a plethora of advantages over random genetic markers, the development and application of functional markers should be conducted with care. The decreasing cost of sequencing will enable more functional markers for rice quality improvement to be developed, and application of these markers in rice quality breeding programs is highly anticipated. PMID:26528304

  8. Review of functional markers for improving cooking, eating, and the nutritional qualities of rice

    PubMed Central

    Lau, Wendy C. P.; Rafii, Mohd Y.; Ismail, Mohd R.; Puteh, Adam; Latif, Mohammad A.; Ramli, Asfaliza

    2015-01-01

    After yield, quality is one of the most important aspects of rice breeding. Preference for rice quality varies among cultures and regions; therefore, rice breeders have to tailor the quality according to the preferences of local consumers. Rice quality assessment requires routine chemical analysis procedures. The advancement of molecular marker technology has revolutionized the strategy in breeding programs. The availability of rice genome sequences and the use of forward and reverse genetics approaches facilitate gene discovery and the deciphering of gene functions. A well-characterized gene is the basis for the development of functional markers, which play an important role in plant genotyping and, in particular, marker-assisted breeding. In addition, functional markers offer advantages that counteract the limitations of random DNA markers. Some functional markers have been applied in marker-assisted breeding programs and have successfully improved rice quality to meet local consumers’ preferences. Although functional markers offer a plethora of advantages over random genetic markers, the development and application of functional markers should be conducted with care. The decreasing cost of sequencing will enable more functional markers for rice quality improvement to be developed, and application of these markers in rice quality breeding programs is highly anticipated. PMID:26528304

  9. Functional diversity of jasmonates in rice.

    PubMed

    Liu, Zheng; Zhang, Shumin; Sun, Ning; Liu, Hongyun; Zhao, Yanhong; Liang, Yuling; Zhang, Liping; Han, Yuanhuai

    2015-12-01

    Phytohormone jasmonates (JA) play essential roles in plants, such as regulating development and growth, responding to environmental changes, and resisting abiotic and biotic stresses. During signaling, JA interacts, either synergistically or antagonistically, with other hormones, such as salicylic acid (SA), gibberellin (GA), ethylene (ET), auxin, brassinosteroid (BR), and abscisic acid (ABA), to regulate gene expression in regulatory networks, conferring physiological and metabolic adjustments in plants. As an important staple crop, rice is a major nutritional source for human beings and feeds one third of the world's population. Recent years have seen significant progress in the understanding of the JA pathway in rice. In this review, we summarize the diverse functions of JA, and discuss the JA interplay with other hormones, as well as light, in this economically important crop. We believe that a better understanding of the JA pathway will lead to practical biotechnological applications in rice breeding and cultivation. PMID:26054241

  10. Genome-wide response to selection and genetic basis of cold tolerance in rice (Oryza sativa L.)

    PubMed Central

    2014-01-01

    Background Cold stress is an important factor limiting rice yield in many areas of high latitude and altitude. Considerable efforts have been taken to genetically dissect cold tolerance (CT) in rice using DNA markers. Because of possible epistasis and gene × environment interactions associated with identified quantitative trait loci, the results of these genetic studies have unfortunately not been directly applicable to marker-assisted selection for improved rice CT. In this study, we demonstrated the utility of a selective introgression strategy for simultaneous improvement and genetic dissection of rice seedling CT. Results A set of japonica introgression lines (ILs) with significantly improved seedling CT were developed from four backcross populations based on two rounds of selection. Genetic characterization of these cold-tolerant ILs revealed two important aspects of genome-wide responses to strong phenotypic selection for rice CT: (1) significant over-introgression of donor alleles at 57 loci in 29 functional genetic units (FGUs) across the rice genome and (2) pronounced non-random associations between or among alleles at many unlinked CT loci. Linkage disequilibrium analyses of the detected CT loci allowed us to construct putative genetic networks (multi-locus structures) underlying the seedling CT of rice. Each network consisted of a single FGU, with high introgression as the putative regulator plus two to three groups of highly associated downstream FGUs. A bioinformatics search of rice genomic regions harboring these putative regulators identified a small set of candidate regulatory genes that are known to be involved in plant stress response. Conclusions Our results suggest that CT in rice is controlled by multiple pathways. Genetic complementarity between parental-derived functional alleles at many loci within a given pathway provides an appropriate explanation for the commonly observed hidden diversity and transgressive segregation of CT and other

  11. Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

    PubMed

    Xie, Weibo; Wang, Gongwei; Yuan, Meng; Yao, Wen; Lyu, Kai; Zhao, Hu; Yang, Meng; Li, Pingbo; Zhang, Xing; Yuan, Jing; Wang, Quanxiu; Liu, Fang; Dong, Huaxia; Zhang, Lejing; Li, Xinglei; Meng, Xiangzhou; Zhang, Wan; Xiong, Lizhong; He, Yuqing; Wang, Shiping; Yu, Sibin; Xu, Caiguo; Luo, Jie; Li, Xianghua; Xiao, Jinghua; Lian, Xingming; Zhang, Qifa

    2015-09-29

    Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts. We detected 200 regions spanning 7.8% of the rice genome that had been differentially selected between IndI and IndII, and thus referred to as breeding signatures. These regions included large numbers of known functional genes and loci associated with important agronomic traits revealed by genome-wide association studies. Grain yield was positively correlated with the number of breeding signatures in a variety, suggesting that the number of breeding signatures in a line may be useful for predicting agronomic potential and the selected loci may provide targets for rice improvement.

  12. Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection

    PubMed Central

    Xie, Weibo; Wang, Gongwei; Yuan, Meng; Yao, Wen; Lyu, Kai; Zhao, Hu; Yang, Meng; Li, Pingbo; Zhang, Xing; Yuan, Jing; Wang, Quanxiu; Liu, Fang; Dong, Huaxia; Zhang, Lejing; Li, Xinglei; Meng, Xiangzhou; Zhang, Wan; Xiong, Lizhong; He, Yuqing; Wang, Shiping; Yu, Sibin; Xu, Caiguo; Luo, Jie; Li, Xianghua; Xiao, Jinghua; Lian, Xingming; Zhang, Qifa

    2015-01-01

    Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts. We detected 200 regions spanning 7.8% of the rice genome that had been differentially selected between IndI and IndII, and thus referred to as breeding signatures. These regions included large numbers of known functional genes and loci associated with important agronomic traits revealed by genome-wide association studies. Grain yield was positively correlated with the number of breeding signatures in a variety, suggesting that the number of breeding signatures in a line may be useful for predicting agronomic potential and the selected loci may provide targets for rice improvement. PMID:26358652

  13. Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism.

    PubMed

    Chen, Wei; Gao, Yanqiang; Xie, Weibo; Gong, Liang; Lu, Kai; Wang, Wensheng; Li, Yang; Liu, Xianqing; Zhang, Hongyan; Dong, Huaxia; Zhang, Wan; Zhang, Lejing; Yu, Sibin; Wang, Gongwei; Lian, Xingming; Luo, Jie

    2014-07-01

    Plant metabolites are important to world food security in terms of maintaining sustainable yield and providing food with enriched phytonutrients. Here we report comprehensive profiling of 840 metabolites and a further metabolic genome-wide association study based on ∼6.4 million SNPs obtained from 529 diverse accessions of Oryza sativa. We identified hundreds of common variants influencing numerous secondary metabolites with large effects at high resolution. We observed substantial heterogeneity in the natural variation of metabolites and their underlying genetic architectures among different subspecies of rice. Data mining identified 36 candidate genes modulating levels of metabolites that are of potential physiological and nutritional importance. As a proof of concept, we functionally identified or annotated five candidate genes influencing metabolic traits. Our study provides insights into the genetic and biochemical bases of rice metabolome variation and can be used as a powerful complementary tool to classical phenotypic trait mapping for rice improvement.

  14. Navigating yeast genome maintenance with functional genomics.

    PubMed

    Measday, Vivien; Stirling, Peter C

    2016-03-01

    Maintenance of genome integrity is a fundamental requirement of all organisms. To address this, organisms have evolved extremely faithful modes of replication, DNA repair and chromosome segregation to combat the deleterious effects of an unstable genome. Nonetheless, a small amount of genome instability is the driver of evolutionary change and adaptation, and thus a low level of instability is permitted in populations. While defects in genome maintenance almost invariably reduce fitness in the short term, they can create an environment where beneficial mutations are more likely to occur. The importance of this fact is clearest in the development of human cancer, where genome instability is a well-established enabling characteristic of carcinogenesis. This raises the crucial question: what are the cellular pathways that promote genome maintenance and what are their mechanisms? Work in model organisms, in particular the yeast Saccharomyces cerevisiae, has provided the global foundations of genome maintenance mechanisms in eukaryotes. The development of pioneering genomic tools inS. cerevisiae, such as the systematic creation of mutants in all nonessential and essential genes, has enabled whole-genome approaches to identifying genes with roles in genome maintenance. Here, we review the extensive whole-genome approaches taken in yeast, with an emphasis on functional genomic screens, to understand the genetic basis of genome instability, highlighting a range of genetic and cytological screening modalities. By revealing the biological pathways and processes regulating genome integrity, these analyses contribute to the systems-level map of the yeast cell and inform studies of human disease, especially cancer.

  15. Navigating yeast genome maintenance with functional genomics.

    PubMed

    Measday, Vivien; Stirling, Peter C

    2016-03-01

    Maintenance of genome integrity is a fundamental requirement of all organisms. To address this, organisms have evolved extremely faithful modes of replication, DNA repair and chromosome segregation to combat the deleterious effects of an unstable genome. Nonetheless, a small amount of genome instability is the driver of evolutionary change and adaptation, and thus a low level of instability is permitted in populations. While defects in genome maintenance almost invariably reduce fitness in the short term, they can create an environment where beneficial mutations are more likely to occur. The importance of this fact is clearest in the development of human cancer, where genome instability is a well-established enabling characteristic of carcinogenesis. This raises the crucial question: what are the cellular pathways that promote genome maintenance and what are their mechanisms? Work in model organisms, in particular the yeast Saccharomyces cerevisiae, has provided the global foundations of genome maintenance mechanisms in eukaryotes. The development of pioneering genomic tools inS. cerevisiae, such as the systematic creation of mutants in all nonessential and essential genes, has enabled whole-genome approaches to identifying genes with roles in genome maintenance. Here, we review the extensive whole-genome approaches taken in yeast, with an emphasis on functional genomic screens, to understand the genetic basis of genome instability, highlighting a range of genetic and cytological screening modalities. By revealing the biological pathways and processes regulating genome integrity, these analyses contribute to the systems-level map of the yeast cell and inform studies of human disease, especially cancer. PMID:26323482

  16. Rapid diversification of five Oryza AA genomes associated with rice adaptation.

    PubMed

    Zhang, Qun-Jie; Zhu, Ting; Xia, En-Hua; Shi, Chao; Liu, Yun-Long; Zhang, Yun; Liu, Yuan; Jiang, Wen-Kai; Zhao, You-Jie; Mao, Shu-Yan; Zhang, Li-Ping; Huang, Hui; Jiao, Jun-Ying; Xu, Ping-Zhen; Yao, Qiu-Yang; Zeng, Fan-Chun; Yang, Li-Li; Gao, Ju; Tao, Da-Yun; Wang, Yue-Ju; Bennetzen, Jeffrey L; Gao, Li-Zhi

    2014-11-18

    Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.

  17. Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences

    PubMed Central

    Wambugu, Peterson W.; Brozynska, Marta; Furtado, Agnelo; Waters, Daniel L.; Henry, Robert J.

    2015-01-01

    Rice is the most important crop in the world, acting as the staple food for over half of the world’s population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genome Oryza species, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species. The pan tropical distribution of these rice relatives was found to be explained by long distance dispersal within the last million years. The analysis resulted in a clustering pattern that showed strong geographical differentiation. The species were defined in two primary clades with a South American/African clade with two species, O glumaepatula and O longistaminata, distinguished from all other species. The largest clade was comprised of an Australian clade including newly identified taxa and the African and Asian clades. This refined knowledge of the relationships between cultivated rice and the related wild species provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation. PMID:26355750

  18. Nongenetic functions of the genome.

    PubMed

    Bustin, Michael; Misteli, Tom

    2016-05-01

    The primary function of the genome is to store, propagate, and express the genetic information that gives rise to a cell's architectural and functional machinery. However, the genome is also a major structural component of the cell. Besides its genetic roles, the genome affects cellular functions by nongenetic means through its physical and structural properties, particularly by exerting mechanical forces and by serving as a scaffold for binding of cellular components. Major cellular processes affected by nongenetic functions of the genome include establishment of nuclear structure, signal transduction, mechanoresponses, cell migration, and vision in nocturnal animals. We discuss the concept, mechanisms, and implications of nongenetic functions of the genome.

  19. Genome-Wide Analysis of Polycistronic MicroRNAs in Cultivated and Wild Rice

    PubMed Central

    Baldrich, Patricia; Hsing, Yue-Ie Caroline; San Segundo, Blanca

    2016-01-01

    MicroRNAs (miRNAs) are small noncoding RNAs that direct posttranscriptional gene silencing in eukaryotes. They are frequently clustered in the genomes of animals and can be independently transcribed or simultaneously transcribed into single polycistronic transcripts. Only a few miRNA clusters have been described in plants, and most of them are generated from independent transcriptional units. Here, we used a combination of bioinformatic tools and experimental analyses to discover new polycistronic miRNAs in rice. A genome-wide analysis of clustering patterns of MIRNA loci in the rice genome was carried out using a criterion of 3 kb as the maximal distance between two miRNAs. This analysis revealed 28 loci with the ability to form the typical hairpin structure of miRNA precursors in which 2 or more mature miRNAs mapped along the same structure. RT-PCR provided evidence for the polycistronic nature of seven miRNA precursors containing homologous or nonhomologous miRNA species. Polycistronic miRNAs and candidate polycistronic miRNAs are located across different rice chromosomes, except chromosome 12, and resided in both duplicated and nonduplicated chromosomal regions. Finally, most polycistronic and candidate polycistronic miRNAs showed a pattern of conservation in the genome of rice species with an AA genome. The diversity in the organization of MIR genes that are transcribed as polycistrons suggests a versatile mechanism for the control of gene expression in different biological processes and supports additional levels of complexity in miRNA functioning in plants. PMID:27190137

  20. Genome sequencing and analysis of a granulovirus isolated from the Asiatic rice leafroller, Cnaphalocrocis medinalis.

    PubMed

    Zhang, Shan; Zhu, Zheng; Sun, Shifeng; Chen, Qijin; Deng, Fei; Yang, Kai

    2015-12-01

    The complete genome of Cnaphalocrocis medinalis granulovirus (CnmeGV) from a serious migratory rice pest, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae), was sequenced using the Roche 454 Genome Sequencer FLX system (GS FLX) with shotgun strategy and assembled by Roche GS De Novo assembler software. Its circular double-stranded genome is 111,246 bp in size with a high A+T content of 64.8% and codes for 118 putative open reading frames (ORFs). It contains 37 conserved baculovirus core ORFs, 13 unique ORFs, 26 ORFs that were found in all Lepidoptera baculoviruses and 42 common ORFs. The analysis of nucleotide sequence repeats revealed that the CnmeGV genome differs from the rest of sequenced GVs by a 23 kb and a 17kb gene block inversions, and does not contain any typical homologous region (hr) except for a region of non-hr-like sequence. Chitinase and cathepsin genes, which are reported to have major roles in the liquefaction of the hosts, were not found in the CnmeGV genome, which explains why CnmeGV infected insects do not show the phenotype of typical liquefaction. Phylogenetic analysis, based on the 37 core baculovirus genes, indicates that CnmeGV is closely related to Adoxophyes orana granulovirus. The genome analysis would contribute to the functional research of CnmeGV, and would benefit to the utilization of CnmeGV as pest control reagent for rice production. PMID:26712716

  1. Genome sequencing and analysis of a granulovirus isolated from the Asiatic rice leafroller, Cnaphalocrocis medinalis.

    PubMed

    Zhang, Shan; Zhu, Zheng; Sun, Shifeng; Chen, Qijin; Deng, Fei; Yang, Kai

    2015-12-01

    The complete genome of Cnaphalocrocis medinalis granulovirus (CnmeGV) from a serious migratory rice pest, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae), was sequenced using the Roche 454 Genome Sequencer FLX system (GS FLX) with shotgun strategy and assembled by Roche GS De Novo assembler software. Its circular double-stranded genome is 111,246 bp in size with a high A+T content of 64.8% and codes for 118 putative open reading frames (ORFs). It contains 37 conserved baculovirus core ORFs, 13 unique ORFs, 26 ORFs that were found in all Lepidoptera baculoviruses and 42 common ORFs. The analysis of nucleotide sequence repeats revealed that the CnmeGV genome differs from the rest of sequenced GVs by a 23 kb and a 17kb gene block inversions, and does not contain any typical homologous region (hr) except for a region of non-hr-like sequence. Chitinase and cathepsin genes, which are reported to have major roles in the liquefaction of the hosts, were not found in the CnmeGV genome, which explains why CnmeGV infected insects do not show the phenotype of typical liquefaction. Phylogenetic analysis, based on the 37 core baculovirus genes, indicates that CnmeGV is closely related to Adoxophyes orana granulovirus. The genome analysis would contribute to the functional research of CnmeGV, and would benefit to the utilization of CnmeGV as pest control reagent for rice production.

  2. The whole chloroplast genome of wild rice (Oryza australiensis).

    PubMed

    Wu, Zhiqiang; Ge, Song

    2016-01-01

    The whole chloroplast genome of wild rice (Oryza australiensis) is characterized in this study. The genome size is 135,224  bp, exhibiting a typical circular structure including a pair of 25,776  bp inverted repeats (IRa,b) separated by a large single-copy region (LSC) of 82,212  bp and a small single-copy region (SSC) of 12,470  bp. The overall GC content of the genome is 38.95%. 110 unique genes were annotated, including 76 protein-coding genes, 4 ribosomal RNA genes, and 30t RNA genes. Among these, 18 are duplicated in the inverted repeat regions, 13 genes contain one intron, and 2 genes (rps12 and ycf3) have two introns.

  3. A genome-wide survey reveals abundant rice blast R-genes in resistant cultivars

    PubMed Central

    Tan, Shengjun; Zhong, Yan; Wang, Ling; Gu, Longjiang; Chen, Jian-Qun; Pan, Qinghua; Bergelson, Joy; Tian, Dacheng

    2015-01-01

    Summary Plant resistance genes (R-genes) harbor tremendous allelic diversity, constituting a robust immune system effective against microbial pathogens. Nevertheless, few functional R-genes have been identified for even the best-studied pathosystems. Does this limited repertoire reflect specificity, with most R-genes having been defeated by former pests, or do plants harbor a rich diversity of functional R-genes whose composite behavior is yet to be characterized? Here, we survey 332 NBS-LRR genes cloned from 5 resistant rice cultivars for their ability to confer recognition of 12 rice blast isolates when transformed into susceptible cultivars. Our survey reveals that 48.5% of the 132 NBS-LRR loci tested contain functional rice blast R-genes, with most R-genes deriving from multi-copy clades containing especially diversified loci. Each R-gene recognized, on average, 2.42 of the 12 isolates screened. The abundant R-genes identified in resistant genomes provide extraordinary redundancy in the ability of host genotypes to recognize particular isolates. If the same is true for other pathogens, many extant NBS-LRR genes retain functionality. Our success at identifying rice blast R-genes also validates a highly efficient cloning and screening strategy. PMID:26248689

  4. Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project.

    PubMed

    Salse, Jérôme; Piégu, Benoit; Cooke, Richard; Delseny, Michel

    2002-06-01

    BLASTX alignment between 189.5 Mb of rice genomic sequence and translated Arabidopsis thaliana annotated coding sequences (CDS) identified 60 syntenic regions involving 4-22 rice orthologs covering < or =3.2 cM (centiMorgan). Most regions are <3 cM in length. A detailed and updated version of a table representing these regions is available on our web site. Thirty-five rice loci match two distinct A.thaliana loci, as expected from the duplicated nature of the A.thaliana genome. One A.thaliana locus matches two distinct rice regions, suggesting that rice chromosomal sequence duplications exist. A high level of rearrangement characterizing the 60 syntenic regions illustrates the ancient nature of the speciation between A.thaliana and rice. The apparent reduced level of microcollinearity implies the dispersion to new genomic locations, via transposon activity, of single or small clusters of genes in the rice genome, which represents a significant additional effector of plant genome evolution.

  5. Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome

    PubMed Central

    Zhao, Keyan; Wright, Mark; Kimball, Jennifer; Eizenga, Georgia; McClung, Anna; Kovach, Michael; Tyagi, Wricha; Ali, Md. Liakat; Tung, Chih-Wei; Reynolds, Andy; Bustamante, Carlos D.; McCouch, Susan R.

    2010-01-01

    Background The domestication of Asian rice (Oryza sativa) was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers. Methodology/Principal Findings In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV) consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations. Conclusions/Significance Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species. PMID:20520727

  6. Mitochondrial Genome Analysis of Wild Rice (Oryza minuta) and Its Comparison with Other Related Species

    PubMed Central

    Asaf, Sajjad; Khan, Abdul Latif; Khan, Abdur Rahim; Waqas, Muhammad; Kang, Sang-Mo; Khan, Muhammad Aaqil; Shahzad, Raheem; Seo, Chang-Woo; Shin, Jae-Ho; Lee, In-Jung

    2016-01-01

    Oryza minuta (Poaceae family) is a tetraploid wild relative of cultivated rice with a BBCC genome. O. minuta has the potential to resist against various pathogenic diseases such as bacterial blight (BB), white backed planthopper (WBPH) and brown plant hopper (BPH). Here, we sequenced and annotated the complete mitochondrial genome of O. minuta. The mtDNA genome is 515,022 bp, containing 60 protein coding genes, 31 tRNA genes and two rRNA genes. The mitochondrial genome organization and the gene content at the nucleotide level are highly similar (89%) to that of O. rufipogon. Comparison with other related species revealed that most of the genes with known function are conserved among the Poaceae members. Similarly, O. minuta mt genome shared 24 protein-coding genes, 15 tRNA genes and 1 ribosomal RNA gene with other rice species (indica and japonica). The evolutionary relationship and phylogenetic analysis revealed that O. minuta is more closely related to O. rufipogon than to any other related species. Such studies are essential to understand the evolutionary divergence among species and analyze common gene pools to combat risks in the current scenario of a changing environment. PMID:27045847

  7. MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress

    PubMed Central

    Arora, Rita; Agarwal, Pinky; Ray, Swatismita; Singh, Ashok Kumar; Singh, Vijay Pal; Tyagi, Akhilesh K; Kapoor, Sanjay

    2007-01-01

    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

  8. Rice-arsenate interactions in hydroponics: whole genome transcriptional analysis.

    PubMed

    Norton, Gareth J; Lou-Hing, Daniel E; Meharg, Andrew A; Price, Adam H

    2008-01-01

    Rice (Oryza sativa) varieties that are arsenate-tolerant (Bala) and -sensitive (Azucena) were used to conduct a transcriptome analysis of the response of rice seedlings to sodium arsenate (AsV) in hydroponic solution. RNA extracted from the roots of three replicate experiments of plants grown for 1 week in phosphate-free nutrient with or without 13.3 muM AsV was used to challenge the Affymetrix (52K) GeneChip Rice Genome array. A total of 576 probe sets were significantly up-regulated at least 2-fold in both varieties, whereas 622 were down-regulated. Ontological classification is presented. As expected, a large number of transcription factors, stress proteins, and transporters demonstrated differential expression. Striking is the lack of response of classic oxidative stress-responsive genes or phytochelatin synthases/synthatases. However, the large number of responses from genes involved in glutathione synthesis, metabolism, and transport suggests that glutathione conjugation and arsenate methylation may be important biochemical responses to arsenate challenge. In this report, no attempt is made to dissect differences in the response of the tolerant and sensitive variety, but analysis in a companion article will link gene expression to the known tolerance loci available in the BalaxAzucena mapping population.

  9. Genome-wide analysis and identification of genes related to expansin gene family in indica rice.

    PubMed

    Hemalatha, N; Rajesh, M K; Narayanan, N K

    2011-01-01

    In this study, we carried out genome-wide analyses to explore expansin gene family in the genome of indica rice. Reference nucleotides were chosen as query sequences for searches in the indica rice genome database. Clones having genomic sequences similar to expansin were taken and converted to amino acid sequences. Putative sequences were subjected to PROSITE and Pfam databases, and 21 signature-sequences-related expansin gene family was obtained. The presence of transmembrane domains was also predicted for all 21 expansin proteins. A phylogenetic tree was generated from the alignments of the proteins sequences to examine the phylogenetic relationship of indica rice expansin proteins.

  10. Whole-genome resequencing and transcriptomic analysis to identify genes involved in leaf-color diversity in ornamental rice plants.

    PubMed

    Kim, Chang-Kug; Seol, Young-Joo; Shin, Younhee; Lim, Hye-Min; Lee, Gang-Seob; Kim, A-Ram; Lee, Tae-Ho; Lee, Jae-Hee; Park, Dong-Suk; Yoo, Seungil; Kim, Yong-Hwan; Kim, Yong-Kab

    2015-01-01

    Rice field art is a large-scale art form in which people design rice fields using various kinds of ornamental rice plants with different leaf colors. Leaf color-related genes play an important role in the study of chlorophyll biosynthesis, chloroplast structure and function, and anthocyanin biosynthesis. Despite the role of different metabolites in the traditional relationship between leaf and color, comprehensive color-specific metabolite studies of ornamental rice have been limited. We performed whole-genome resequencing and transcriptomic analysis of regulatory patterns and genetic diversity among different rice cultivars to discover new genetic mechanisms that promote enhanced levels of various leaf colors. We resequenced the genomes of 10 rice leaf-color accessions to an average of 40× reads depth and >95% coverage and performed 30 RNA-seq experiments using the 10 rice accessions sampled at three developmental stages. The sequencing results yielded a total of 1,814 × 106 reads and identified an average of 713,114 SNPs per rice accession. Based on our analysis of the DNA variation and gene expression, we selected 47 candidate genes. We used an integrated analysis of the whole-genome resequencing data and the RNA-seq data to divide the candidate genes into two groups: genes related to macronutrient (i.e., magnesium and sulfur) transport and genes related to flavonoid pathways, including anthocyanidin biosynthesis. We verified the candidate genes with quantitative real-time PCR using transgenic T-DNA insertion mutants. Our study demonstrates the potential of integrated screening methods combined with genetic-variation and transcriptomic data to isolate genes involved in complex biosynthetic networks and pathways.

  11. Whole-Genome Resequencing and Transcriptomic Analysis to Identify Genes Involved in Leaf-Color Diversity in Ornamental Rice Plants

    PubMed Central

    Shin, Younhee; Lim, Hye-Min; Lee, Gang-Seob; Kim, A-Ram; Lee, Tae-Ho; Lee, Jae-Hee; Park, Dong-Suk; Yoo, Seungil; Kim, Yong-Hwan; Kim, Yong-Kab

    2015-01-01

    Rice field art is a large-scale art form in which people design rice fields using various kinds of ornamental rice plants with different leaf colors. Leaf color-related genes play an important role in the study of chlorophyll biosynthesis, chloroplast structure and function, and anthocyanin biosynthesis. Despite the role of different metabolites in the traditional relationship between leaf and color, comprehensive color-specific metabolite studies of ornamental rice have been limited. We performed whole-genome resequencing and transcriptomic analysis of regulatory patterns and genetic diversity among different rice cultivars to discover new genetic mechanisms that promote enhanced levels of various leaf colors. We resequenced the genomes of 10 rice leaf-color accessions to an average of 40× reads depth and >95% coverage and performed 30 RNA-seq experiments using the 10 rice accessions sampled at three developmental stages. The sequencing results yielded a total of 1,814 × 106 reads and identified an average of 713,114 SNPs per rice accession. Based on our analysis of the DNA variation and gene expression, we selected 47 candidate genes. We used an integrated analysis of the whole-genome resequencing data and the RNA-seq data to divide the candidate genes into two groups: genes related to macronutrient (i.e., magnesium and sulfur) transport and genes related to flavonoid pathways, including anthocyanidin biosynthesis. We verified the candidate genes with quantitative real-time PCR using transgenic T-DNA insertion mutants. Our study demonstrates the potential of integrated screening methods combined with genetic-variation and transcriptomic data to isolate genes involved in complex biosynthetic networks and pathways. PMID:25897514

  12. Functional characterization of open chromatin in bidirectional promoters of rice.

    PubMed

    Fang, Yuan; Wang, Ximeng; Wang, Lei; Pan, Xiucai; Xiao, Jin; Wang, Xiu-E; Wu, Yufeng; Zhang, Wenli

    2016-01-01

    Bidirectional gene pairs tend to be highly coregulated and function in similar biological processes in eukaryotic genomes. Structural features and functional consequences of bidirectional promoters (BDPs) have received considerable attention among diverse species. However, the underlying mechanisms responsible for the bidirectional transcription and coexpression of BDPs remain poorly understood in plants. In this study, we integrated DNase-seq, RNA-seq, ChIP-seq and MNase-seq data and investigated the effect of physical DNase I hypersensitive site (DHS) positions on the transcription of rice BDPs. We found that the physical position of a DHS relative to the TSS of bidirectional gene pairs can affect the expression of the corresponding genes: the closer a DHS is to the TSS, the higher is the expression level of the genes. Most importantly, we observed that the distribution of DHSs plays a significant role in the regulation of transcription and the coexpression of gene pairs, which are possibly mediated by orchestrating the positioning of histone marks and canonical nucleosomes around BDPs. Our results demonstrate that the combined actions of chromatin structures with DHSs, which contain functional cis-elements for interaction with transcriptional machinery, may play an important role in the regulation of the bidirectional transcription or coexpression in rice BDPs. Our findings may help to enhance the understanding of DHSs in the regulation of bidirectional gene pairs. PMID:27558448

  13. Functional characterization of open chromatin in bidirectional promoters of rice

    PubMed Central

    Fang, Yuan; Wang, Ximeng; Wang, Lei; Pan, Xiucai; Xiao, Jin; Wang, Xiu-e; Wu, Yufeng; Zhang, Wenli

    2016-01-01

    Bidirectional gene pairs tend to be highly coregulated and function in similar biological processes in eukaryotic genomes. Structural features and functional consequences of bidirectional promoters (BDPs) have received considerable attention among diverse species. However, the underlying mechanisms responsible for the bidirectional transcription and coexpression of BDPs remain poorly understood in plants. In this study, we integrated DNase-seq, RNA-seq, ChIP-seq and MNase-seq data and investigated the effect of physical DNase I hypersensitive site (DHS) positions on the transcription of rice BDPs. We found that the physical position of a DHS relative to the TSS of bidirectional gene pairs can affect the expression of the corresponding genes: the closer a DHS is to the TSS, the higher is the expression level of the genes. Most importantly, we observed that the distribution of DHSs plays a significant role in the regulation of transcription and the coexpression of gene pairs, which are possibly mediated by orchestrating the positioning of histone marks and canonical nucleosomes around BDPs. Our results demonstrate that the combined actions of chromatin structures with DHSs, which contain functional cis-elements for interaction with transcriptional machinery, may play an important role in the regulation of the bidirectional transcription or coexpression in rice BDPs. Our findings may help to enhance the understanding of DHSs in the regulation of bidirectional gene pairs. PMID:27558448

  14. Isolation and Functional Characterization of Bidirectional Promoters in Rice

    PubMed Central

    Wang, Rui; Yan, Yan; Zhu, Menglin; Yang, Mei; Zhou, Fei; Chen, Hao; Lin, Yongjun

    2016-01-01

    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. PMID:27303432

  15. Rice hoja blanca virus genome characterization and expression in vitro.

    PubMed

    Ramirez, B C; Macaya, G; Calvert, L A; Haenni, A L

    1992-06-01

    No information exists on the organization and mechanisms of expression of the genome of rice hoja blanca virus (RHBV), a member of the tenuivirus group, but here we describe the first steps in its characterization. RHBV contains four ssRNA and three dsRNA species, the sizes of which were estimated by native and denaturing gel electrophoresis. Hybridization analyses using 32P-labelled riboprobes of viral and viral complementary polarities showed that unequal amounts of the two polarities of at least the smallest RNA are present in the virion, and indicated that the dsRNA species contain the same information as the ssRNA species of corresponding size. Total RHBV RNA directs the synthesis of two major proteins of 23K and 21K in vitro. RNA3 directs the synthesis of a 23K protein designated NS3, and RNA4 of a 21K protein designated NS4. The NS4 protein corresponds to the non-structural protein that accumulates in RHBV-infected rice tissue. The nuclecocapsid protein is not translated from either total RHBV RNA or any individual RHBV RNA in vitro. PMID:1607863

  16. Rice Molecular Breeding Laboratories in the Genomics Era: Current Status and Future Considerations

    PubMed Central

    Collard, Bert C. Y.; Vera Cruz, Casiana M.; McNally, Kenneth L.; Virk, Parminder S.; Mackill, David J.

    2008-01-01

    Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information—coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools—provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to “bridge the application gap” between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs. PMID:18528527

  17. Rice transglutaminase gene: Identification, protein expression, functionality, light dependence and specific cell location.

    PubMed

    Campos, N; Castañón, S; Urreta, I; Santos, M; Torné, J M

    2013-05-01

    Transglutaminases (TGases), that catalyze post-translational modification of proteins, are scarcely known in plants. As part of a project to characterize transglutaminase genes in new plant species, the identification and characterization of a TGase in rice is presented. Using differential primers, a cDNA (tgo) of 1767bp from genomic rice DNA amplification was obtained. The primers were designed from the rice DNA sequence relatively homologous to the gene encoding active maize chloroplast TGase. Amino acid sequence of the deduced rice TGase protein (TGO) indicated that it contains the enzyme catalytic triad (Cys-His-Asp), three repeats, myristoylation domains and a leucine zipper motif. The TGO recombinant protein was characterized, showing specific activity regulation, and indicating that tgo encoded for an authentic TGase. Substrate preference and Ca(2+) dependent activity were also detected. In the rice plant TGO protein was immunolocalized in the grana chloroplasts, in protein vesicles near them, and in the bulliform cells. Immunoblot analyses, tgo mRNA expression, and TGase activity indicated that TGO expression in rice was light dependent and regulated by the illumination period. This work increases significantly our plant TGase understanding. Its functional role in rice, which is a good model system for C3 plants, is discussed.

  18. Functional properties as affected by laboratory-scale parboiling of rough rice and brown rice.

    PubMed

    Patindol, J; Newton, J; Wang, Y-J

    2008-10-01

    Rough rice (RR) is the conventional feedstock for parboiling. The use of brown rice (BR) instead of RR is gaining interest because it results in shorter processing time and lower energy requirement. This study compared the functional properties of milled parboiled rice under different parboiling conditions from RR and BR. Presoaked RR and BR from cultivars Bolivar, Cheniere, Dixiebelle, and Wells were parboiled under mild (20 min, 100 degrees C, 0 kPa) and severe (20 min, 120 degrees C, 98 kPa) laboratory-scale conditions. Head rice yield improved on the RR and BR samples subjected to severe parboiling and was comparable to that of a commercially parboiled sample. Mild parboiling of BR resulted in lower head rice yields. Parboiling generally resulted in decreased head rice whiteness, decreased apparent amylose, increased total lipid, and sparingly changed protein content. Under the same parboiling conditions, the extent of starch gelatinization was higher for BR compared to RR as manifested by some distinct differences in pasting and thermal properties. The cooking characteristics (water uptake ratio, leached materials, and volumetric expansion) and cooked rice texture (hardness and stickiness) of RR and BR subjected to severe parboiling were fairly comparable. Differences in parboiled rice functional properties due to cultivar effect were evident. PMID:19019108

  19. Tissue-Specific Transcriptomic Profiling of Sorghum propinquum using a Rice Genome Array

    PubMed Central

    Zhang, Ting; Zhao, Xiuqin; Huang, Liyu; Liu, Xiaoyue; Zong, Ying; Zhu, Linghua; Yang, Daichang; Fu, Binying

    2013-01-01

    Sorghum (Sorghum bicolor) is one of the world's most important cereal crops. S. propinquum is a perennial wild relative of S. bicolor with well-developed rhizomes. Functional genomics analysis of S. propinquum, especially with respect to molecular mechanisms related to rhizome growth and development, can contribute to the development of more sustainable grain, forage, and bioenergy cropping systems. In this study, we used a whole rice genome oligonucleotide microarray to obtain tissue-specific gene expression profiles of S. propinquum with special emphasis on rhizome development. A total of 548 tissue-enriched genes were detected, including 31 and 114 unique genes that were expressed predominantly in the rhizome tips (RT) and internodes (RI), respectively. Further GO analysis indicated that the functions of these tissue-enriched genes corresponded to their characteristic biological processes. A few distinct cis-elements, including ABA-responsive RY repeat CATGCA, sugar-repressive TTATCC, and GA-responsive TAACAA, were found to be prevalent in RT-enriched genes, implying an important role in rhizome growth and development. Comprehensive comparative analysis of these rhizome-enriched genes and rhizome-specific genes previously identified in Oryza longistaminata and S. propinquum indicated that phytohormones, including ABA, GA, and SA, are key regulators of gene expression during rhizome development. Co-localization of rhizome-enriched genes with rhizome-related QTLs in rice and sorghum generated functional candidates for future cloning of genes associated with rhizome growth and development. PMID:23536906

  20. A genome-wide view of miniature inverted-repeat transposable elements (MITEs) in rice, Oryza sativa ssp. japonica.

    PubMed

    Oki, Nobuhiko; Yano, Kentaro; Okumoto, Yutaka; Tsukiyama, Takuji; Teraishi, Masayoshi; Tanisaka, Takatoshi

    2008-08-01

    Transposable elements (TEs) have played important roles in the evolution of genes and genomes of higher eukaryotes. Among the TEs in the rice genome, miniature inverted-repeat transposable elements (MITEs) exist at the highest copy number. Some of MITEs in the rice genome contain poly(A) signals and putative cis-acting regulatory domains. Insertion events of such MITEs may have caused many structural and functional changes of genomes. The genome-wide examination of MITE-derived sequences could elucidate the contribution of MITEs to gene evolution. Here we report on the MITEs in the rice genome that have contributed to the emergence of novel genes and the expansion of the sequence diversity of the genome and mRNAs. Of the MITE-derived sequences, approximately 6000 were found in gene regions (exons and introns) and 67,000 in intergenic regions. In gene regions, most MITEs are located in introns rather than exons. For over 300 protein-coding genes, coding sequences, poly(A) sites, transcription start sites, and splicing sites overlap with MITEs. These sequence alterations via MITE insertions potentially affect the biological functions of gene products. Many MITE insertions also exist in 5'-untranslated regions (UTRs), 3'-UTRs, and in the proximity of genes. Although mutations in these non-protein coding regions do not alter protein sequences, these regions have key roles for gene regulation. Moreover, MITE family sequences (Tourist, Stowaway, and others) are unevenly distributed in introns. Our findings suggest that MITEs may have contributed to expansion of genome diversity by causing alterations not only in gene functions but also in regulation of many genes. PMID:18931457

  1. Genome-Wide Characterization and Expression Analysis of the Germin-Like Protein Family in Rice and Arabidopsis

    PubMed Central

    Li, Lu; Xu, Xihui; Chen, Chen; Shen, Zhenguo

    2016-01-01

    Previous studies have shown that germin-like proteins (GLPs) are present ubiquitously in rice and Arabidopsis. However, the understanding regarding their role in development and abiotic/biotic stress resistance remains limited. In the present study, we report genome-wide identification, characterisation, subcellular localization, enzyme activity, and expression analysis of the GLP gene family in rice and Arabidopsis to study their functions. In total, 43 and 32 GLPs in the rice and Arabidopsis genome were identified based on a systematic analysis, respectively. The GLP genes were clustered into six clades based on phylogenetic analysis, and many stress and developmental-related cis-elements were detected in promoters of GLP genes. In addition, subcellular location and superoxide dismutase (SOD) analysis demonstrated that the random selected OsGLP genes on chromosomes 8 and 4 of rice were expressed in the cell wall with SOD activity. Overall, our results showed that tandem duplication events, especially the clusters of tandem duplication genes on chromosome 8 in rice, play a major role in expansion of the GLP family and thus increase our understanding of the role of the GLP family in abiotic/biotic stress and development. PMID:27669230

  2. Genome-Wide Characterization and Expression Analysis of the Germin-Like Protein Family in Rice and Arabidopsis.

    PubMed

    Li, Lu; Xu, Xihui; Chen, Chen; Shen, Zhenguo

    2016-01-01

    Previous studies have shown that germin-like proteins (GLPs) are present ubiquitously in rice and Arabidopsis. However, the understanding regarding their role in development and abiotic/biotic stress resistance remains limited. In the present study, we report genome-wide identification, characterisation, subcellular localization, enzyme activity, and expression analysis of the GLP gene family in rice and Arabidopsis to study their functions. In total, 43 and 32 GLPs in the rice and Arabidopsis genome were identified based on a systematic analysis, respectively. The GLP genes were clustered into six clades based on phylogenetic analysis, and many stress and developmental-related cis-elements were detected in promoters of GLP genes. In addition, subcellular location and superoxide dismutase (SOD) analysis demonstrated that the random selected OsGLP genes on chromosomes 8 and 4 of rice were expressed in the cell wall with SOD activity. Overall, our results showed that tandem duplication events, especially the clusters of tandem duplication genes on chromosome 8 in rice, play a major role in expansion of the GLP family and thus increase our understanding of the role of the GLP family in abiotic/biotic stress and development. PMID:27669230

  3. Genomic survey and gene expression analysis of the VDAC gene family in rice.

    PubMed

    Xu, X; Tan, Y P; Cheng, G; Liu, X Q; Xia, C J; Luo, F Y; Wang, C T

    2015-12-02

    The voltage-dependent anion channel (VDAC), also known as a mitochondrial porin, plays an important role in the regulation of metabolic and energetic functions of mitochondria, as well as in mitochondria-mediated apoptosis. Cytoplasmic male sterility (CMS) is of major economic importance for commercial hybrid production and a research model for the interaction be-tween nuclear and cytoplasmic genomes. Recent research has revealed that CMS is associated with programmed cell death. Here, we used the Honglian (HL)-CMS line of rice (Oryza sativa) as material to investigate the association of O. sativa VDAC (OsVDAC) expression to CMS. Eight VDACs were extracted from rice in this study. Bioinformatic analysis of the rice VDACs was conducted at the DNA, cDNA, and protein level. Expression patterns of OsVDACs were analyzed in different organs and during different stages of pollen development using sterile line YuetaiA (YTA), and its maintainer line YuetaiB (YTB). Differential expression of OsVDACs between YTA and YTB was observed, suggesting that VDACs may be involved in the formation of HL-CMS.

  4. Functional analysis of Pid3-A4, an ortholog of rice blast resistance gene Pid3 revealed by allele mining in common wild rice.

    PubMed

    Lv, Qiming; Xu, Xiao; Shang, Junjun; Jiang, Guanghuai; Pang, Zhiqian; Zhou, Zhuangzhi; Wang, Jing; Liu, Ya; Li, Ting; Li, Xiaobing; Xu, Jichen; Cheng, Zhukuan; Zhao, Xianfeng; Li, Shigui; Zhu, Lihuang

    2013-06-01

    The rice blast resistance gene Pid3 encodes a nucleotide-binding-site leucine-rich repeat (NBS-LRR) protein. This gene was cloned from the rice 'Digu' (indica) by performing a genome-wide comparison of the NBS-LRR gene family between two genome-sequenced varieties, '9311' (indica) and 'Nipponbare' (japonica). In this study, we performed functional analysis of Pid3-A4, an ortholog of Pid3 revealed by allele mining in the common wild rice A4 (Oryza rufipogon). The predicted protein encoded by Pid3-A4 shares 99.03% sequence identity with Pid3, with only nine amino-acid substitutions. In wild rice plants, Pid3-A4 is constitutively expressed, and its expression is not induced by Magnaporthe oryzae isolate Zhong-10-8-14 infection. Importantly, in transgenic plants, Pid3-A4, as compared with Pid3, displays a distinct resistance spectrum to a set of M. oryzae isolates, including those that prevail in the rice fields of Sichuan Province. Therefore, Pid3-A4 should be quite useful for the breeding of rice blast resistance, especially in southwestern China.

  5. The organelle genomes of Hassawi rice (Oryza sativa L.) and its hybrid in saudi arabia: genome variation, rearrangement, and origins.

    PubMed

    Zhang, Tongwu; Hu, Songnian; Zhang, Guangyu; Pan, Linlin; Zhang, Xiaowei; Al-Mssallem, Ibrahim S; Yu, Jun

    2012-01-01

    Hassawi rice (Oryza sativa L.) is a landrace adapted to the climate of Saudi Arabia, characterized by its strong resistance to soil salinity and drought. Using high quality sequencing reads extracted from raw data of a whole genome sequencing project, we assembled both chloroplast (cp) and mitochondrial (mt) genomes of the wild-type Hassawi rice (Hassawi-1) and its dwarf hybrid (Hassawi-2). We discovered 16 InDels (insertions and deletions) but no SNP (single nucleotide polymorphism) is present between the two Hassawi cp genomes. We identified 48 InDels and 26 SNPs in the two Hassawi mt genomes and a new type of sequence variation, termed reverse complementary variation (RCV) in the rice cp genomes. There are two and four RCVs identified in Hassawi-1 when compared to 93-11 (indica) and Nipponbare (japonica), respectively. Microsatellite sequence analysis showed there are more SSRs in the genic regions of both cp and mt genomes in the Hassawi rice than in the other rice varieties. There are also large repeats in the Hassawi mt genomes, with the longest length of 96,168 bp and 96,165 bp in Hassawi-1 and Hassawi-2, respectively. We believe that frequent DNA rearrangement in the Hassawi mt and cp genomes indicate ongoing dynamic processes to reach genetic stability under strong environmental pressures. Based on sequence variation analysis and the breeding history, we suggest that both Hassawi-1 and Hassawi-2 originated from the Indonesian variety Peta since genetic diversity between the two Hassawi cultivars is very low albeit an unknown historic origin of the wild-type Hassawi rice. PMID:22870184

  6. Genome-wide DNA polymorphisms in low Phosphate tolerant and sensitive rice genotypes

    PubMed Central

    Mehra, Poonam; Pandey, Bipin K.; Giri, Jitender

    2015-01-01

    Soil Phosphorus (P) deficiency is one of the major challenges to rice crop world-wide. Modern rice genotypes are highly P-responsive and rely on high input of P fertilizers. However, low P tolerant traditional cultivars and landraces have genetic potential to sustain well under low P. Identification of high resolution DNA polymorphisms (SNPs and InDels) in such contrasting genotypes is largely missing for low P response at gene levels. Here, we report high quality DNA polymorphisms in low P sensitive genotype, PB1 and tolerant traditional genotype, Dular. We performed whole genome resequencing using Illumina NGS platform and identified a total of 5,157,939 sequence variants in PB1 and Dular with reference to Nipponbare genome. We have identified approximately 2.3 million and 2.9 million high quality polymorphisms in PB1 and Dular, respectively, with an average read depth of ≥24X. We further mapped several DNA polymorphisms (non-synonymous and regulatory variants) having potential functional significance to key Phosphate Starvation Responsive (PSR) and root architecture genes in Dular and Kasalath using a compiled list of low P responsive genes. These identified variants can serve as a useful source of genetic variability for improving low P tolerance and root architecture of high yielding modern genotypes. PMID:26278778

  7. Functional genomics in the mouse.

    PubMed

    Perkins, Archibald S

    2002-08-01

    The mouse is the premier genetic model organism for the study of human disease and development. With the recent advances in sequencing of the human and mouse genomes, there is strong interest now in large-scale approaches to decipher the function of mouse genes using various mutagenesis technologies. This review discusses what tools are currently available for manipulating and mutagenizing the mouse genome, such as ethylnitrosourea and gene trap mutagenesis, engineered inversions and deletions using the cre-lox system, and proviral insertional mutagenesis in somatic cells, and how these are being used to uncover gene function.

  8. The Complete Mitochondrial Genome of the Rice Moth, Corcyra cephalonica

    PubMed Central

    Wu, Yu-Peng; Li, Jie; Zhao, Jin-Liang; Su, Tian-Juan; Luo, A-Rong; Fan, Ren-Jun; Chen, Ming-Chang; Wu, Chun-Sheng; Zhu, Chao-Dong

    2012-01-01

    The complete mitochondrial genome (mitogenome) of the rice moth, Corcyra cephalonica Stainton (Lepidoptera: Pyralidae) was determined as a circular molecular of 15,273 bp in size. The mitogenome composition (37 genes) and gene order are the same as the other lepidopterans. Nucleotide composition of the C. cephalonica mitogenome is highly A+T biased (80.43%) like other insects. Twelve protein-coding genes start with a typical ATN codon, with the exception of coxl gene, which uses CGA as the initial codon. Nine protein-coding genes have the common stop codon TAA, and the nad2, cox1, cox2, and nad4 have single T as the incomplete stop codon. 22 tRNA genes demonstrated cloverleaf secondary structure. The mitogenome has several large intergenic spacer regions, the spacer1 between trnQ gene and nad2 gene, which is common in Lepidoptera. The spacer 3 between trnE and trnF includes microsatellite-like repeat regions (AT)18 and (TTAT)3. The spacer 4 (16 bp) between trnS2 gene and nad1 gene has a motif ATACTAT; another species, Sesamia inferens encodes ATCATAT at the same position, while other lepidopteran insects encode a similar ATACTAA motif. The spacer 6 is A+T rich region, include motif ATAGA and a 20-bp poly(T) stretch and two microsatellite (AT)9, (AT)8 elements. PMID:23413968

  9. Comparative Genomics Analysis of Rice and Pineapple Contributes to Understand the Chromosome Number Reduction and Genomic Changes in Grasses

    PubMed Central

    Wang, Jinpeng; Yu, Jiaxiang; Sun, Pengchuan; Li, Yuxian; Xia, Ruiyan; Liu, Yinzhe; Ma, Xuelian; Yu, Jigao; Yang, Nanshan; Lei, Tianyu; Wang, Zhenyi; Wang, Li; Ge, Weina; Song, Xiaoming; Liu, Xiaojian; Sun, Sangrong; Liu, Tao; Jin, Dianchuan; Pan, Yuxin; Wang, Xiyin

    2016-01-01

    Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ∼100 million years ago. There has been a standing controversy whether there had been five or seven basic chromosomes, before the tetraploidization, which were tackled but could not be well solved for the lacking of a sequenced and assembled outgroup plant to have a conservative genome structure. Recently, the availability of pineapple genome, which has not been subjected to the grass-common tetraploidization, provides a precious opportunity to solve the above controversy and to research into genome changes of rice and other grasses. Here, we performed a comparative genomics analysis of pineapple and rice, and found solid evidence that grass-common ancestor had 2n = 2x = 14 basic chromosomes before the tetraploidization and duplicated to 2n = 4x = 28 after the event. Moreover, we proposed that enormous gene missing from duplicated regions in rice should be explained by an allotetraploid produced by prominently divergent parental lines, rather than gene losses after their divergence. This means that genome fractionation might have occurred before the formation of the allotetraploid grass ancestor. PMID:27757123

  10. Whole genome sequencing and analysis of Swarna, a widely cultivated indica rice variety with low glycemic index

    PubMed Central

    Rathinasabapathi, Pasupathi; Purushothaman, Natarajan; VL, Ramprasad; Parani, Madasamy

    2015-01-01

    Swarna is a popular cultivated indica rice variety with low glycemic index (GI) but its genetic basis is not known. The whole genome of Swarna was sequenced using Illumina’s paired-end technology, and the reads were mapped to the Nipponbare reference genome. Overall, 65,984 non-synonymous SNPs were identified in 20,350 genes, and in silico analysis predicted that 4,847 of them in 2,214 genes may have deleterious effect on protein functions. Polymorphisms were found in all the starch biosynthesis genes, except the gene for branching enzyme IIa. It was found that T/G SNP at position 246, ‘A’ at position 2,386, and ‘C’ at position 3,378 in the granule bound starch synthase I gene, and C/T SNP at position 1,188 in the glucose-6-phosphate translocator gene may contribute to the low GI phenotype in Swarna. All these variants were also found in the genome of another low GI indica rice variety from Columbia, Fedearroz 50. The whole genome analysis of Swarna helped to understand the genetic basis of GI in rice, which is a complex trait involving multiple factors. PMID:26068787

  11. Seamless Genome Editing in Rice via Gene Targeting and Precise Marker Elimination.

    PubMed

    Nishizawa-Yokoi, Ayako; Saika, Hiroaki; Toki, Seiichi

    2016-01-01

    Positive-negative selection using hygromycin phosphotransferase (hpt) and diphtheria toxin A-fragment (DT-A) as positive and negative selection markers, respectively, allows enrichment of cells harboring target genes modified via gene targeting (GT). We have developed a successful GT system employing positive-negative selection and subsequent precise marker excision via the piggyBac transposon derived from the cabbage looper moth to introduce desired modifications into target genes in the rice genome. This approach could be applied to the precision genome editing of almost all endogenous genes throughout the genome, at least in rice. PMID:27557691

  12. Genomic and expression analysis of glycosyl hydrolase family 35 genes from rice (Oryza sativa L.)

    PubMed Central

    Tanthanuch, Waraporn; Chantarangsee, Mallika; Maneesan, Janjira; Ketudat-Cairns, James

    2008-01-01

    Background Many plant β-galactosidases (Bgals) have been well characterized and their deduced biological functions mainly involve degradation of structural pectins, xyloglucans or arabinogalactoproteins in plant cell walls. However, gene multiplicity in glycosyl hydrolase family 35 (GH35), to which these proteins belong, implies diverse functions. In this study, the gene multiplicity, apparent evolutionary relationships and transcript expression of rice Bgal genes were examined, in order to predict their biological functions. Results Fifteen rice Bgal genes were identified in the plant genome, one of which encodes a protein similar to animal Bgals (OsBgal9), and the remaining 14 fall in a nearly plant-specific subfamily of Bgals. The presence of both classes of Bgals in bryophytes, as well as vascular plants, suggests both gene lineages were present early in plant evolution. All 15 proteins were predicted to contain secretory signal sequences, suggesting they have secretory pathway or external roles. RT-PCR and database analysis found two distinct lineages to be expressed nearly exclusively in reproductive tissues and to be closely related to Arabidopsis Bgals expressed most highly in flower and pollen. On the other hand, OsBgal6 is expressed primarily in young vegetative tissues, and alternative splicing in panicle prevents its production of full-length protein in this reproductive tissue. OsBgal11 also showed alternative splicing to produce different length proteins. OsBgal13 produced by recombinant expression in Escherichia coli hydrolyzed α-L-arabinoside in addition to β-D-galactoside and β-(1→3)-, β-(1→4)- and β-(1→6)- linked galacto-oligosaccharides. Conclusion Rice GH35 contains fifteen genes with a diversity of protein sequences, predicted locations and expression and splicing patterns that suggest that OsBgals enzymes may play a variety of roles in metabolism of cell wall polysaccharides, glycoproteins and glycolipids. PMID:18664295

  13. Comparative analyses of genomic locations and race specificities of loci for quantitative resistance to Pyricularia grisea in rice and barley.

    PubMed

    Chen, Huilan; Wang, Shiping; Xing, Yongzhong; Xu, Caiguo; Hayes, Patrick M; Zhang, Qifa

    2003-03-01

    Comparative genomic analyses have revealed extensive colinearity in gene orders in distantly related taxa in mammals and grasses, which opened new horizons for evolutionary study. The objective of our study was to assess syntenic relationships of quantitative trait loci (QTL) for disease resistance in cereals by using a model system in which rice and barley were used as the hosts and the blast fungus Pyricularia grisea Sacc. as the pathogen. In total, 12 QTL against three isolates were identified in rice; two had effects on all three isolates, and the other 10 had effects on only one or two of the three isolates. Twelve QTL for blast resistance were identified in barley; one had effect on all three isolates, and the other 11 had effects on only one or two of the three isolates. The observed isolate specificity led to a hypothesis about the durability of quantitative resistance commonly observed in many plant host-pathogen systems. Four pairs of the QTL showed corresponding map positions between rice and barley, two of the four QTL pairs had complete conserved isolate specificity, and another two QTL pairs had partial conserved isolate specificity. Such corresponding locations and conserved specificity suggested a common origin and conserved functionality of the genes underlying the QTL for quantitative resistance and may have utility in gene discovery, understanding the function of the genomes, and identifying the evolutionary forces that structured the organization of the grass genomes.

  14. Plant Gene and Alternatively Spliced Variant Annotator. A plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species.

    PubMed

    Chen, Feng-Chi; Wang, Sheng-Shun; Chaw, Shu-Miaw; Huang, Yao-Ting; Chuang, Trees-Juen

    2007-03-01

    The completion of the rice (Oryza sativa) genome draft has brought unprecedented opportunities for genomic studies of the world's most important food crop. Previous rice gene annotations have relied mainly on ab initio methods, which usually yield a high rate of false-positive predictions and give only limited information regarding alternative splicing in rice genes. Comparative approaches based on expressed sequence tags (ESTs) can compensate for the drawbacks of ab initio methods because they can simultaneously identify experimental data-supported genes and alternatively spliced transcripts. Furthermore, cross-species EST information can be used to not only offset the insufficiency of same-species ESTs but also derive evolutionary implications. In this study, we used ESTs from seven plant species, rice, wheat (Triticum aestivum), maize (Zea mays), barley (Hordeum vulgare), sorghum (Sorghum bicolor), soybean (Glycine max), and Arabidopsis (Arabidopsis thaliana), to annotate the rice genome. We developed a plant genome annotation pipeline, Plant Gene and Alternatively Spliced Variant Annotator (PGAA). Using this approach, we identified 852 genes (931 isoforms) not annotated in other widely used databases (i.e. the Institute for Genomic Research, National Center for Biotechnology Information, and Rice Annotation Project) and found 87% of them supported by both rice and nonrice EST evidence. PGAA also identified more than 44,000 alternatively spliced events, of which approximately 20% are not observed in the other three annotations. These novel annotations represent rich opportunities for rice genome research, because the functions of most of our annotated genes are currently unknown. Also, in the PGAA annotation, the isoforms with non-rice-EST-supported exons are significantly enriched in transporter activity but significantly underrepresented in transcription regulator activity. We have also identified potential lineage-specific and conserved isoforms, which are

  15. Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice

    PubMed Central

    2010-01-01

    Background Weedy rice (red rice), a conspecific weed of cultivated rice (Oryza sativa L.), is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP) variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution. Results We find greater population structure than has been previously reported for U.S. weedy rice, and that the multiple, genetically divergent populations have separate origins. The two main U.S. weedy rice populations share genetic backgrounds with cultivated O. sativa varietal groups not grown commercially in the U.S., suggesting weed origins from domesticated ancestors. Hybridization between weedy groups and between weedy rice and local crops has also led to the evolution of distinct U.S. weedy rice populations. Demographic simulations indicate differences among the main weedy groups in the impact of bottlenecks on their establishment in the U.S., and in the timing of divergence from their cultivated relatives. Conclusions Unlike prior research, we did not find unambiguous evidence for U.S. weedy rice originating via hybridization between cultivated and wild Oryza species. Our results demonstrate the potential for weedy life-histories to evolve directly from within domesticated lineages. The diverse origins of U.S. weedy rice populations demonstrate the multiplicity of evolutionary forces that can influence the emergence of weeds from a single species complex. PMID:20550656

  16. Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping.

    PubMed

    Shinada, Hiroshi; Yamamoto, Toshio; Sato, Hirokazu; Yamamoto, Eiji; Hori, Kiyosumi; Yonemaru, Junichi; Sato, Takashi; Fujino, Kenji

    2015-12-01

    Plant breeding programs aim to develop cultivars with high adaptability to the specific conditions in a local region. As a result, unique genes and gene combinations have been accumulated in local elite breeding populations during the long history of plant breeding. Genetic analyses on such genes and combinations may be useful for developing new cultivars with more-desirable agronomic traits. Here, we attempted to detect quantitative trait loci (QTL) for rice blast resistance (BR) using a local breeding rice population from Hokkaido, Japan. Using genotyping data on single nucleotide polymorphisms and simple sequence repeat markers distributed throughout the whole genomic region, we detected genetic regions associated with phenotypic variation in BR by a genome-wide association mapping study (GWAS). An additional association analysis using other breeding cultivars verified the effect and inheritance of the associated region. Furthermore, the existence of a gene for BR in the associated region was confirmed by QTL mapping. The results from these studies enabled us to estimate potential of the Hokkaido rice population as a gene pool for improving BR. The results of this study could be useful for developing novel cultivars with vigorous BR in rice breeding programs.

  17. Functional genomics of pathogenic bacteria.

    PubMed Central

    Moxon, E R; Hood, D W; Saunders, N J; Schweda, E K H; Richards, J C

    2002-01-01

    Microbial diseases remain the commonest cause of global mortality and morbidity. Automated-DNA sequencing has revolutionized the investigation of pathogenic microbes by making the immense fund of information contained in their genomes available at reasonable cost. The challenge is how this information can be used to increase current understanding of the biology of commensal and virulence behaviour of pathogens with particular emphasis on in vivo function and novel approaches to prevention. One example of the application of whole-genome-sequence information is afforded by investigations of the pathogenic role of Haemophilus influenzae lipopolysaccharide and its candidacy as a vaccine. PMID:11839188

  18. Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by whole-genome sequencing.

    PubMed

    Arai-Kichise, Yuko; Shiwa, Yuh; Nagasaki, Hideki; Ebana, Kaworu; Yoshikawa, Hirofumi; Yano, Masahiro; Wakasa, Kyo

    2011-02-01

    Molecular breeding approaches are of growing importance to crop improvement. However, closely related cultivars generally used for crossing material lack sufficient known DNA polymorphisms due to their genetic relatedness. Next-generation sequencing allows the identification of a massive number of DNA polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) between highly homologous genomes. Using this technology, we performed whole-genome sequencing of a landrace of japonica rice, Omachi, which is used for sake brewing and is an important source for modern cultivars. A total of 229 million reads, each comprising 75 nucleotides of the Omachi genome, was generated with 45-fold coverage and uniquely mapped to 89.7% of the Nipponbare genome, a closely related cultivar. We identified 132,462 SNPs, 16,448 insertions and 19,318 deletions between the Omachi and Nipponbare genomes. An SNP array was designed to validate 731 selected SNPs, resulting in validation rates of 95 and 88% for the Omachi and Nipponbare genomes, respectively. Among the 577 SNPs validated in both genomes, 532 are entirely new SNP markers not previously reported between related rice cultivars. We also validated InDels on a part of chromosome 2 as DNA markers and successfully genotyped five japonica rice cultivars. Our results present the methodology and extensive data on SNPs and InDels available for whole-genome genotyping and marker-assisted breeding. The polymorphism information between Omachi and Nipponbare is available at NGRC_Rice_Omachi (http://www.nodai-genome.org/oryza_sativa_en.html).

  19. 2004 Structural, Function and Evolutionary Genomics

    SciTech Connect

    Douglas L. Brutlag Nancy Ryan Gray

    2005-03-23

    This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

  20. Genomes with distinct function composition.

    PubMed

    Tamames, J; Ouzounis, C; Sander, C; Valencia, A

    1996-06-24

    The functional composition of organisms can be analysed for the first time with the appearance of complete or sizeable parts of various genomes. We have reduced the problem of protein function classification to a simple scheme with three classes of protein function: energy-, information- and communication-associated proteins. Finer classification schemes can be easily mapped to the above three classes. To deal with the vast amount of information, a system for automatic function classification using database annotations has been developed. The system is able to classify correctly about 80% of the query sequences with annotations. Using this system, we can analyse samples from the genomes of the most represented species in sequence databases and compare their genomic composition. The similarities and differences for different taxonomic groups are strikingly intuitive. Viruses have the highest proportion of proteins involved in the control and expression of genetic information. Bacteria have the highest proportion of their genes dedicated to the production of proteins associated with small molecule transformations and transport. Animals have a very large proportion of proteins associated with intra- and intercellular communication and other regulatory processes. In general, the proportion of communication-related proteins increases during evolution, indicating trends that led to the emergence of the eukaryotic cell and later the transition from unicellular to multicellular organisms. PMID:8682215

  1. Genetic variation in the chloroplast genome suggests multiple domestication of cultivated Asian rice (Oryza sativa L.).

    PubMed

    Kawakami, Shin-ichi; Ebana, Kaworu; Nishikawa, Tomotaro; Sato, Yo-ichiro; Vaughan, Duncan A; Kadowaki, Koh-ichi

    2007-02-01

    Two hundred and seventy-five accessions of cultivated Asian rice and 44 accessions of AA genome Oryza species were classified into 8 chloroplast (cp) genome types (A-H) based on insertion-deletion events at 3 regions (8K, 57K, and 76K) of the cp genome. The ancestral cp genome type was determined according to the frequency of occurrence in Oryza species and the likely evolution of the variable 57K region of the cp genome. When 2 nucleotide substitutions (AA or TT) were taken into account, these 8 cp types were subdivided into 11 cp types. Most indica cultivars had 1 of 3 cp genome types that were also identified in the wild relatives of rice, O. nivara and O. rufipogon, suggesting that the 3 indica cp types had evolved from distinct gene pools of the O. rufipogon - O. nivara complex. The majority of japonica cultivars had 1 of 3 different cp genome types. One of these 3 was identified in O. rufipogon, suggesting that at least 1 japonica type is derived from O. rufipogon with the same cp genome type. These results provide evidence to support a polyphyletic origin of cultivated Asian rice from at least 4 principal lineages in the O. rufipogon - O. nivara complex.

  2. Genome sequence of Xanthomonas sacchari R1, a biocontrol bacterium isolated from the rice seed.

    PubMed

    Fang, Yunxia; Lin, Haiyan; Wu, Liwen; Ren, Deyong; Ye, Weijun; Dong, Guojun; Zhu, Li; Guo, Longbiao

    2015-07-20

    Xanthomonas sacchari, was first identified as a pathogenic bacterium isolated from diseased sugarcane in Guadeloupe. In this study, R1 was first isolated from rice seed samples from Philippines in 2002. The antagonistic ability against several rice pathogens raises our attention. The genomic feature of this strain was described in this paper. The total genome size of X. sacchari R1 is 5,000,479 bp with 4315 coding sequences (CDS), 59 tRNAs, 2rRNAs and one plasmid. PMID:25931193

  3. Insights into the Musa genome: Syntenic relationships to rice and between Musa species

    PubMed Central

    Lescot, Magali; Piffanelli, Pietro; Ciampi, Ana Y; Ruiz, Manuel; Blanc, Guillaume; Leebens-Mack, Jim; da Silva, Felipe R; Santos, Candice MR; D'Hont, Angélique; Garsmeur, Olivier; Vilarinhos, Alberto D; Kanamori, Hiroyuki; Matsumoto, Takashi; Ronning, Catherine M; Cheung, Foo; Haas, Brian J; Althoff, Ryan; Arbogast, Tammy; Hine, Erin; Pappas, Georgios J; Sasaki, Takuji; Souza, Manoel T; Miller, Robert NG; Glaszmann, Jean-Christophe; Town, Christopher D

    2008-01-01

    Background Musa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of Musa genomic sequence have been conducted. This study compares genomic sequence in two Musa species with orthologous regions in the rice genome. Results We produced 1.4 Mb of Musa sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for Musa-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication event in the Musa lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from M. acuminata and M. balbisiana revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya. Conclusion These results point to the utility of comparative analyses between distantly-related monocot species such as rice and Musa for improving our understanding of monocot genome evolution. Sequencing the genome of M. acuminata would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated Musa polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic traits for breeding purposes

  4. Saturated Molecular Map of the Rice Genome Based on an Interspecific Backcross Population

    PubMed Central

    Causse, M. A.; Fulton, T. M.; Cho, Y. G.; Ahn, S. N.; Chunwongse, J.; Wu, K.; Xiao, J.; Yu, Z.; Ronald, P. C.; Harrington, S. E.; Second, G.; McCouch, S. R.; Tanksley, S. D.

    1994-01-01

    A molecular map has been constructed for the rice genome comprised of 726 markers (mainly restriction fragment length polymorphisms; RFLPs). The mapping population was derived from a backcross between cultivated rice, Oryza sativa, and its wild African relative, Oryza longistaminata. The very high level of polymorphism between these species, combined with the use of polymerase chain reaction-amplified cDNA libraries, contributed to mapping efficiency. A subset of the probes used in this study was previously used to construct an RFLP map derived from an inter subspecific cross, providing a basis for comparison of the two maps and of the relative mapping efficiencies in the two crosses. In addition to the previously described PstI genomic rice library, three cDNA libraries from rice (Oryza), oat (Avena) and barley (Hordeum) were used in this mapping project. Levels of polymorphism detected by each and the frequency of identifying heterologous sequences for use in rice mapping are discussed. Though strong reproductive barriers isolate O. sativa from O. longistaminata, the percentage of markers showing distorted segregation in this backcross population was not significantly different than that observed in an intraspecific F(2) population previously used for mapping. The map contains 1491 cM with an average interval size of 4.0 cM on the framework map, and 2.0 cM overall. A total of 238 markers from the previously described PstI genomic rice library, 250 markers from a cDNA library of rice (Oryza), 112 cDNA markers from oat (Avena), and 20 cDNA markers from a barley (Hordeum) library, two genomic clones from maize (Zea), 11 microsatellite markers, three telomere markers, eleven isozymes, 26 cloned genes, six RAPD, and 47 mutant phenotypes were used in this mapping project. Applications of a molecular map for plant improvement are discussed. PMID:7896104

  5. Natural and artificial mutants as valuable resources for functional genomics and molecular breeding.

    PubMed

    Jiang, Shu-Ye; Ramachandran, Srinivasan

    2010-01-01

    With the completion of rice genome sequencing, large collection of expression data and the great efforts in annotating rice genomes, the next challenge is to systematically assign functions to all predicted genes in the genome. The generations and collections of mutants at the genome-wide level form technological platform of functional genomics. In this study, we have reviewed currently employed tools to generate such mutant populations. These tools include natural, physical, chemical, tissue culture, T-DNA, transposon or gene silencing based mutagenesis. We also reviewed how these tools were used to generate a large collection of mutants and how these mutants can be screened and detected for functional analysis of a gene. The data suggested that the current population of mutants might be large enough to tag all predicted genes. However, the collection of flanking sequencing tags (FSTs) is limited due to the relatively higher cost. Thus, we have proposed a new strategy to generate gene-silencing mutants at the genome-wide level. Due to the large collection of insertion mutants, the next step to rice functional genomics should be focusing on functional characterization of tagged genes by detailed survey of corresponding mutants. Additionally, we also evaluated the utilization of these mutants as valuable resources for molecular breeding.

  6. Functional Insights from Structural Genomics

    SciTech Connect

    Forouhar,F.; Kuzin, A.; Seetharaman, J.; Lee, I.; Zhou, W.; Abashidze, M.; Chen, Y.; Montelione, G.; Tong, L.; et al

    2007-01-01

    Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been characterized at the functional level. The structural information has provided valuable functional insights on some of these proteins, through careful structural analyses, serendipity, and structure-guided functional screening. Some of the success stories based on structures solved at the Northeast Structural Genomics Consortium (NESG) are reported here. These include a novel methyl salicylate esterase with important role in plant innate immunity, a novel RNA methyltransferase (H. influenzae yggJ (HI0303)), a novel spermidine/spermine N-acetyltransferase (B. subtilis PaiA), a novel methyltransferase or AdoMet binding protein (A. fulgidus AF{_}0241), an ATP:cob(I)alamin adenosyltransferase (B. subtilis YvqK), a novel carboxysome pore (E. coli EutN), a proline racemase homolog with a disrupted active site (B. melitensis BME11586), an FMN-dependent enzyme (S. pneumoniae SP{_}1951), and a 12-stranded {beta}-barrel with a novel fold (V. parahaemolyticus VPA1032).

  7. Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice

    PubMed Central

    Badoni, Saurabh; Das, Sweta; Sayal, Yogesh K.; Gopalakrishnan, S.; Singh, Ashok K.; Rao, Atmakuri R.; Agarwal, Pinky; Parida, Swarup K.; Tyagi, Akhilesh K.

    2016-01-01

    We developed genome-wide 84634 ISM (intron-spanning marker) and 16510 InDel-fragment length polymorphism-based ILP (intron-length polymorphism) markers from genes physically mapped on 12 rice chromosomes. These genic markers revealed much higher amplification-efficiency (80%) and polymorphic-potential (66%) among rice accessions even by a cost-effective agarose gel-based assay. A wider level of functional molecular diversity (17–79%) and well-defined precise admixed genetic structure was assayed by 3052 genome-wide markers in a structured population of indica, japonica, aromatic and wild rice. Six major grain weight QTLs (11.9–21.6% phenotypic variation explained) were mapped on five rice chromosomes of a high-density (inter-marker distance: 0.98 cM) genetic linkage map (IR 64 x Sonasal) anchored with 2785 known/candidate gene-derived ISM and ILP markers. The designing of multiple ISM and ILP markers (2 to 4 markers/gene) in an individual gene will broaden the user-preference to select suitable primer combination for efficient assaying of functional allelic variation/diversity and realistic estimation of differential gene expression profiles among rice accessions. The genomic information generated in our study is made publicly accessible through a user-friendly web-resource, “Oryza ISM-ILP marker” database. The known/candidate gene-derived ISM and ILP markers can be enormously deployed to identify functionally relevant trait-associated molecular tags by optimal-resource expenses, leading towards genomics-assisted crop improvement in rice. PMID:27032371

  8. A genome-wide microsatellite polymorphism database for the indica and japonica rice.

    PubMed

    Zhang, Zhonghua; Deng, Yajun; Tan, Jun; Hu, Songnian; Yu, Jun; Xue, Qingzhong

    2007-02-28

    Microsatellite (MS) polymorphism is an important source of genetic diversity, providing support for map-based cloning and molecular breeding. We have developed a new database that contains 52 845 polymorphic MS loci between indica and japonica, composed of ample Class II MS markers, and integrated 18 828 MS loci from IRGSP and genetic markers from RGP. Based on genetic marker positions on the rice genome (http://rise.genomics.org.cn/rice2/index.jsp ), we determined the approximate genetic distances of these MS loci and validated 100 randomly selected markers experimentally with 90% success rate. In addition, we recorded polymorphic MS positions in indica cv. 9311 that is the most important paternal parent of the two-line hybrid rice in China. Our database will undoubtedly facilitate the application of MS markers in genetic researches and marker-assisted breeding. The data set is freely available from www.wigs.zju.edu.cn/achievment/polySSR. PMID:17452422

  9. Gene Chips and Functional Genomics

    NASA Astrophysics Data System (ADS)

    Hamadeh, Hisham; Afshari, Cynthia

    2000-11-01

    These past few years of scientific discovery will undoubtedly be remembered as the "genomics era," the period in which biologists succeeded in enumerating the sequence of nucleotides making up all, or at least most, of human DNA. And while this achievement has been heralded as a technological feat equal to the moon landing, it is only the first of many advances in DNA technology. Scientists are now faced with the task of understanding the meaning of the DNA sequence. Specifically, they want to learn how the DNA code relates to protein function. An important tool in the study of "functional genomics," is the cDNA microarray—also known as the gene chip. Inspired by computer microchips, gene chips allow scientists to monitor the expression of hundreds, even thousands, of genes in a fraction of the time it used to take to monitor the expression of a single one. By altering the conditions under which a particular tissue expresses genes—say, by exposing it to toxins or growth factors—scientists can determine the suite of genes expressed in different situations and hence start to get a handle on the function of these genes. The authors discuss this important new technology and some of its practical applications.

  10. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Current advances in sequencing technologies and bioinformatics allow to determine a nearly complete genomic background of rice, a staple food for the poor people. Consequently, comprehensive databases of variation among thousands of varieties is currently being assembled and released. Proper analysi...

  11. Effects of Milling on Functional Properties of Rice Flour

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A commercial available long grain rice flour ( RL-100) and the flours made by using a pin mill and the Udy mill from the same batch of broken second-head white long grain were evaluated for their particle size and functional properties. The results showed that pin milled flour had more uniform parti...

  12. Evolution, language and analogy in functional genomics.

    PubMed

    Benner, S A; Gaucher, E A

    2001-07-01

    Almost a century ago, Wittgenstein pointed out that theory in science is intricately connected to language. This connection is not a frequent topic in the genomics literature. But a case can be made that functional genomics is today hindered by the paradoxes that Wittgenstein identified. If this is true, until these paradoxes are recognized and addressed, functional genomics will continue to be limited in its ability to extrapolate information from genomic sequences.

  13. Evolution, language and analogy in functional genomics

    NASA Technical Reports Server (NTRS)

    Benner, S. A.; Gaucher, E. A.

    2001-01-01

    Almost a century ago, Wittgenstein pointed out that theory in science is intricately connected to language. This connection is not a frequent topic in the genomics literature. But a case can be made that functional genomics is today hindered by the paradoxes that Wittgenstein identified. If this is true, until these paradoxes are recognized and addressed, functional genomics will continue to be limited in its ability to extrapolate information from genomic sequences.

  14. Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

    PubMed

    Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R

    2015-02-01

    Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline. PMID:25689273

  15. Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines

    PubMed Central

    Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R.

    2015-01-01

    Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline. PMID:25689273

  16. Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

    PubMed

    Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R

    2015-02-01

    Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

  17. Unlocking the variation hidden in rice germplasm collections with genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cultivated Asian rice (Oryza sativa) was domesticated from O. rufipogon (O. nivara). The O. sativa subspecies indica and japonica diverged in ancient times, and based on DNA markers, further subdivided into the five major subpopulations, aus, indica, aromatic, tropical japonica and temperate japoni...

  18. Comparative analyses of distributions and functions of Z-DNA in Arabidopsis and rice.

    PubMed

    Zhou, Chan; Zhou, Fengfeng; Xu, Ying

    2009-04-01

    Left-handed Z-DNA is an energetically unfavorable DNA structure that could form mostly under certain physiological conditions and was known to be involved in a number of cellular activities such as transcription regulation. We have compared the distributions and functions of Z-DNA in the genomes of Arabidopsis and rice, and observed that Z-DNA occurs in rice at least 9 times more often than in Arabidopsis; similar observations hold for other monocots and dicots. In addition, Z-DNA is significantly enriched in the coding regions of Arabidopsis, and in the high-GC-content regions of rice. Based on our analyses, we speculate that Z-DNA may play a role in regulating the expression of transcription factors, inhibitors, translation repressors, succinate dehydrogenases and glutathione-disulfide reductases in Arabidopsis, and it may affect the expression of vesicle and nucleosome genes and genes involved in alcohol transporter activity, stem cell maintenance, meristem development and reproductive structure development in rice. PMID:19103278

  19. Biallelic and Genome Wide Association Mapping of Germanium Tolerant Loci in Rice (Oryza sativa L.)

    PubMed Central

    Talukdar, Partha; Douglas, Alex; Price, Adam H.; Norton, Gareth J.

    2015-01-01

    Rice plants accumulate high concentrations of silicon. Silicon has been shown to be involved in plant growth, high yield, and mitigating biotic and abiotic stresses. However, it has been demonstrated that inorganic arsenic is taken up by rice through silicon transporters under anaerobic conditions, thus the ability to efficiently take up silicon may be considered either a positive or a negative trait in rice. Germanium is an analogue of silicon that produces brown lesions in shoots and leaves, and germanium toxicity has been used to identify mutants in silicon and arsenic transport. In this study, two different genetic mapping methods were performed to determine the loci involved in germanium sensitivity in rice. Genetic mapping in the biparental cross of Bala × Azucena (an F6 population) and a genome wide association (GWA) study with 350 accessions from the Rice Diversity Panel 1 were conducted using 15 μM of germanic acid. This identified a number of germanium sensitive loci: some co-localised with previously identified quantitative trait loci (QTL) for tissue silicon or arsenic concentration, none co-localised with Lsi1 or Lsi6, while one single nucleotide polymorphism (SNP) was detected within 200 kb of Lsi2 (these are genes known to transport silicon, whose identity was discovered using germanium toxicity). However, examining candidate genes that are within the genomic region of the loci detected above reveals genes homologous to both Lsi1 and Lsi2, as well as a number of other candidate genes, which are discussed. PMID:26356220

  20. Biallelic and Genome Wide Association Mapping of Germanium Tolerant Loci in Rice (Oryza sativa L.).

    PubMed

    Talukdar, Partha; Douglas, Alex; Price, Adam H; Norton, Gareth J

    2015-01-01

    Rice plants accumulate high concentrations of silicon. Silicon has been shown to be involved in plant growth, high yield, and mitigating biotic and abiotic stresses. However, it has been demonstrated that inorganic arsenic is taken up by rice through silicon transporters under anaerobic conditions, thus the ability to efficiently take up silicon may be considered either a positive or a negative trait in rice. Germanium is an analogue of silicon that produces brown lesions in shoots and leaves, and germanium toxicity has been used to identify mutants in silicon and arsenic transport. In this study, two different genetic mapping methods were performed to determine the loci involved in germanium sensitivity in rice. Genetic mapping in the biparental cross of Bala × Azucena (an F6 population) and a genome wide association (GWA) study with 350 accessions from the Rice Diversity Panel 1 were conducted using 15 μM of germanic acid. This identified a number of germanium sensitive loci: some co-localised with previously identified quantitative trait loci (QTL) for tissue silicon or arsenic concentration, none co-localised with Lsi1 or Lsi6, while one single nucleotide polymorphism (SNP) was detected within 200 kb of Lsi2 (these are genes known to transport silicon, whose identity was discovered using germanium toxicity). However, examining candidate genes that are within the genomic region of the loci detected above reveals genes homologous to both Lsi1 and Lsi2, as well as a number of other candidate genes, which are discussed.

  1. Space environment induced mutations prefer to occur at polymorphic sites of rice genomes

    NASA Astrophysics Data System (ADS)

    Li, Y.; Liu, M.; Cheng, Z.; Sun, Y.

    To explore the genomic characteristics of rice mutants induced by space environment, space-induced mutants 971-5, 972-4, and R955, which acquired new traits after space flight such as increased yield, reduced resistance to rice blast, and semi-dwarfism compared with their on-ground controls, 971ck, 972ck, and Bing95-503, respectively, together with other 8 japonica and 3 indica rice varieties, 17 in total, were analyzed by amplified fragment length polymorphism (AFLP) method. We chose 16 AFLP primer-pairs which generated a total of 1251 sites, of which 745 (59.6%) were polymorphic over all the genotypes. With the 16 pairs of primer combinations, 54 space-induced mutation sites were observed in 971-5, 86 in 972-4, and 5 in R955 compared to their controls, and the mutation rates were 4.3%, 6.9% and 0.4%, respectively. Interestingly, 75.9%, 84.9% and 100% of the mutation sites identified in 971-5, 972-4, and R955 occurred in polymorphic sites. This result suggests that the space environment preferentially induced mutations at polymorphic sites in rice genomes and might share a common mechanism with other types of mutagens. It also implies that polymorphic sites in genomes are potential "hotspots" for mutations induced by the space environment.

  2. A simplified genomic DNA extraction protocol for pre-germination genotyping in rice.

    PubMed

    Duan, Y B; Zhao, F L; Chen, H D; Li, H; Ni, D H; Wei, P C; Sheng, W; Teng, J T; Zhang, A M; Xue, J P

    2015-06-11

    Genotyping is a critical step for molecular marker-assisted selection in rice. Rice genomic DNA samples for genotyping are typically isolated from living tissues such as seedlings. This requires the germination of all candidate seeds and extraction of DNA from the seedlings. Currently, an ideal individual is selected from a very large number of plants, which is time- and labor-consuming, requiring several transplantations of materials and sampling processes. In this study, we developed a simplified genomic DNA extraction protocol in rice by using amylase to treat half-seeds. The yields of genomic DNA from a half-seed of Indica and Japonica rice were greater than 203.8 ± 32.5 and 143.2 ± 25.5 ng, respectively, and the 260/280 nm absorbance ratio was 1.75-2.10. The DNA was confirmed to be sufficient for polymerase chain reaction amplification and can be used in a marker-assisted selection program.

  3. Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis

    PubMed Central

    2012-01-01

    Background GDSL esterases/lipases are a newly discovered subclass of lipolytic enzymes that are very important and attractive research subjects because of their multifunctional properties, such as broad substrate specificity and regiospecificity. Compared with the current knowledge regarding these enzymes in bacteria, our understanding of the plant GDSL enzymes is very limited, although the GDSL gene family in plant species include numerous members in many fully sequenced plant genomes. Only two genes from a large rice GDSL esterase/lipase gene family were previously characterised, and the majority of the members remain unknown. In the present study, we describe the rice OsGELP (Oryza sativa GDSL esterase/lipase protein) gene family at the genomic and proteomic levels, and use this knowledge to provide insights into the multifunctionality of the rice OsGELP enzymes. Results In this study, an extensive bioinformatics analysis identified 114 genes in the rice OsGELP gene family. A complete overview of this family in rice is presented, including the chromosome locations, gene structures, phylogeny, and protein motifs. Among the OsGELPs and the plant GDSL esterase/lipase proteins of known functions, 41 motifs were found that represent the core secondary structure elements or appear specifically in different phylogenetic subclades. The specification and distribution of identified putative conserved clade-common and -specific peptide motifs, and their location on the predicted protein three dimensional structure may possibly signify their functional roles. Potentially important regions for substrate specificity are highlighted, in accordance with protein three-dimensional model and location of the phylogenetic specific conserved motifs. The differential expression of some representative genes were confirmed by quantitative real-time PCR. The phylogenetic analysis, together with protein motif architectures, and the expression profiling were analysed to predict the

  4. Genome-wide association of rice blast disease resistance and yield-related components of rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Robust disease resistance may require an expenditure of energy that may limit crop yield potential. In the present study, a subset of a USDA rice core collection consisting of 151 accessions was selected using a major blast resistance (R) gene Pi-ta marker, and was genotyped with 156 simple sequence...

  5. Cereal genome analysis using rice as a model.

    PubMed

    Havukkala, I J

    1996-12-01

    Researchers are eagerly waiting for the physical map of rice to become completed and available for use as a model for all cereals. The most significant advances of the past year have been the progress toward positional cloning of genes and the identification of quantitative trait loci (QTL) from detailed restriction fragment length polymorphism maps. Future focus will be: first, the enhanced dissemination and integration of the available data in World Wide Web accessible databases for easy comparison of genetic and physical mapping data across various species; second, the expanded distribution of a wide variety of DNA materials (cDNA clones, yeast artificial chromosomes, bacterial artificial chromosomes and other probes) for use in other cereals on the basis of the rice model map; and third, the applied breeding by locating and isolating sequences corresponding to important agronomic traits, often correlating with QTL.

  6. Relationships among Genetic, Structural, and Functional Properties of Rice Starch.

    PubMed

    Kong, Xiangli; Chen, Yaling; Zhu, Ping; Sui, Zhongquan; Corke, Harold; Bao, Jinsong

    2015-07-15

    We determined the relationships among the structural properties, in vitro digestibility, and genetic factors in starches of 14 rice cultivars. Weight-based chain-length distributions in amylopectin ranged from 18.07% to 24.71% (fa, DP 6-12), 45.01% to 55.67% (fb1, DP 13-24), 12.72% to 14.05% (fb2, DP 25-36), and 10.80 to 20.72% (fb3, DP > 36), respectively. The contents of rapidly digestible starch (RDS), slowly digestible starch (SDS), and resistant starch (RS) ranged from 78.5% to 87.5%, 1.2% to 6.0%, and 10.1% to 18.0%, respectively. AAC was negatively correlated with RDS content but positively correlated with RS content in rice starch. The proportion of short chains in amylopectin, i.e. the amount of fraction IIa (FrIIa) fractionated by gel permeation chromatography (GPC), was positively correlated with RDS. Starch synthase IIa (SSIIa) gene controlled the degree of crystallinity, the amount of fa chains of amylopectin. SSIIIa gene controlled the amount of fb1 chains. Wx gene controlled the FrI, FrIIa, RDS, and RS. Starch debranching enzyme isoamylase II (ISA2) gene also controlled the RDS, which may suggest that RDS was also affected by amylopectin structure, although no correlation between them was found. This study indicated that genetics (i.e., starch biosynthesis related genes) controlled the structural properties of starch, and both amylose content and amylopectin fine structure determined functional properties of rice starch (i.e., the digestion), each in a different way. Understanding the "genetics-structure-function" relationships in rice starches will assist plant breeders and food processors in developing new rice varieties and functional foods.

  7. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.

    PubMed

    Zhang, Jianwei; Chen, Ling-Ling; Xing, Feng; Kudrna, David A; Yao, Wen; Copetti, Dario; Mu, Ting; Li, Weiming; Song, Jia-Ming; Xie, Weibo; Lee, Seunghee; Talag, Jayson; Shao, Lin; An, Yue; Zhang, Chun-Liu; Ouyang, Yidan; Sun, Shuai; Jiao, Wen-Biao; Lv, Fang; Du, Bogu; Luo, Meizhong; Maldonado, Carlos Ernesto; Goicoechea, Jose Luis; Xiong, Lizhong; Wu, Changyin; Xing, Yongzhong; Zhou, Dao-Xiu; Yu, Sibin; Zhao, Yu; Wang, Gongwei; Yu, Yeisoo; Luo, Yijie; Zhou, Zhi-Wei; Hurtado, Beatriz Elena Padilla; Danowitz, Ann; Wing, Rod A; Zhang, Qifa

    2016-08-30

    Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059-2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement. PMID:27535938

  8. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.

    PubMed

    Zhang, Jianwei; Chen, Ling-Ling; Xing, Feng; Kudrna, David A; Yao, Wen; Copetti, Dario; Mu, Ting; Li, Weiming; Song, Jia-Ming; Xie, Weibo; Lee, Seunghee; Talag, Jayson; Shao, Lin; An, Yue; Zhang, Chun-Liu; Ouyang, Yidan; Sun, Shuai; Jiao, Wen-Biao; Lv, Fang; Du, Bogu; Luo, Meizhong; Maldonado, Carlos Ernesto; Goicoechea, Jose Luis; Xiong, Lizhong; Wu, Changyin; Xing, Yongzhong; Zhou, Dao-Xiu; Yu, Sibin; Zhao, Yu; Wang, Gongwei; Yu, Yeisoo; Luo, Yijie; Zhou, Zhi-Wei; Hurtado, Beatriz Elena Padilla; Danowitz, Ann; Wing, Rod A; Zhang, Qifa

    2016-08-30

    Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059-2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement.

  9. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63

    PubMed Central

    Zhang, Jianwei; Chen, Ling-Ling; Xing, Feng; Kudrna, David A.; Yao, Wen; Copetti, Dario; Mu, Ting; Li, Weiming; Song, Jia-Ming; Lee, Seunghee; Talag, Jayson; Shao, Lin; An, Yue; Zhang, Chun-Liu; Ouyang, Yidan; Sun, Shuai; Jiao, Wen-Biao; Lv, Fang; Du, Bogu; Luo, Meizhong; Maldonado, Carlos Ernesto; Goicoechea, Jose Luis; Xiong, Lizhong; Wu, Changyin; Xing, Yongzhong; Zhou, Dao-Xiu; Yu, Sibin; Zhao, Yu; Wang, Gongwei; Yu, Yeisoo; Luo, Yijie; Zhou, Zhi-Wei; Hurtado, Beatriz Elena Padilla; Danowitz, Ann; Wing, Rod A.; Zhang, Qifa

    2016-01-01

    Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica. Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059–2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement. PMID:27535938

  10. Genomic DNA sequence and cytosine methylation changes of adult rice leaves after seeds space flight

    NASA Astrophysics Data System (ADS)

    Shi, Jinming

    In this study, cytosine methylation on CCGG site and genomic DNA sequence changes of adult leaves of rice after seeds space flight were detected by methylation-sensitive amplification polymorphism (MSAP) and Amplified fragment length polymorphism (AFLP) technique respectively. Rice seeds were planted in the trial field after 4 days space flight on the shenzhou-6 Spaceship of China. Adult leaves of space-treated rice including 8 plants chosen randomly and 2 plants with phenotypic mutation were used for AFLP and MSAP analysis. Polymorphism of both DNA sequence and cytosine methylation were detected. For MSAP analysis, the average polymorphic frequency of the on-ground controls, space-treated plants and mutants are 1.3%, 3.1% and 11% respectively. For AFLP analysis, the average polymorphic frequencies are 1.4%, 2.9%and 8%respectively. Total 27 and 22 polymorphic fragments were cloned sequenced from MSAP and AFLP analysis respectively. Nine of the 27 fragments from MSAP analysis show homology to coding sequence. For the 22 polymorphic fragments from AFLP analysis, no one shows homology to mRNA sequence and eight fragments show homology to repeat region or retrotransposon sequence. These results suggest that although both genomic DNA sequence and cytosine methylation status can be effected by space flight, the genomic region homology to the fragments from genome DNA and cytosine methylation analysis were different.

  11. Genome-wide DNA polymorphisms in Kavuni, a traditional rice cultivar with nutritional and therapeutic properties.

    PubMed

    Rathinasabapathi, Pasupathi; Purushothaman, Natarajan; Parani, Madasamy

    2016-05-01

    Although rice genome was sequenced in the year 2002, efforts in resequencing the large number of available accessions, landraces, traditional cultivars, and improved varieties of this important food crop are limited. We have initiated resequencing of the traditional cultivars from India. Kavuni is an important traditional rice cultivar from South India that attracts premium price for its nutritional and therapeutic properties. Whole-genome sequencing of Kavuni using Illumina platform and SNPs analysis using Nipponbare reference genome identified 1 150 711 SNPs of which 377 381 SNPs were located in the genic regions. Non-synonymous SNPs (62 708) were distributed in 19 251 genes, and their number varied between 1 and 115 per gene. Large-effect DNA polymorphisms (7769) were present in 3475 genes. Pathway mapping of these polymorphisms revealed the involvement of genes related to carbohydrate metabolism, translation, protein-folding, and cell death. Analysis of the starch biosynthesis related genes revealed that the granule-bound starch synthase I gene had T/G SNPs at the first intron/exon junction and a two-nucleotide combination, which were reported to favour high amylose content and low glycemic index. The present study provided a valuable genomics resource to study the rice varieties with nutritional and medicinal properties.

  12. Open access resources for genome-wide association mapping in rice.

    PubMed

    McCouch, Susan R; Wright, Mark H; Tung, Chih-Wei; Maron, Lyza G; McNally, Kenneth L; Fitzgerald, Melissa; Singh, Namrata; DeClerck, Genevieve; Agosto-Perez, Francisco; Korniliev, Pavel; Greenberg, Anthony J; Naredo, Ma Elizabeth B; Mercado, Sheila Mae Q; Harrington, Sandra E; Shi, Yuxin; Branchini, Darcy A; Kuser-Falcão, Paula R; Leung, Hei; Ebana, Kowaru; Yano, Masahiro; Eizenga, Georgia; McClung, Anna; Mezey, Jason

    2016-01-01

    Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement. PMID:26842267

  13. Open access resources for genome-wide association mapping in rice

    PubMed Central

    McCouch, Susan R.; Wright, Mark H.; Tung, Chih-Wei; Maron, Lyza G.; McNally, Kenneth L.; Fitzgerald, Melissa; Singh, Namrata; DeClerck, Genevieve; Agosto-Perez, Francisco; Korniliev, Pavel; Greenberg, Anthony J.; Naredo, Ma. Elizabeth B.; Mercado, Sheila Mae Q.; Harrington, Sandra E.; Shi, Yuxin; Branchini, Darcy A.; Kuser-Falcão, Paula R.; Leung, Hei; Ebana, Kowaru; Yano, Masahiro; Eizenga, Georgia; McClung, Anna; Mezey, Jason

    2016-01-01

    Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement. PMID:26842267

  14. Open access resources for genome-wide association mapping in rice.

    PubMed

    McCouch, Susan R; Wright, Mark H; Tung, Chih-Wei; Maron, Lyza G; McNally, Kenneth L; Fitzgerald, Melissa; Singh, Namrata; DeClerck, Genevieve; Agosto-Perez, Francisco; Korniliev, Pavel; Greenberg, Anthony J; Naredo, Ma Elizabeth B; Mercado, Sheila Mae Q; Harrington, Sandra E; Shi, Yuxin; Branchini, Darcy A; Kuser-Falcão, Paula R; Leung, Hei; Ebana, Kowaru; Yano, Masahiro; Eizenga, Georgia; McClung, Anna; Mezey, Jason

    2016-01-01

    Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement.

  15. QTL Mapping in Three Rice Populations Uncovers Major Genomic Regions Associated with African Rice Gall Midge Resistance.

    PubMed

    Yao, Nasser; Lee, Cheng-Ruei; Semagn, Kassa; Sow, Mounirou; Nwilene, Francis; Kolade, Olufisayo; Bocco, Roland; Oyetunji, Olumoye; Mitchell-Olds, Thomas; Ndjiondjop, Marie-Noëlle

    2016-01-01

    African rice gall midge (AfRGM) is one of the most destructive pests of irrigated and lowland African ecologies. This study aimed to identify the quantitative trait loci (QTL) associated with AfRGM pest incidence and resistance in three independent bi-parental rice populations (ITA306xBW348-1, ITA306xTOG7106 and ITA306xTOS14519), and to conduct meta QTL (mQTL) analysis to explore whether any genomic regions are conserved across different genetic backgrounds. Composite interval mapping (CIM) conducted on the three populations independently uncovered a total of 28 QTLs associated with pest incidence (12) and pest severity (16). The number of QTLs per population associated with AfRGM resistance varied from three in the ITA306xBW348-1 population to eight in the ITA306xTOG7106 population. Each QTL individually explained 1.3 to 34.1% of the phenotypic variance. The major genomic region for AfRGM resistance had a LOD score and R2 of 60.0 and 34.1% respectively, and mapped at 111 cM on chromosome 4 (qAfrGM4) in the ITA306xTOS14519 population. The meta-analysis reduced the number of QTLs from 28 to 17 mQTLs, each explaining 1.3 to 24.5% of phenotypic variance, and narrowed the confidence intervals by 2.2 cM. There was only one minor effect mQTL on chromosome 1 that was common in the TOS14519 and TOG7106 genetic backgrounds; all other mQTLs were background specific. We are currently fine-mapping and validating the major effect genomic region on chromosome 4 (qAfRGM4). This is the first report in mapping the genomic regions associated with the AfRGM resistance, and will be highly useful for rice breeders. PMID:27508500

  16. QTL Mapping in Three Rice Populations Uncovers Major Genomic Regions Associated with African Rice Gall Midge Resistance

    PubMed Central

    Semagn, Kassa; Sow, Mounirou; Nwilene, Francis; Kolade, Olufisayo; Bocco, Roland; Oyetunji, Olumoye; Mitchell-Olds, Thomas; Ndjiondjop, Marie-Noëlle

    2016-01-01

    African rice gall midge (AfRGM) is one of the most destructive pests of irrigated and lowland African ecologies. This study aimed to identify the quantitative trait loci (QTL) associated with AfRGM pest incidence and resistance in three independent bi-parental rice populations (ITA306xBW348-1, ITA306xTOG7106 and ITA306xTOS14519), and to conduct meta QTL (mQTL) analysis to explore whether any genomic regions are conserved across different genetic backgrounds. Composite interval mapping (CIM) conducted on the three populations independently uncovered a total of 28 QTLs associated with pest incidence (12) and pest severity (16). The number of QTLs per population associated with AfRGM resistance varied from three in the ITA306xBW348-1 population to eight in the ITA306xTOG7106 population. Each QTL individually explained 1.3 to 34.1% of the phenotypic variance. The major genomic region for AfRGM resistance had a LOD score and R2 of 60.0 and 34.1% respectively, and mapped at 111 cM on chromosome 4 (qAfrGM4) in the ITA306xTOS14519 population. The meta-analysis reduced the number of QTLs from 28 to 17 mQTLs, each explaining 1.3 to 24.5% of phenotypic variance, and narrowed the confidence intervals by 2.2 cM. There was only one minor effect mQTL on chromosome 1 that was common in the TOS14519 and TOG7106 genetic backgrounds; all other mQTLs were background specific. We are currently fine-mapping and validating the major effect genomic region on chromosome 4 (qAfRGM4). This is the first report in mapping the genomic regions associated with the AfRGM resistance, and will be highly useful for rice breeders. PMID:27508500

  17. Genome-wide association mapping of salinity tolerance in rice (Oryza sativa).

    PubMed

    Kumar, Vinod; Singh, Anshuman; Mithra, S V Amitha; Krishnamurthy, S L; Parida, Swarup K; Jain, Sourabh; Tiwari, Kapil K; Kumar, Pankaj; Rao, Atmakuri R; Sharma, S K; Khurana, Jitendra P; Singh, Nagendra K; Mohapatra, Trilochan

    2015-04-01

    Salinity tolerance in rice is highly desirable to sustain production in areas rendered saline due to various reasons. It is a complex quantitative trait having different components, which can be dissected effectively by genome-wide association study (GWAS). Here, we implemented GWAS to identify loci controlling salinity tolerance in rice. A custom-designed array based on 6,000 single nucleotide polymorphisms (SNPs) in as many stress-responsive genes, distributed at an average physical interval of <100 kb on 12 rice chromosomes, was used to genotype 220 rice accessions using Infinium high-throughput assay. Genetic association was analysed with 12 different traits recorded on these accessions under field conditions at reproductive stage. We identified 20 SNPs (loci) significantly associated with Na(+)/K(+) ratio, and 44 SNPs with other traits observed under stress condition. The loci identified for various salinity indices through GWAS explained 5-18% of the phenotypic variance. The region harbouring Saltol, a major quantitative trait loci (QTLs) on chromosome 1 in rice, which is known to control salinity tolerance at seedling stage, was detected as a major association with Na(+)/K(+) ratio measured at reproductive stage in our study. In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7. The current association mapping panel contained mostly indica accessions that can serve as source of novel salt tolerance genes and alleles. The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.

  18. Selection Under Domestication: Evidence for a Sweep in the Rice Waxy Genomic Region

    PubMed Central

    Olsen, Kenneth M.; Caicedo, Ana L.; Polato, Nicholas; McClung, Anna; McCouch, Susan; Purugganan, Michael D.

    2006-01-01

    Rice (Oryza sativa) was cultivated by Asian Neolithic farmers >11,000 years ago, and different cultures have selected for divergent starch qualities in the rice grain during and after the domestication process. An intron 1 splice donor site mutation of the Waxy gene is responsible for the absence of amylose in glutinous rice varieties. This mutation appears to have also played an important role in the origin of low amylose, nonglutinous temperate japonica rice varieties, which form a primary component of Northeast Asian cuisines. Waxy DNA sequence analyses indicate that the splice donor mutation is prevalent in temperate japonica rice varieties, but rare or absent in tropical japonica, indica, aus, and aromatic varieties. Sequence analysis across a 500-kb genomic region centered on Waxy reveals patterns consistent with a selective sweep in the temperate japonicas associated with the mutation. The size of the selective sweep (>250 kb) indicates very strong selection in this region, with an inferred selection coefficient that is higher than similar estimates from maize domestication genes or wild species. These findings demonstrate that selection pressures associated with crop domestication regimes can exceed by one to two orders of magnitude those observed for genes under even strong selection in natural systems. PMID:16547098

  19. The rice endophyte Harpophora oryzae genome reveals evolution from a pathogen to a mutualistic endophyte.

    PubMed

    Xu, Xi-Hui; Su, Zhen-Zhu; Wang, Chen; Kubicek, Christian P; Feng, Xiao-Xiao; Mao, Li-Juan; Wang, Jia-Ying; Chen, Chen; Lin, Fu-Cheng; Zhang, Chu-Long

    2014-07-22

    The fungus Harpophora oryzae is a close relative of the pathogen Magnaporthe oryzae and a beneficial endosymbiont of wild rice. Here, we show that H. oryzae evolved from a pathogenic ancestor. The overall genomic structures of H. and M. oryzae were found to be similar. However, during interactions with rice, the expression of 11.7% of all genes showed opposing trends in the two fungi, suggesting differences in gene regulation. Moreover, infection patterns, triggering of host defense responses, signal transduction and nutritional preferences exhibited remarkable differentiation between the two fungi. In addition, the H. oryzae genome was found to contain thousands of loci of transposon-like elements, which led to the disruption of 929 genes. Our results indicate that the gain or loss of orphan genes, DNA duplications, gene family expansions and the frequent translocation of transposon-like elements have been important factors in the evolution of this endosymbiont from a pathogenic ancestor.

  20. Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice.

    PubMed

    Yan, Huihuang; Kikuchi, Shinji; Neumann, Pavel; Zhang, Wenli; Wu, Yufeng; Chen, Feng; Jiang, Jiming

    2010-08-01

    We conducted genome-wide mapping of cytosine methylation using methylcytosine immunoprecipitation combined with Illumina sequencing. The chromosomal distribution pattern of methylated DNA is similar to the heterochromatin distribution pattern on rice chromosomes. The DNA methylation patterns of rice genes are similar to those in Arabidopsis thaliana, including distinct methylation patterns asssociated with gene bodies and promoters. The DNA sequences in the core domains of rice Cen4, Cen5 and Cen8 showed elevated methylation levels compared with sequences in the pericentromeric regions. In addition, elevated methylation levels were associated with the DNA sequences in the CENH3-binding subdomains, compared with the sequences in the flanking H3 subdomains. In contrast, the centromeric domain of Cen11, which is composed exclusively of centromeric satellite DNA, is hypomethylated compared with the pericentromeric domains. Thus, the DNA sequences associated with functional centromeres can be either hypomethylated or hypermethylated. The methylation patterns of centromeric DNA appear to be correlated with the composition of the associated DNA sequences. We propose that both hypomethylation and hypermethylation of CENH3-associated DNA sequences can serve as epigenetic marks to distinguish where CENH3 deposition will occur within the surrounding H3 chromatin.

  1. Physicochemical and functional properties of yeast fermented brown rice flour.

    PubMed

    Ilowefah, Muna; Bakar, Jamilah; Ghazali, Hasanah M; Mediani, Ahmed; Muhammad, Kharidah

    2015-09-01

    In the current study, effects of fermentation on physicochemical and functional properties of brown rice flour (BRF) were investigated. Fermentation conditions were optimized using response surface methodology to achieve moderate acidity (pH 5-6), specifically pH 5.5 of brown rice batter with time, temperature and yeast concentration as the independent variables. The results indicated that brown rice batter was well fermented to maintain pH 5.5 at optimum conditions of 32 °C for 6.26 h using 1 % yeast concentration. Fermentation at moderate acidity significantly increased the levels of protein, total ash, insoluble fiber, soluble fibre, minerals, phenolics, antioxidants, resistant starch, riboflavin, pyridoxine, nicotinic acid, γ-tocotrienol, and δ-tocotrienol. However, it reduced the contents of γ-oryzanol, γ-tocopherol, α-tocopherol, phytic acid, amylose and total starch. Foaming capacity, foaming stability, oil holding capacity, gelatinization temperatures, enthalpy and whiteness of BRF were increased after fermentation. In contrast, its swelling power, water solubility index, hot paste viscosity, breakdown, and setback significantly decreased. Microstructure of BRF was also influenced, where its starch granules released from its enclosed structure after fermentation. This investigation shows evidence that yeast fermentation modified the functionality of BRF and can be used as a functional food ingredient.

  2. Physicochemical and functional properties of yeast fermented brown rice flour.

    PubMed

    Ilowefah, Muna; Bakar, Jamilah; Ghazali, Hasanah M; Mediani, Ahmed; Muhammad, Kharidah

    2015-09-01

    In the current study, effects of fermentation on physicochemical and functional properties of brown rice flour (BRF) were investigated. Fermentation conditions were optimized using response surface methodology to achieve moderate acidity (pH 5-6), specifically pH 5.5 of brown rice batter with time, temperature and yeast concentration as the independent variables. The results indicated that brown rice batter was well fermented to maintain pH 5.5 at optimum conditions of 32 °C for 6.26 h using 1 % yeast concentration. Fermentation at moderate acidity significantly increased the levels of protein, total ash, insoluble fiber, soluble fibre, minerals, phenolics, antioxidants, resistant starch, riboflavin, pyridoxine, nicotinic acid, γ-tocotrienol, and δ-tocotrienol. However, it reduced the contents of γ-oryzanol, γ-tocopherol, α-tocopherol, phytic acid, amylose and total starch. Foaming capacity, foaming stability, oil holding capacity, gelatinization temperatures, enthalpy and whiteness of BRF were increased after fermentation. In contrast, its swelling power, water solubility index, hot paste viscosity, breakdown, and setback significantly decreased. Microstructure of BRF was also influenced, where its starch granules released from its enclosed structure after fermentation. This investigation shows evidence that yeast fermentation modified the functionality of BRF and can be used as a functional food ingredient. PMID:26344967

  3. Functional Analysis of Jasmonates in Rice through Mutant Approaches

    PubMed Central

    Dhakarey, Rohit; Kodackattumannil Peethambaran, Preshobha; Riemann, Michael

    2016-01-01

    Jasmonic acid, one of the major plant hormones, is, unlike other hormones, a lipid-derived compound that is synthesized from the fatty acid linolenic acid. It has been studied intensively in many plant species including Arabidopsis thaliana, in which most of the enzymes participating in its biosynthesis were characterized. In the past 15 years, mutants and transgenic plants affected in the jasmonate pathway became available in rice and facilitate studies on the functions of this hormone in an important crop. Those functions are partially conserved compared to other plant species, and include roles in fertility, response to mechanical wounding and defense against herbivores. However, new and surprising functions have also been uncovered by mutant approaches, such as a close link between light perception and the jasmonate pathway. This was not only useful to show a phenomenon that is unique to rice but also helped to establish this role in plant species where such links are less obvious. This review aims to provide an overview of currently available rice mutants and transgenic plants in the jasmonate pathway and highlights some selected roles of jasmonate in this species, such as photomorphogenesis, and abiotic and biotic stress. PMID:27135235

  4. Draft Genome Sequence of Pseudomonas fluorescens Strain ET76, Isolated from Rice Rhizosphere in Northwestern Morocco

    PubMed Central

    Aarab, Saida; Arakrak, Abdelhay; Ollero, Francisco Javier; Megías, Manuel; Gomes, Douglas Fabiano; Ribeiro, Renan Augusto

    2016-01-01

    Pseudomonas fluorescens ET76 was isolated from rice rhizosphere in northwestern Morocco. Its draft genome was estimated to be 6,681,652 bp with 5,789 coding sequences (CDSs). Genes encoding for type I to VI secretion systems, PvdQ, proteases, siderophores, hydrogen cyanide synthase, ACC-deaminase, among others, highlight its potential use in biological control of plant pathogens. PMID:27198014

  5. Draft Genome Sequence of Pseudomonas fluorescens Strain ET76, Isolated from Rice Rhizosphere in Northwestern Morocco.

    PubMed

    Aarab, Saida; Arakrak, Abdelhay; Ollero, Francisco Javier; Megías, Manuel; Gomes, Douglas Fabiano; Ribeiro, Renan Augusto; Hungria, Mariangela

    2016-01-01

    Pseudomonas fluorescens ET76 was isolated from rice rhizosphere in northwestern Morocco. Its draft genome was estimated to be 6,681,652 bp with 5,789 coding sequences (CDSs). Genes encoding for type I to VI secretion systems, PvdQ, proteases, siderophores, hydrogen cyanide synthase, ACC-deaminase, among others, highlight its potential use in biological control of plant pathogens. PMID:27198014

  6. Draft Genome Sequence of Pseudomonas fluorescens Strain ET76, Isolated from Rice Rhizosphere in Northwestern Morocco.

    PubMed

    Aarab, Saida; Arakrak, Abdelhay; Ollero, Francisco Javier; Megías, Manuel; Gomes, Douglas Fabiano; Ribeiro, Renan Augusto; Hungria, Mariangela

    2016-05-19

    Pseudomonas fluorescens ET76 was isolated from rice rhizosphere in northwestern Morocco. Its draft genome was estimated to be 6,681,652 bp with 5,789 coding sequences (CDSs). Genes encoding for type I to VI secretion systems, PvdQ, proteases, siderophores, hydrogen cyanide synthase, ACC-deaminase, among others, highlight its potential use in biological control of plant pathogens.

  7. Open chromatin reveals the functional maize genome

    PubMed Central

    Rodgers-Melnick, Eli; Vera, Daniel L.; Bass, Hank W.

    2016-01-01

    Cellular processes mediated through nuclear DNA must contend with chromatin. Chromatin structural assays can efficiently integrate information across diverse regulatory elements, revealing the functional noncoding genome. In this study, we use a differential nuclease sensitivity assay based on micrococcal nuclease (MNase) digestion to discover open chromatin regions in the maize genome. We find that maize MNase-hypersensitive (MNase HS) regions localize around active genes and within recombination hotspots, focusing biased gene conversion at their flanks. Although MNase HS regions map to less than 1% of the genome, they consistently explain a remarkably large amount (∼40%) of heritable phenotypic variance in diverse complex traits. MNase HS regions are therefore on par with coding sequences as annotations that demarcate the functional parts of the maize genome. These results imply that less than 3% of the maize genome (coding and MNase HS regions) may give rise to the overwhelming majority of phenotypic variation, greatly narrowing the scope of the functional genome. PMID:27185945

  8. Genome analysis of rice-blast fungus Magnaporthe oryzae field isolates from southern India

    PubMed Central

    Gowda, Malali; Shirke, Meghana D.; Mahesh, H.B.; Chandarana, Pinal; Rajamani, Anantharamanan; Chattoo, Bharat B.

    2015-01-01

    The Indian subcontinent is the center of origin and diversity for rice (Oryza sativa L.). The O. sativa ssp. indica is a major food crop grown in India, which occupies the first and second position in area and production, respectively. Blast disease caused by Magnaporthe oryzae is a major constraint to rice production. Here, we report the analysis of genome architecture and sequence variation of two field isolates, B157 and MG01, of the blast fungus from southern India. The 40 Mb genome of B157 and 43 Mb genome of MG01 contained 11,344 and 11,733 predicted genes, respectively. Genomic comparisons unveiled a large set of SNPs and several isolate specific genes in the Indian blast isolates. Avr genes were analyzed in several sequenced Magnaporthe strains; this analysis revealed the presence of Avr-Pizt and Avr-Ace1 genes in all the sequenced isolates. Availability of whole genomes of field isolates from India will contribute to global efforts to understand genetic diversity of M. oryzae population and to track the emergence of virulent pathotypes. PMID:26484270

  9. Rice epigenomics and epigenetics: challenges and opportunities.

    PubMed

    Chen, Xiangsong; Zhou, Dao-Xiu

    2013-05-01

    During recent years rice genome-wide epigenomic information such as DNA methylation and histone modifications, which are important for genome activity has been accumulated. The function of a number of rice epigenetic regulators has been studied, many of which are found to be involved in a diverse range of developmental and stress-responsive pathways. Analysis of epigenetic variations among different rice varieties indicates that epigenetic modification may lead to inheritable phenotypic variation. Characterizing phenotypic consequences of rice epigenomic variations and the underlining chromatin mechanism and identifying epialleles related to important agronomic traits may provide novel strategies to enhance agronomically favorable traits and grain productivity in rice.

  10. Transport Function of Rice Amino Acid Permeases (AAPs).

    PubMed

    Taylor, Margaret R; Reinders, Anke; Ward, John M

    2015-07-01

    The transport function of four rice (Oryza sativa) amino acid permeases (AAPs), OsAAP1 (Os07g04180), OsAAP3 (Os06g36180), OsAAP7 (Os05g34980) and OsAAP16 (Os12g08090), was analyzed by expression in Xenopus laevis oocytes and electrophysiology. OsAAP1, OsAAP7 and OsAAP16 functioned, similarly to Arabidopsis AAPs, as general amino acid permeases. OsAAP3 had a distinct substrate specificity compared with other rice or Arabidopsis AAPs. OsAAP3 transported the basic amino acids lysine and arginine well but selected against aromatic amino acids. The transport of basic amino acids was further analyzed for OsAAP1 and OsAAP3, and the results support the transport of both neutral and positively charged forms of basic amino acids by the rice AAPs. Cellular localization using the tandem enhanced green fluorescent protein (EGFP)-red fluorescent protein (RFP) reporter pHusion showed that OsAAP1 and OsAAP3 localized to the plasma membrane after transient expression in onion epidermal cells or stable expression in Arabidopsis. PMID:25907566

  11. Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution[W

    PubMed Central

    Salse, Jérôme; Bolot, Stéphanie; Throude, Michaël; Jouffe, Vincent; Piegu, Benoît; Quraishi, Umar Masood; Calcagno, Thomas; Cooke, Richard; Delseny, Michel; Feuillet, Catherine

    2008-01-01

    The grass family comprises the most important cereal crops and is a good system for studying, with comparative genomics, mechanisms of evolution, speciation, and domestication. Here, we identified and characterized the evolution of shared duplications in the rice (Oryza sativa) and wheat (Triticum aestivum) genomes by comparing 42,654 rice gene sequences with 6426 mapped wheat ESTs using improved sequence alignment criteria and statistical analysis. Intraspecific comparisons identified 29 interchromosomal duplications covering 72% of the rice genome and 10 duplication blocks covering 67.5% of the wheat genome. Using the same methodology, we assessed orthologous relationships between the two genomes and detected 13 blocks of colinearity that represent 83.1 and 90.4% of the rice and wheat genomes, respectively. Integration of the intraspecific duplications data with colinearity relationships revealed seven duplicated segments conserved at orthologous positions. A detailed analysis of the length, composition, and divergence time of these duplications and comparisons with sorghum (Sorghum bicolor) and maize (Zea mays) indicated common and lineage-specific patterns of conservation between the different genomes. This allowed us to propose a model in which the grass genomes have evolved from a common ancestor with a basic number of five chromosomes through a series of whole genome and segmental duplications, chromosome fusions, and translocations. PMID:18178768

  12. Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima).

    PubMed

    Nabholz, Benoit; Sarah, Gautier; Sabot, François; Ruiz, Manuel; Adam, Hélène; Nidelet, Sabine; Ghesquière, Alain; Santoni, Sylvain; David, Jacques; Glémin, Sylvain

    2014-05-01

    The African cultivated rice (Oryza glaberrima) was domesticated in West Africa 3000 years ago. Although less cultivated than the Asian rice (O. sativa), O. glaberrima landraces often display interesting adaptation to rustic environment (e.g. drought). Here, using RNA-seq technology, we were able to compare more than 12,000 transcripts between 9 O. glaberrima, 10 wild O. barthii and one O. meridionalis individuals. With a synonymous nucleotide diversity πs = 0.0006 per site, O. glaberrima appears as the least genetically diverse crop grass ever documented. Using approximate Bayesian computation, we estimated that O. glaberrima experienced a severe bottleneck during domestication. This demographic scenario almost fully accounts for the pattern of genetic diversity across O. glaberrima genome as we detected very few outliers regions where positive selection may have further impacted genetic diversity. Moreover, the large excess of derived nonsynonymous substitution that we detected suggests that the O. glaberrima population suffered from the 'cost of domestication'. In addition, we used this genome-scale data set to demonstrate that (i) O. barthii genetic diversity is positively correlated with recombination rate and negatively with gene density, (ii) expression level is negatively correlated with evolutionary constraint, and (iii) one region on chromosome 5 (position 4-6 Mb) exhibits a clear signature of introgression with a yet unidentified Oryza species. This work represents the first genome-wide survey of the African rice genetic diversity and paves the way for further comparison between the African and the Asian rice, notably regarding the genetics underlying domestication traits.

  13. Nucleotide diversity analysis highlights functionally important genomic regions

    PubMed Central

    Tatarinova, Tatiana V.; Chekalin, Evgeny; Nikolsky, Yuri; Bruskin, Sergey; Chebotarov, Dmitry; McNally, Kenneth L.; Alexandrov, Nickolai

    2016-01-01

    We analyzed functionality and relative distribution of genetic variants across the complete Oryza sativa genome, using the 40 million single nucleotide polymorphisms (SNPs) dataset from the 3,000 Rice Genomes Project (http://snp-seek.irri.org), the largest and highest density SNP collection for any higher plant. We have shown that the DNA-binding transcription factors (TFs) are the most conserved group of genes, whereas kinases and membrane-localized transporters are the most variable ones. TFs may be conserved because they belong to some of the most connected regulatory hubs that modulate transcription of vast downstream gene networks, whereas signaling kinases and transporters need to adapt rapidly to changing environmental conditions. In general, the observed profound patterns of nucleotide variability reveal functionally important genomic regions. As expected, nucleotide diversity is much higher in intergenic regions than within gene bodies (regions spanning gene models), and protein-coding sequences are more conserved than untranslated gene regions. We have observed a sharp decline in nucleotide diversity that begins at about 250 nucleotides upstream of the transcription start and reaches minimal diversity exactly at the transcription start. We found the transcription termination sites to have remarkably symmetrical patterns of SNP density, implying presence of functional sites near transcription termination. Also, nucleotide diversity was significantly lower near 3′ UTRs, the area rich with regulatory regions. PMID:27774999

  14. Comparative genomic analysis of the Sm gene family in rice and maize.

    PubMed

    Chen, Yuzhu; Cao, Jun

    2014-04-15

    Sm proteins are a group of ubiquitous ring-shaped oligomers that function in multiple aspects of RNA metabolism. However, until this study, no comprehensive study incorporating phylogeny, chromosomal location, gene organization, adaptive evolution, expression profiling and functional networks has been reported for rice and maize. In this study, twenty-five and thirty-three Sm genes have been identified in rice and maize, respectively. Phylogenetic analyses identified eighteen gene groups. Results by gene locations indicated that segmental duplication contributes to the expansion of this gene family in rice and maize. Gene organization and motif compositions of the Sm members are highly conserved in each group, indicative of their functional conservation. Expression profiles have provided insights into the possible functional divergence among members of the Sm gene family. Adaptive evolution analyses suggested that purifying selection was the main force driving Sm evolution, but some critical sites might be responsible for functional divergence. In addition, four hundred and seventy-nine interactions were identified by functional network analyses, and most of which were associated with binding, cellular macromolecule biosynthesis, pre-mRNA processing and transferase activity. Overall, the data contribute to a better understanding of the complexity of Sm gene family in rice and maize and will provide a solid foundation for future functional studies.

  15. Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data.

    PubMed

    Edwards, J D; Baldo, A M; Mueller, L A

    2016-01-01

    Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice. PMID:27515824

  16. Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data

    PubMed Central

    Edwards, J. D.; Baldo, A. M.; Mueller, L. A.

    2016-01-01

    Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice. PMID:27515824

  17. Draft Genome Sequence of Lactobacillus namurensis Chizuka 01, Isolated from Nukadoko, a Pickling Bed of Fermented Rice Bran.

    PubMed

    Kato, Keita; Toh, Hidehiro; Sakamoto, Naoshige; Mori, Kazuki; Tashiro, Kosuke; Hibi, Naruhiro; Sonomoto, Kenji; Nakayama, Jiro

    2014-01-01

    Lactobacillus namurensis Chizuka 01 was isolated from nukadoko, which is a fermented rice bran bed traditionally used in Japan for pickling vegetables. Here, we report the first draft of an annotated genome sequence of this organism. This paper is the first published report of the genomic sequence of L. namurensis. PMID:24504001

  18. Conservation of Microstructure between a Sequenced Region of the Genome of Rice and Multiple Segments of the Genome of Arabidopsis thaliana

    PubMed Central

    Mayer, Klaus; Murphy, George; Tarchini, Renato; Wambutt, Rolf; Volckaert, Guido; Pohl, Thomas; Düsterhöft, Andreas; Stiekema, Willem; Entian, Karl-Dieter; Terryn, Nancy; Lemcke, Kai; Haase, Dirk; Hall, Caroline R.; van Dodeweerd, Anne-Marie; Tingey, Scott V.; Mewes, Hans-Werner; Bevan, Michael W.; Bancroft, Ian

    2001-01-01

    The nucleotide sequence was determined for a 340-kb segment of rice chromosome 2, revealing 56 putative protein-coding genes. This represents a density of one gene per 6.1 kb, which is higher than was reported for a previously sequenced segment of the rice genome. Sixteen of the putative genes were supported by matches to ESTs. The predicted products of 29 of the putative genes showed similarity to known proteins, and a further 17 genes showed similarity only to predicted or hypothetical proteins identified in genome sequence data. The region contains a few transposable elements: one retrotransposon, and one transposon. The segment of the rice genome studied had previously been identified as representing a part of rice chromosome 2 that may be homologous to a segment of Arabidopsis chromosome 4. We confirmed the conservation of gene content and order between the two genome segments. In addition, we identified a further four segments of the Arabidopsis genome that contain conserved gene content and order. In total, 22 of the 56 genes identified in the rice genome segment were represented in this set of Arabidopsis genome segments, with at least five genes present, in conserved order, in each segment. These data are consistent with the hypothesis that the Arabidopsis genome has undergone multiple duplication events. Our results demonstrate that conservation of the genome microstructure can be identified even between monocot and dicot species. However, the frequent occurrence of duplication, and subsequent microstructure divergence, within plant genomes may necessitate the integration of subsets of genes present in multiple redundant segments to deduce evolutionary relationships and identify orthologous genes. PMID:11435398

  19. A Unified and Comprehensible View of Parametric and Kernel Methods for Genomic Prediction with Application to Rice

    PubMed Central

    Jacquin, Laval; Cao, Tuong-Vi; Ahmadi, Nourollah

    2016-01-01

    One objective of this study was to provide readers with a clear and unified understanding of parametric statistical and kernel methods, used for genomic prediction, and to compare some of these in the context of rice breeding for quantitative traits. Furthermore, another objective was to provide a simple and user-friendly R package, named KRMM, which allows users to perform RKHS regression with several kernels. After introducing the concept of regularized empirical risk minimization, the connections between well-known parametric and kernel methods such as Ridge regression [i.e., genomic best linear unbiased predictor (GBLUP)] and reproducing kernel Hilbert space (RKHS) regression were reviewed. Ridge regression was then reformulated so as to show and emphasize the advantage of the kernel “trick” concept, exploited by kernel methods in the context of epistatic genetic architectures, over parametric frameworks used by conventional methods. Some parametric and kernel methods; least absolute shrinkage and selection operator (LASSO), GBLUP, support vector machine regression (SVR) and RKHS regression were thereupon compared for their genomic predictive ability in the context of rice breeding using three real data sets. Among the compared methods, RKHS regression and SVR were often the most accurate methods for prediction followed by GBLUP and LASSO. An R function which allows users to perform RR-BLUP of marker effects, GBLUP and RKHS regression, with a Gaussian, Laplacian, polynomial or ANOVA kernel, in a reasonable computation time has been developed. Moreover, a modified version of this function, which allows users to tune kernels for RKHS regression, has also been developed and parallelized for HPC Linux clusters. The corresponding KRMM package and all scripts have been made publicly available. PMID:27555865

  20. A Unified and Comprehensible View of Parametric and Kernel Methods for Genomic Prediction with Application to Rice.

    PubMed

    Jacquin, Laval; Cao, Tuong-Vi; Ahmadi, Nourollah

    2016-01-01

    One objective of this study was to provide readers with a clear and unified understanding of parametric statistical and kernel methods, used for genomic prediction, and to compare some of these in the context of rice breeding for quantitative traits. Furthermore, another objective was to provide a simple and user-friendly R package, named KRMM, which allows users to perform RKHS regression with several kernels. After introducing the concept of regularized empirical risk minimization, the connections between well-known parametric and kernel methods such as Ridge regression [i.e., genomic best linear unbiased predictor (GBLUP)] and reproducing kernel Hilbert space (RKHS) regression were reviewed. Ridge regression was then reformulated so as to show and emphasize the advantage of the kernel "trick" concept, exploited by kernel methods in the context of epistatic genetic architectures, over parametric frameworks used by conventional methods. Some parametric and kernel methods; least absolute shrinkage and selection operator (LASSO), GBLUP, support vector machine regression (SVR) and RKHS regression were thereupon compared for their genomic predictive ability in the context of rice breeding using three real data sets. Among the compared methods, RKHS regression and SVR were often the most accurate methods for prediction followed by GBLUP and LASSO. An R function which allows users to perform RR-BLUP of marker effects, GBLUP and RKHS regression, with a Gaussian, Laplacian, polynomial or ANOVA kernel, in a reasonable computation time has been developed. Moreover, a modified version of this function, which allows users to tune kernels for RKHS regression, has also been developed and parallelized for HPC Linux clusters. The corresponding KRMM package and all scripts have been made publicly available. PMID:27555865

  1. Genomewide Variation in an Introgression Line of Rice-Zizania Revealed by Whole-Genome re-Sequencing

    PubMed Central

    Bai, Yan; Zhang, Yun-Hong; Liu, Ying; Wu, Ying; Lin, Xiu-Yun; Wen, Jia-Wei; Xu, Chun-Ming; Li, Lin-Feng; Liu, Bao

    2013-01-01

    Background Hybridization between genetically diverged organisms is known as an important avenue that drives plant genome evolution. The possible outcomes of hybridization would be the occurrences of genetic instabilities in the resultant hybrids. It remained under-investigated however whether pollination by alien pollens of a closely related but sexually "incompatible" species could evoke genomic changes and to what extent it may result in phenotypic novelties in the derived progenies. Methodology/Principal Findings In this study, we have re-sequenced the genomes of Oryza sativa ssp. japonica cv. Matsumae and one of its derived introgressant RZ35 that was obtained from an introgressive hybridization between Matsumae and Zizanialatifolia Griseb. in general, 131 millions 90 base pair (bp) paired-end reads were generated which covered 13.2 and 21.9 folds of the Matsumae and RZ35 genomes, respectively. Relative to Matsumae, a total of 41,724 homozygous single nucleotide polymorphisms (SNPs) and 17,839 homozygous insertions/deletions (indels) were identified in RZ35, of which 3,797 SNPs were nonsynonymous mutations. Furthermore, rampant mobilization of transposable elements (TEs) was found in the RZ35 genome. The results of pathogen inoculation revealed that RZ35 exhibited enhanced resistance to blast relative to Matsumae. Notably, one nonsynonymous mutation was found in the known blast resistance gene Pid3/Pi25 and real-time quantitative (q) RT-PCR analysis revealed constitutive up-regulation of its expression, suggesting both altered function and expression of Pid3/Pi25 may be responsible for the enhanced resistance to rice blast by RZ35. Conclusions/Significance Our results demonstrate that introgressive hybridization by Zizania has provoked genomewide, extensive genomic changes in the rice genome, and some of which have resulted in important phenotypic novelties. These findings suggest that introgressive hybridization by alien pollens of even a sexually incompatible

  2. Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine

    PubMed Central

    Lu, Yi Chen; Feng, Sheng Jun; Zhang, Jing Jing; Luo, Fang; Zhang, Shuang; Yang, Hong

    2016-01-01

    Atrazine (ATR) is a pesticide widely used for controlling weeds for crop production. Crop contamination with ATR negatively affects crop growth and development. This study presents the first genome-wide single-base-resolution maps of DNA methylation in ATR-exposed rice. Widespread differences were identified in CG and non-CG methylation marks between the ATR-exposed and ATR-free (control) rice. Most of DNA methyltransferases, histone methyltransferases and DNA demethylase were differentially regulated by ATR. We found more genes hypermethylated than those hypomethylated in the regions of upstream, genebody and downstream under ATR exposure. A stringent group of 674 genes (p < 0.05, two-fold change) with a strong preference of differential expression in ATR-exposed rice was identified. Some of the genes were identified in a subset of loss of function mutants defective in DNA methylation/demethylation. Provision of 5-azacytidine (AZA, inhibitor of DNA methylation) promoted the rice growth and reduced ATR content. By UPLC/Q-TOF-MS/MS, 8 degraded products and 9 conjugates of ATR in AZA-treated rice were characterized. Two of them has been newly identified in this study. Our data show that ATR-induced changes in DNA methylation marks are possibly involved in an epigenetic mechanism associated with activation of specific genes responsible for ATR degradation and detoxification. PMID:26739616

  3. Characteristics and inheritance of space flight induced mutations in rice genomes

    NASA Astrophysics Data System (ADS)

    Cheng, Zhenlong; Feng, Jie; Kong, Fanding; Wang, Chunli; Zhang, Meng; Jinming Shi, Mrs; Guan, Shuanghong; Sun, Yeqing

    In order to determine the mutagenic effects of space flight and the properties of space induced mutations, the seeds of 5 japonica rice varieties, Zhenzhuhong, Lianjing-2, Yuguang, Beijinghong and Lianjing-1, were carried on-board by Shenzhou-6 spaceship for 5-day-flight. In M1 generation, 20-30 individuals were selected at random from each variety for determination of genomic changes with AFLP method. Sixteen pairs of selective amplification primers were used and 1061, 933, 1054, 749, and 673 loci were detected in each variety. Mutation rates were 3.4% 10.1%, 3.3% 8.5%, 4.0% 10.1%, 0.93% 6.54% and 1.19% 4.46%. Three individuals with significant phenotypic changes which in significant differences in height, tillering, length of spike, seeds per spike and per individual, the mutation rates were 13.7%, 12.1% and 13.1% respectively,. These results suggested that space flight induced mutations in rice genomes and the phenotypic mutants showed higher genomic mutation rates. Nineteen mutant loci were amplified for sequence analysis. BlastN program performance showed that 10 (52.6%) were matched with sequences in GenBank, 5 single copies and 5 multi-copies in rice genome. Among 5 single copy sequences, 2 were located at exons, 2 at introns. One was combined with exon and intron sequences. Three multi-copy sequences were related to transposons or retroposon, one of which was combination of two fragments in different chromosomes, indicating that chromosome recombination may be involved in spaceflight induced mutation. Inheritance of one mutation at transposon related region and another mutation at non-coding region was checked in M1, 2 and 3 generations. Results showed that mutation loci can be inherited to some but all progenies. Interestingly, mutations were detected in M3 individuals, whose M2 parents were with no mutation at corresponding loci, suggesting that space flight may induce genomic instability on rice seeds (Supported by National Natural Science Foundation No

  4. Rice Glycosyltransferase (GT) Phylogenomic Database

    DOE Data Explorer

    Ronald, Pamela

    The Ronald Laboratory staff at the University of California-Davis has a primary research focus on the genes of the rice plant. They study the role that genetics plays in the way rice plants respond to their environment. They created the Rice GT Database in order to integrate functional genomic information for putative rice Glycosyltransferases (GTs). This database contains information on nearly 800 putative rice GTs (gene models) identified by sequence similarity searches based on the Carbohydrate Active enZymes (CAZy) database. The Rice GT Database provides a platform to display user-selected functional genomic data on a phylogenetic tree. This includes sequence information, mutant line information, expression data, etc. An interactive chromosomal map shows the position of all rice GTs, and links to rice annotation databases are included. The format is intended to "facilitate the comparison of closely related GTs within different families, as well as perform global comparisons between sets of related families." [From http://ricephylogenomics.ucdavis.edu/cellwalls/gt/genInfo.shtml] See also the primary paper discussing this work: Peijian Cao, Laura E. Bartley, Ki-Hong Jung and Pamela C. Ronalda. Construction of a Rice Glycosyltransferase Phylogenomic Database and Identification of Rice-Diverged Glycosyltransferases. Molecular Plant, 2008, 1(5): 858-877.

  5. Unmasking Novel Loci for Internal Phosphorus Utilization Efficiency in Rice Germplasm through Genome-Wide Association Analysis.

    PubMed

    Wissuwa, Matthias; Kondo, Katsuhiko; Fukuda, Takuya; Mori, Asako; Rose, Michael T; Pariasca-Tanaka, Juan; Kretzschmar, Tobias; Haefele, Stephan M; Rose, Terry J

    2015-01-01

    Depletion of non-renewable rock phosphate reserves and phosphorus (P) fertilizer price increases has renewed interest in breeding P-efficient varieties. Internal P utilization efficiency (PUE) is of prime interest because there has been no progress to date in breeding for high PUE. We characterized the genotypic variation for PUE present within the rice gene pool by using a hydroponic system that assured equal plant P uptake, followed by mapping of loci controlling PUE via Genome-Wide Association Studies (GWAS). Loci associated with PUE were mapped on chromosomes 1, 4, 11 and 12. The highest PUE was associated with a minor indica-specific haplotype on chromosome 1 and a rare aus-specific haplotype on chromosome 11. Comparative variant and expression analysis for genes contained within the chromosome 1 haplotype identified high priority candidate genes. Differences in coding regions and expression patterns between genotypes of contrasting haplotypes, suggested functional alterations for two predicted nucleic acid-interacting proteins that are likely causative for the observed differences in PUE. The loci reported here are the first identified for PUE in any crop that is not confounded by differential P uptake among genotypes. Importantly, modern rice varieties lacked haplotypes associated with superior PUE, and would thus benefit from targeted introgressions of these loci from traditional donors to improve plant growth in phosphorus-limited cropping systems. PMID:25923470

  6. Unmasking Novel Loci for Internal Phosphorus Utilization Efficiency in Rice Germplasm through Genome-Wide Association Analysis

    PubMed Central

    Wissuwa, Matthias; Kondo, Katsuhiko; Fukuda, Takuya; Mori, Asako; Rose, Michael T.; Pariasca-Tanaka, Juan; Kretzschmar, Tobias; Haefele, Stephan M.; Rose, Terry J.

    2015-01-01

    Depletion of non-renewable rock phosphate reserves and phosphorus (P) fertilizer price increases has renewed interest in breeding P-efficient varieties. Internal P utilization efficiency (PUE) is of prime interest because there has been no progress to date in breeding for high PUE. We characterized the genotypic variation for PUE present within the rice gene pool by using a hydroponic system that assured equal plant P uptake, followed by mapping of loci controlling PUE via Genome-Wide Association Studies (GWAS). Loci associated with PUE were mapped on chromosomes 1, 4, 11 and 12. The highest PUE was associated with a minor indica-specific haplotype on chromosome 1 and a rare aus-specific haplotype on chromosome 11. Comparative variant and expression analysis for genes contained within the chromosome 1 haplotype identified high priority candidate genes. Differences in coding regions and expression patterns between genotypes of contrasting haplotypes, suggested functional alterations for two predicted nucleic acid-interacting proteins that are likely causative for the observed differences in PUE. The loci reported here are the first identified for PUE in any crop that is not confounded by differential P uptake among genotypes. Importantly, modern rice varieties lacked haplotypes associated with superior PUE, and would thus benefit from targeted introgressions of these loci from traditional donors to improve plant growth in phosphorus-limited cropping systems. PMID:25923470

  7. Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach.

    PubMed

    Bhattacharyya, P; Roy, K S; Das, M; Ray, S; Balachandar, D; Karthikeyan, S; Nayak, A K; Mohapatra, T

    2016-01-15

    Carbon (C) and nitrogen (N) mineralization is one of the key processes of biogeochemical cycling in terrestrial ecosystem in general and rice ecology in particular. Rice rhizosphere is a rich niche of microbial diversity influenced by change in atmospheric temperature and concentration of carbon dioxide (CO2). Structural changes in microbial communities in rhizosphere influence the nutrient cycling. In the present study, the bacterial diversity and population dynamics were studied under ambient CO2 (a-CO2) and elevated CO2+temperature (e-CO2T) in lowland rice rhizosphere using whole genome metagenomic approach. The whole genome metagenomic sequence data of lowland rice exhibited the dominance of bacterial communities including Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria and Planctomycetes. Interestingly, four genera related to methane production namely, Methanobacterium, Methanosphaera, Methanothermus and Methanothermococcus were absent in a-CO2 but noticed under e-CO2T. The acetoclastic pathway was found as the predominant pathway for methanogenesis, whereas, the serine pathway was found as the principal metabolic pathway for CH4 oxidation in lowland rice. The abundances of reads of enzymes in the acetoclastic methanogenesis pathway and serine pathways of methanotrophy were much higher in e-CO2T (328 and 182, respectively) as compared with a-CO2 (118 and 98, respectively). Rice rhizosphere showed higher structural diversities and functional activities in relation to N metabolism involving nitrogen fixation, assimilatory and dissimilatory nitrate reduction and denitrification under e-CO2T than that of a-CO2. Among the three pathways of N metabolism, dissimilarity pathways were predominant in lowland rice rhizosphere and more so under e-CO2T. Consequently, under e-CO2T, CH4 emission, microbial biomass nitrogen (MBN) and dehydrogenase activities were 45%, 20% and 35% higher than a-CO2, respectively. Holistically, a high bacterial diversity and

  8. A Genome-Wide Survey of Imprinted Genes in Rice Seeds Reveals Imprinting Primarily Occurs in the Endosperm

    PubMed Central

    Luo, Ming; Taylor, Jennifer M.; Spriggs, Andrew; Zhang, Hongyu; Wu, Xianjun; Russell, Scott; Singh, Mohan; Koltunow, Anna

    2011-01-01

    Genomic imprinting causes the expression of an allele depending on its parental origin. In plants, most imprinted genes have been identified in Arabidopsis endosperm, a transient structure consumed by the embryo during seed formation. We identified imprinted genes in rice seed where both the endosperm and embryo are present at seed maturity. RNA was extracted from embryos and endosperm of seeds obtained from reciprocal crosses between two subspecies Nipponbare (Japonica rice) and 93-11 (Indica rice). Sequenced reads from cDNA libraries were aligned to their respective parental genomes using single-nucleotide polymorphisms (SNPs). Reads across SNPs enabled derivation of parental expression bias ratios. A continuum of parental expression bias states was observed. Statistical analyses indicated 262 candidate imprinted loci in the endosperm and three in the embryo (168 genic and 97 non-genic). Fifty-six of the 67 loci investigated were confirmed to be imprinted in the seed. Imprinted loci are not clustered in the rice genome as found in mammals. All of these imprinted loci were expressed in the endosperm, and one of these was also imprinted in the embryo, confirming that in both rice and Arabidopsis imprinted expression is primarily confined to the endosperm. Some rice imprinted genes were also expressed in vegetative tissues, indicating that they have additional roles in plant growth. Comparison of candidate imprinted genes found in rice with imprinted candidate loci obtained from genome-wide surveys of imprinted genes in Arabidopsis to date shows a low degree of conservation, suggesting that imprinting has evolved independently in eudicots and monocots. PMID:21731498

  9. Tomato functional genomics database (TFGD): a comprehensive collection and analysis package for tomato functional genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tomato Functional Genomics Database (TFGD; http://ted.bti.cornell.edu) provides a comprehensive systems biology resource to store, mine, analyze, visualize and integrate large-scale tomato functional genomics datasets. The database is expanded from the previously described Tomato Expression Database...

  10. Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis

    PubMed Central

    Huang, Xuehui; Yang, Shihua; Gong, Junyi; Zhao, Yan; Feng, Qi; Gong, Hao; Li, Wenjun; Zhan, Qilin; Cheng, Benyi; Xia, Junhui; Chen, Neng; Hao, Zhongna; Liu, Kunyan; Zhu, Chuanrang; Huang, Tao; Zhao, Qiang; Zhang, Lei; Fan, Danlin; Zhou, Congcong; Lu, Yiqi; Weng, Qijun; Wang, Zi-Xuan; Li, Jiayang; Han, Bin

    2015-01-01

    Exploitation of heterosis is one of the most important applications of genetics in agriculture. However, the genetic mechanisms of heterosis are only partly understood, and a global view of heterosis from a representative number of hybrid combinations is lacking. Here we develop an integrated genomic approach to construct a genome map for 1,495 elite hybrid rice varieties and their inbred parental lines. We investigate 38 agronomic traits and identify 130 associated loci. In-depth analyses of the effects of heterozygous genotypes reveal that there are only a few loci with strong overdominance effects in hybrids, but a strong correlation is observed between the yield and the number of superior alleles. While most parental inbred lines have only a small number of superior alleles, high-yielding hybrid varieties have several. We conclude that the accumulation of numerous rare superior alleles with positive dominance is an important contributor to the heterotic phenomena. PMID:25651972

  11. Genome-wide transcriptome analysis of expression in rice seedling roots in response to supplemental nitrogen.

    PubMed

    Chandran, Anil Kumar Nalini; Priatama, Ryza A; Kumar, Vikranth; Xuan, Yuanhu; Je, Byoung Il; Kim, Chul Min; Jung, Ki-Hong; Han, Chang-Deok

    2016-08-01

    Nitrogen (N) is the most important macronutrient for plant growth and grain yields. For rice crops, nitrate and ammonium are the major N sources. To explore the genomic responses to ammonium supplements in rice roots, we used 17-day-old seedlings grown in the absence of external N that were then exposed to 0.5mM (NH4)2SO4 for 3h. Transcriptomic profiles were examined by microarray experiments. In all, 634 genes were up-regulated at least two-fold by the N-supplement when compared with expression in roots from untreated control plants. Gene Ontology (GO) enrichment analysis revealed that those upregulated genes are associated with 23 GO terms. Among them, metabolic processes for diverse amino acids (i.e., aspartate, threonine, tryptophan, glutamine, l-phenylalanine, and thiamin) as well as nitrogen compounds are highly over-represented, demonstrating that our selected genes are suitable for studying the N-response in roots. This enrichment analysis also indicated that nitrogen is closely linked to diverse transporter activities by primary metabolites, including proteins (amino acids), lipids, and carbohydrates, and is associated with carbohydrate catabolism and cell wall organization. Integration of results from omics analysis of metabolic pathways and transcriptome data using the MapMan tool suggested that the TCA cycle and pathway for mitochondrial electron transport are co-regulated when rice roots are exposed to ammonium. We also investigated the expression of N-responsive marker genes by performing a comparative analysis with root samples from plants grown under different NH4(+) treatments. The diverse responses to such treatment provide useful insight into the global changes related to the shift from an N-deficiency to an enhanced N-supply in rice, a model crop plant. PMID:27340859

  12. From genome to function: the Arabidopsis aquaporins

    PubMed Central

    Quigley, Francoise; Rosenberg, Joshua M; Shachar-Hill, Yair; Bohnert, Hans J

    2002-01-01

    Background In the post-genomic era newly sequenced genomes can be used to deduce organismal functions from our knowledge of other systems. Here we apply this approach to analyzing the aquaporin gene family in Arabidopsis thaliana. The aquaporins are intrinsic membrane proteins that have been characterized as facilitators of water flux. Originally termed major intrinsic proteins (MIPs), they are now also known as water channels, glycerol facilitators and aqua-glyceroporins, yet recent data suggest that they facilitate the movement of other low-molecular-weight metabolites as well. Results The Arabidopsis genome contains 38 sequences with homology to aquaporin in four subfamilies, termed PIP, TIP, NIP and SIP. We have analyzed aquaporin family structure and expression using the A. thaliana genome sequence, and introduce a new NMR approach for the purpose of analyzing water movement in plant roots in vivo. Conclusions Our preliminary data indicate a strongly transcellular component for the flux of water in roots. PMID:11806824

  13. Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites

    PubMed Central

    Studt, Lena; Niehaus, Eva-Maria; Espino, Jose J.; Huß, Kathleen; Michielse, Caroline B.; Albermann, Sabine; Wagner, Dominik; Bergner, Sonja V.; Connolly, Lanelle R.; Fischer, Andreas; Reuter, Gunter; Kleigrewe, Karin; Bald, Till; Wingfield, Brenda D.; Ophir, Ron; Freeman, Stanley; Hippler, Michael; Smith, Kristina M.; Brown, Daren W.; Proctor, Robert H.; Münsterkötter, Martin; Freitag, Michael; Humpf, Hans-Ulrich; Güldener, Ulrich; Tudzynski, Bettina

    2013-01-01

    The fungus Fusarium fujikuroi causes “bakanae” disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we present a high-quality genome sequence of F. fujikuroi that was assembled into 12 scaffolds corresponding to the 12 chromosomes described for the fungus. We used the genome sequence along with ChIP-seq, transcriptome, proteome, and HPLC-FTMS-based metabolome analyses to identify the potential secondary metabolite biosynthetic gene clusters and to examine their regulation in response to nitrogen availability and plant signals. The results indicate that expression of most but not all gene clusters correlate with proteome and ChIP-seq data. Comparison of the F. fujikuroi genome to those of six other fusaria revealed that only a small number of gene clusters are conserved among these species, thus providing new insights into the divergence of secondary metabolism in the genus Fusarium. Noteworthy, GA biosynthetic genes are present in some related species, but GA biosynthesis is limited to F. fujikuroi, suggesting that this provides a selective advantage during infection of the preferred host plant rice. Among the genome sequences analyzed, one cluster that includes a polyketide synthase gene (PKS19) and another that includes a non-ribosomal peptide synthetase gene (NRPS31) are unique to F. fujikuroi. The metabolites derived from these clusters were identified by HPLC-FTMS-based analyses of engineered F. fujikuroi strains overexpressing cluster genes. In planta expression studies suggest a specific role for the PKS19-derived product during rice infection. Thus, our results indicate that combined comparative genomics and genome-wide experimental analyses identified novel genes and secondary metabolites that contribute to the evolutionary success of F

  14. Phenolic Phytoalexins in Rice: Biological Functions and Biosynthesis

    PubMed Central

    Cho, Man-Ho; Lee, Sang-Won

    2015-01-01

    Phytoalexins are inducible secondary metabolites possessing antimicrobial activity against phytopathogens. Rice produces a wide array of phytoalexins in response to pathogen attacks and environmental stresses. With few exceptions, most phytoalexins identified in rice are diterpenoid compounds. Until very recently, flavonoid sakuranetin was the only known phenolic phytoalexin in rice. However, recent studies have shown that phenylamides are involved in defense against pathogen attacks in rice. Phenylamides are amine-conjugated phenolic acids that are induced by pathogen infections and abiotic stresses including ultra violet (UV) radiation in rice. Stress-induced phenylamides, such as N-trans-cinnamoyltryptamine, N-p-coumaroylserotonin and N-cinnamoyltyramine, have been reported to possess antimicrobial activities against rice bacterial and fungal pathogens, an indication of their direct inhibitory roles against invading pathogens. This finding suggests that phenylamides act as phytoalexins in rice and belong to phenolic phytoalexins along with sakuranetin. Phenylamides also have been implicated in cell wall reinforcement for disease resistance and allelopathy of rice. Synthesis of phenolic phytoalexins is stimulated by phytopathogen attacks and abiotic challenges including UV radiation. Accumulating evidence has demonstrated that biosynthetic pathways including the shikimate, phenylpropanoid and arylmonoamine pathways are coordinately activated for phenolic phytoalexin synthesis, and related genes are induced by biotic and abiotic stresses in rice. PMID:26690131

  15. An evolutionary classification of genomic function.

    PubMed

    Graur, Dan; Zheng, Yichen; Azevedo, Ricardo B R

    2015-03-01

    The pronouncements of the ENCODE Project Consortium regarding "junk DNA" exposed the need for an evolutionary classification of genomic elements according to their selected-effect function. In the classification scheme presented here, we divide the genome into "functional DNA," that is, DNA sequences that have a selected-effect function, and "rubbish DNA," that is, sequences that do not. Functional DNA is further subdivided into "literal DNA" and "indifferent DNA." In literal DNA, the order of nucleotides is under selection; in indifferent DNA, only the presence or absence of the sequence is under selection. Rubbish DNA is further subdivided into "junk DNA" and "garbage DNA." Junk DNA neither contributes to nor detracts from the fitness of the organism and, hence, evolves under selective neutrality. Garbage DNA, on the other hand, decreases the fitness of its carriers. Garbage DNA exists in the genome only because natural selection is neither omnipotent nor instantaneous. Each of these four functional categories can be 1) transcribed and translated, 2) transcribed but not translated, or 3) not transcribed. The affiliation of a DNA segment to a particular functional category may change during evolution: Functional DNA may become junk DNA, junk DNA may become garbage DNA, rubbish DNA may become functional DNA, and so on; however, determining the functionality or nonfunctionality of a genomic sequence must be based on its present status rather than on its potential to change (or not to change) in the future. Changes in functional affiliation are divided into pseudogenes, Lazarus DNA, zombie DNA, and Jekyll-to-Hyde DNA. PMID:25635041

  16. Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees, and whole-genome-based data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining data sets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data, and mol...

  17. Open chromatin reveals the functional maize genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Every cellular process mediated through nuclear DNA must contend with chromatin. As results from ENCODE show, open chromatin assays can efficiently integrate across diverse regulatory elements, revealing functional non-coding genome. In this study, we use a MNase hypersensitivity assay to discover o...

  18. Genome-Wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm.

    PubMed

    Qiu, Xianjin; Pang, Yunlong; Yuan, Zhihua; Xing, Danying; Xu, Jianlong; Dingkuhn, Michael; Li, Zhikang; Ye, Guoyou

    2015-01-01

    Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding. PMID:26714258

  19. Functional Annotation Analytics of Rhodopseudomonas palustris Genomes

    PubMed Central

    Simmons, Shaneka S.; Isokpehi, Raphael D.; Brown, Shyretha D.; McAllister, Donee L.; Hall, Charnia C.; McDuffy, Wanaki M.; Medley, Tamara L.; Udensi, Udensi K.; Rajnarayanan, Rajendram V.; Ayensu, Wellington K.; Cohly, Hari H.P.

    2011-01-01

    Rhodopseudomonas palustris, a nonsulphur purple photosynthetic bacteria, has been extensively investigated for its metabolic versatility including ability to produce hydrogen gas from sunlight and biomass. The availability of the finished genome sequences of six R. palustris strains (BisA53, BisB18, BisB5, CGA009, HaA2 and TIE-1) combined with online bioinformatics software for integrated analysis presents new opportunities to determine the genomic basis of metabolic versatility and ecological lifestyles of the bacteria species. The purpose of this investigation was to compare the functional annotations available for multiple R. palustris genomes to identify annotations that can be further investigated for strain-specific or uniquely shared phenotypic characteristics. A total of 2,355 protein family Pfam domain annotations were clustered based on presence or absence in the six genomes. The clustering process identified groups of functional annotations including those that could be verified as strain-specific or uniquely shared phenotypes. For example, genes encoding water/glycerol transport were present in the genome sequences of strains CGA009 and BisB5, but absent in strains BisA53, BisB18, HaA2 and TIE-1. Protein structural homology modeling predicted that the two orthologous 240 aa R. palustris aquaporins have water-specific transport function. Based on observations in other microbes, the presence of aquaporin in R. palustris strains may improve freeze tolerance in natural conditions of rapid freezing such as nitrogen fixation at low temperatures where access to liquid water is a limiting factor for nitrogenase activation. In the case of adaptive loss of aquaporin genes, strains may be better adapted to survive in conditions of high-sugar content such as fermentation of biomass for biohydrogen production. Finally, web-based resources were developed to allow for interactive, user-defined selection of the relationship between protein family annotations and the R

  20. SNP in starch biosynthesis genes associated with nutritional and functional properties of rice

    PubMed Central

    Kharabian-Masouleh, Ardashir; Waters, Daniel L. E.; Reinke, Russell F.; Ward, Rachelle; Henry, Robert J.

    2012-01-01

    Starch is a major component of human diets. The relative contribution of variation in the genes of starch biosynthesis to the nutritional and functional properties of the rice was evaluated in a rice breeding population. Sequencing 18 genes involved in starch synthesis in a population of 233 rice breeding lines discovered 66 functional SNPs in exonic regions. Five genes, AGPS2b, Isoamylase1, SPHOL, SSIIb and SSIVb showed no polymorphism. Association analysis found 31 of the SNP were associated with differences in pasting and cooking quality properties of the rice lines. Two genes appear to be the major loci controlling traits under human selection in rice, GBSSI (waxy gene) and SSIIa. GBSSI influenced amylose content and retrogradation. Other genes contributing to retrogradation were GPT1, SSI, BEI and SSIIIa. SSIIa explained much of the variation in cooking characteristics. Other genes had relatively small effects. PMID:22870386

  1. Comparisons of mutation rate variation at genome-wide microsatellites: evolutionary insights from two cultivated rice and their wild relatives

    PubMed Central

    2008-01-01

    Background Mutation rate (μ) per generation per locus is an important parameter in the models of population genetics. Studies on mutation rate and its variation are of significance to elucidate the extent and distribution of genetic variation, further infer evolutionary relationships among closely related species, and deeply understand genetic variation of genomes. However, patterns of rate variation of microsatellite loci are still poorly understood in plant species. Furthermore, how their mutation rates vary in di-, tri-, and tetra-nucleotide repeats within the species is largely uninvestigated across related plant genomes. Results Genome-wide variation of mutation rates was first investigated by means of the composite population parameter θ (θ = 4Nμ, where N is the effective population size and μ is the mutation rate per locus per generation) in four subspecies of Asian cultivated rice O. sativa and its three related species, O. rufipogon, O. glaberrima, and O. officinalis. On the basis of three data sets of microsatellite allele frequencies throughout the genome, population mutation rate (θ) was estimated for each locus. Our results reveal that the variation of population mutation rates at microsatellites within each studied species or subspecies of cultivated rice can be approximated with a gamma distribution. The mean population mutation rates of microsatellites do not significantly differ in motifs of di-, tri-, and tetra-nucleotide repeats for the studied rice species. The shape parameter was also estimated for each subspecies of rice as well as other related rice species. Of them, different subspecies of O. sativa possesses similar shape parameters (α) of the gamma distribution, while other species extensively vary in their population mutation rates. Conclusion Through the analysis of genome-wide microsatellite data, the population mutation rate can be approximately fitted with a gamma distribution in most of the studied species. In general

  2. Non-coding genome functions in diabetes.

    PubMed

    Cebola, Inês; Pasquali, Lorenzo

    2016-01-01

    Most of the genetic variation associated with diabetes, through genome-wide association studies, does not reside in protein-coding regions, making the identification of functional variants and their eventual translation to the clinic challenging. In recent years, high-throughput sequencing-based methods have enabled genome-scale high-resolution epigenomic profiling in a variety of human tissues, allowing the exploration of the human genome outside of the well-studied coding regions. These experiments unmasked tens of thousands of regulatory elements across several cell types, including diabetes-relevant tissues, providing new insights into their mechanisms of gene regulation. Regulatory landscapes are highly dynamic and cell-type specific and, being sensitive to DNA sequence variation, can vary with individual genomes. The scientific community is now in place to exploit the regulatory maps of tissues central to diabetes etiology, such as pancreatic progenitors and adult islets. This giant leap forward in the understanding of pancreatic gene regulation is revolutionizing our capacity to discriminate between functional and non-functional non-coding variants, opening opportunities to uncover regulatory links between sequence variation and diabetes susceptibility. In this review, we focus on the non-coding regulatory landscape of the pancreatic endocrine cells and provide an overview of the recent developments in this field. PMID:26438568

  3. Bioengineering nitrogen acquisition in rice: can novel initiatives in rice genomics and physiology contribute to global food security?

    PubMed

    Britto, Dev T; Kronzucker, Herbert J

    2004-06-01

    Rice is the most important crop species on earth, providing staple food for 70% of the world's human population. Over the past four decades, successes in classical breeding, fertilization, pest control, irrigation and expansion of arable land have massively increased global rice production, enabling crop scientists and farmers to stave off anticipated famines. If current projections for human population growth are correct, however, present rice yields will be insufficient within a few years. Rice yields will have to increase by an estimated 60% in the next 30 years, or global food security will be in danger. The classical methods of previous green revolutions alone will probably not be able to meet this challenge, without being coupled to recombinant DNA technology. Here, we focus on the promise of these modern technologies in the area of nitrogen acquisition in rice, recognizing that nitrogen deficiency compromises the realization of rice yield potential in the field more than any other single factor. We summarize rice-specific advances in four key areas of research: (1). nitrogen fixation, (2). primary nitrogen acquisition, (3). manipulations of internal nitrogen metabolism, and (4). interactions between nitrogen and photosynthesis. We develop a model for future plant breeding possibilities, pointing out the importance of coming to terms with the complex interactions among the physiological components under manipulation, in the context of ensuring proper targeting of intellectual and financial resources in this crucial area of research.

  4. [The ENCODE project and functional genomics studies].

    PubMed

    Ding, Nan; Qu, Hongzhu; Fang, Xiangdong

    2014-03-01

    Upon the completion of the Human Genome Project, scientists have been trying to interpret the underlying genomic code for human biology. Since 2003, National Human Genome Research Institute (NHGRI) has invested nearly $0.3 billion and gathered over 440 scientists from more than 32 institutions in the United States, China, United Kingdom, Japan, Spain and Singapore to initiate the Encyclopedia of DNA Elements (ENCODE) project, aiming to identify and analyze all regulatory elements in the human genome. Taking advantage of the development of next-generation sequencing technologies and continuous improvement of experimental methods, ENCODE had made remarkable achievements: identified methylation and histone modification of DNA sequences and their regulatory effects on gene expression through altering chromatin structures, categorized binding sites of various transcription factors and constructed their regulatory networks, further revised and updated database for pseudogenes and non-coding RNA, and identified SNPs in regulatory sequences associated with diseases. These findings help to comprehensively understand information embedded in gene and genome sequences, the function of regulatory elements as well as the molecular mechanism underlying the transcriptional regulation by noncoding regions, and provide extensive data resource for life sciences, particularly for translational medicine. We re-viewed the contributions of high-throughput sequencing platform development and bioinformatical technology improve-ment to the ENCODE project, the association between epigenetics studies and the ENCODE project, and the major achievement of the ENCODE project. We also provided our prospective on the role of the ENCODE project in promoting the development of basic and clinical medicine.

  5. Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Weedy rice is a significant problem in cultivated rice fields throughout the world, and is an emerging threat in regions where it was previously absent. Prior research has classified weedy rice as the same species as Asian cultivated rice (Oryza sativa L.). This close genetic relationship makes cont...

  6. QTL scanning for rice yield using a whole genome SNP array.

    PubMed

    Tan, Cong; Han, Zhongmin; Yu, Huihui; Zhan, Wei; Xie, Weibo; Chen, Xun; Zhao, Hu; Zhou, Fasong; Xing, Yongzhong

    2013-12-20

    High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred line (RIL) population derived from the cross between the indica variety, Zhenshan 97, and the japonica variety, Xizang 2. A total of 3324 SNP markers of high quality were identified and were grouped into 1495 recombination bins in the RIL population. A high-density linkage map, consisting of the 1495 bins, was developed, covering 1591.2 cM and with average length of 1.1 cM per bin. Segregation distortions were observed in 24 regions of the 11 chromosomes in the RILs. One half of the distorted regions contained fertility genes that had been previously reported. A total of 23 QTLs were identified for yield. Seven QTLs were firstly detected in this study. The positive alleles from about half of the identified QTLs came from Zhenshan 97 and they had lower phenotypic values than Xizang 2. This indicated that favorable alleles for breeding were dispersed in both parents and pyramiding favorable alleles could develop elite lines. The size of the mapping population for QTL analysis using high throughput SNP genotyping platform is also discussed.

  7. Responses to light intensity in a genome-scale model of rice metabolism.

    PubMed

    Poolman, Mark G; Kundu, Sudip; Shaw, Rahul; Fell, David A

    2013-06-01

    We describe the construction and analysis of a genome-scale metabolic model representing a developing leaf cell of rice (Oryza sativa) primarily derived from the annotations in the RiceCyc database. We used flux balance analysis to determine that the model represents a network capable of producing biomass precursors (amino acids, nucleotides, lipid, starch, cellulose, and lignin) in experimentally reported proportions, using carbon dioxide as the sole carbon source. We then repeated the analysis over a range of photon flux values to examine responses in the solutions. The resulting flux distributions show that (1) redox shuttles between the chloroplast, cytosol, and mitochondrion may play a significant role at low light levels, (2) photorespiration can act to dissipate excess energy at high light levels, and (3) the role of mitochondrial metabolism is likely to vary considerably according to the balance between energy demand and availability. It is notable that these organelle interactions, consistent with many experimental observations, arise solely as a result of the need for mass and energy balancing without any explicit assumptions concerning kinetic or other regulatory mechanisms.

  8. Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing

    PubMed Central

    Park, Doori; Kim, Dongin; Jang, Green; Lim, Jongsung; Shin, Yun-Ji; Kim, Jina; Seo, Mi-Seong; Park, Su-Hyun; Kim, Ju-Kon

    2015-01-01

    Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to living modified and non-modified organisms. Next generation sequencing (NGS) methodology is suggested as an effective means in genome characterization and detection of transgenic insertion locations. In the present study, we applied NGS to insert transgenic loci, specifically the epidermal growth factor (EGF) in genetically modified rice cells. A total of 29.3 Gb (~72× coverage) was sequenced with a 2 × 150 bp paired end method by Illumina HiSeq2500, which was consecutively mapped to the rice genome and T-vector sequence. The compatible pairs of reads were successfully mapped to 10 loci on the rice chromosome and vector sequences were validated to the insertion location by polymerase chain reaction (PCR) amplification. The EGF transgenic site was confirmed only on chromosome 4 by PCR. Results of this study demonstrated the success of NGS data to characterize the rice genome. Bioinformatics analyses must be developed in association with NGS data to identify highly accurate transgenic sites. PMID:26523132

  9. Impact of transgenic technologies on functional genomics.

    PubMed

    Shashikant, Cooduvalli S; Ruddle, Frank H

    2003-07-01

    Gene transfer technologies in mammals are the focus of renewed interest owing to the recent emphasis on analyzing gene function in the postgenomic era. Three important developments in this area include transgenics, gene targeting and nuclear transfer or animal cloning. These technological innovations have enhanced our ability to analyze gene function at the level of the whole organism and have provided the means to modify gene expression. This review discusses the origins and current status of transgenic technologies. Various applications and technologies including chromosome engineering, stem cells, gene traps and modification of livestock are presented. The impact of mouse technologies and genomics on functional analyses is also discussed.

  10. The tillering phenotype of the rice plastid terminal oxidase (PTOX) loss-of-function mutant is associated with strigolactone deficiency.

    PubMed

    Tamiru, Muluneh; Abe, Akira; Utsushi, Hiroe; Yoshida, Kakoto; Takagi, Hiroki; Fujisaki, Koki; Undan, Jerwin R; Rakshit, Sujay; Takaichi, Shinichi; Jikumaru, Yusuke; Yokota, Takao; Terry, Matthew J; Terauchi, Ryohei

    2014-04-01

    The significance of plastid terminal oxidase (PTOX) in phytoene desaturation and chloroplast function has been demonstrated using PTOX-deficient mutants, particularly in Arabidopsis. However, studies on its role in monocots are lacking. Here, we report cloning and characterization of the rice (Oryza sativa) PTOX1 gene. Using Ecotype Targeting Induced Local Lesions IN Genomes (EcoTILLING) and TILLING as forward genetic tools, we identified the causative mutation of an EMS mutant characterized by excessive tillering, semi-dwarfism and leaf variegation that corresponded to the PTOX1 gene. The tillering and semi-dwarf phenotypes of the ptox1 mutant are similar to phenotypes of known strigolactone (SL)-related rice mutants, and both phenotypic traits could be rescued by application of the synthetic SL GR24. The ptox1 mutant accumulated phytoene in white leaf sectors with a corresponding deficiency in β-carotene, consistent with the expected function of PTOX1 in promoting phytoene desaturase activity. There was also no accumulation of the carotenoid-derived SL ent-2'-epi-5-deoxystrigol in root exudates. Elevated concentrations of auxin were detected in the mutant, supporting previous observations that SL interaction with auxin is important in shoot branching control. Our results demonstrate that PTOX1 is required for both carotenoid and SL synthesis resulting in SL-deficient phenotypes in rice. PMID:24350905

  11. Effects of retroviruses on host genome function.

    PubMed

    Jern, Patric; Coffin, John M

    2008-01-01

    For millions of years, retroviral infections have challenged vertebrates, occasionally leading to germline integration and inheritance as ERVs, genetic parasites whose remnants today constitute some 7% to 8% of the human genome. Although they have had significant evolutionary side effects, it is useful to view ERVs as fossil representatives of retroviruses extant at the time of their insertion into the germline and not as direct players in the evolutionary process itself. Expression of particular ERVs is associated with several positive physiological functions as well as certain diseases, although their roles in human disease as etiological agents, possible contributing factors, or disease markers-well demonstrated in animal models-remain to be established. Here we discuss ERV contributions to host genome structure and function, including their ability to mediate recombination, and physiological effects on the host transcriptome resulting from their integration, expression, and other events.

  12. Functional genomics approaches in parasitic helminths.

    PubMed

    Hagen, J; Lee, E F; Fairlie, W D; Kalinna, B H

    2012-01-01

    As research on parasitic helminths is moving into the post-genomic era, an enormous effort is directed towards deciphering gene function and to achieve gene annotation. The sequences that are available in public databases undoubtedly hold information that can be utilized for new interventions and control but the exploitation of these resources has until recently remained difficult. Only now, with the emergence of methods to genetically manipulate and transform parasitic worms will it be possible to gain a comprehensive understanding of the molecular mechanisms involved in nutrition, metabolism, developmental switches/maturation and interaction with the host immune system. This review focuses on functional genomics approaches in parasitic helminths that are currently used, to highlight potential applications of these technologies in the areas of cell biology, systems biology and immunobiology of parasitic helminths.

  13. Characterization of functional trait diversity among Indian cultivated and weedy rice populations

    PubMed Central

    Rathore, M.; Singh, Raghwendra; Kumar, B.; Chauhan, B. S.

    2016-01-01

    Weedy rice, a menace in rice growing areas globally, is biosimilar having attributes similar to cultivated and wild rice, and therefore is difficult to manage. A study was initiated to characterize the functional traits of 76 weedy rice populations and commonly grown rice cultivars from different agro-climatic zones for nine morphological, five physiological, and three phenological parameters in a field experiment under an augmented block design. Comparison between weedy and cultivated rice revealed a difference in duration (days) from panicle emergence to heading as the most variable trait and awn length as the least variable one, as evidenced from their coefficients of variation. The results of principal component analysis revealed the first three principal components to represent 47.3% of the total variation, which indicates an important role of transpiration, conductance, leaf-air temperature difference, days to panicle emergence, days to heading, flag leaf length, SPAD (soil-plant analysis development), grain weight, plant height, and panicle length to the diversity in weedy rice populations. The variations existing in weedy rice population are a major reason for its wider adaptability to varied environmental conditions and also a problem while trying to manage it. PMID:27072282

  14. Characterization of functional trait diversity among Indian cultivated and weedy rice populations.

    PubMed

    Rathore, M; Singh, Raghwendra; Kumar, B; Chauhan, B S

    2016-04-13

    Weedy rice, a menace in rice growing areas globally, is biosimilar having attributes similar to cultivated and wild rice, and therefore is difficult to manage. A study was initiated to characterize the functional traits of 76 weedy rice populations and commonly grown rice cultivars from different agro-climatic zones for nine morphological, five physiological, and three phenological parameters in a field experiment under an augmented block design. Comparison between weedy and cultivated rice revealed a difference in duration (days) from panicle emergence to heading as the most variable trait and awn length as the least variable one, as evidenced from their coefficients of variation. The results of principal component analysis revealed the first three principal components to represent 47.3% of the total variation, which indicates an important role of transpiration, conductance, leaf-air temperature difference, days to panicle emergence, days to heading, flag leaf length, SPAD (soil-plant analysis development), grain weight, plant height, and panicle length to the diversity in weedy rice populations. The variations existing in weedy rice population are a major reason for its wider adaptability to varied environmental conditions and also a problem while trying to manage it.

  15. Draft Genome Sequence of Methylosinus sp. Strain 3S-1, an Isolate from Rice Root in a Low-Nitrogen Paddy Field.

    PubMed

    Bao, Zhihua; Shinoda, Ryo; Minamisawa, Kiwamu

    2016-01-01

    N2-fixing methanotrophs play an important role in the methane-nitrogen cycle in rice paddies. We report here the draft genome sequence of Methylosinus sp. strain 3S-1 isolated from rice root in a paddy field without N fertilizer input. PMID:27587832

  16. Draft Genome Sequence of Methylosinus sp. Strain 3S-1, an Isolate from Rice Root in a Low-Nitrogen Paddy Field

    PubMed Central

    Bao, Zhihua; Shinoda, Ryo

    2016-01-01

    N2-fixing methanotrophs play an important role in the methane-nitrogen cycle in rice paddies. We report here the draft genome sequence of Methylosinus sp. strain 3S-1 isolated from rice root in a paddy field without N fertilizer input. PMID:27587832

  17. Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding.

    PubMed

    Grenier, Cécile; Cao, Tuong-Vi; Ospina, Yolima; Quintero, Constanza; Châtel, Marc Henri; Tohme, Joe; Courtois, Brigitte; Ahmadi, Nourollah

    2015-01-01

    Genomic selection (GS) is a promising strategy for enhancing genetic gain. We investigated the accuracy of genomic estimated breeding values (GEBV) in four inter-related synthetic populations that underwent several cycles of recurrent selection in an upland rice-breeding program. A total of 343 S2:4 lines extracted from those populations were phenotyped for flowering time, plant height, grain yield and panicle weight, and genotyped with an average density of one marker per 44.8 kb. The relative effect of the linkage disequilibrium (LD) and minor allele frequency (MAF) thresholds for selecting markers, the relative size of the training population (TP) and of the validation population (VP), the selected trait and the genomic prediction models (frequentist and Bayesian) on the accuracy of GEBVs was investigated in 540 cross validation experiments with 100 replicates. The effect of kinship between the training and validation populations was tested in an additional set of 840 cross validation experiments with a single genomic prediction model. LD was high (average r2 = 0.59 at 25 kb) and decreased slowly, distribution of allele frequencies at individual loci was markedly skewed toward unbalanced frequencies (MAF average value 15.2% and median 9.6%), and differentiation between the four synthetic populations was low (FST ≤0.06). The accuracy of GEBV across all cross validation experiments ranged from 0.12 to 0.54 with an average of 0.30. Significant differences in accuracy were observed among the different levels of each factor investigated. Phenotypic traits had the biggest effect, and the size of the incidence matrix had the smallest. Significant first degree interaction was observed for GEBV accuracy between traits and all the other factors studied, and between prediction models and LD, MAF and composition of the TP. The potential of GS to accelerate genetic gain and breeding options to increase the accuracy of predictions are discussed. PMID:26313446

  18. Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding.

    PubMed

    Grenier, Cécile; Cao, Tuong-Vi; Ospina, Yolima; Quintero, Constanza; Châtel, Marc Henri; Tohme, Joe; Courtois, Brigitte; Ahmadi, Nourollah

    2015-01-01

    Genomic selection (GS) is a promising strategy for enhancing genetic gain. We investigated the accuracy of genomic estimated breeding values (GEBV) in four inter-related synthetic populations that underwent several cycles of recurrent selection in an upland rice-breeding program. A total of 343 S2:4 lines extracted from those populations were phenotyped for flowering time, plant height, grain yield and panicle weight, and genotyped with an average density of one marker per 44.8 kb. The relative effect of the linkage disequilibrium (LD) and minor allele frequency (MAF) thresholds for selecting markers, the relative size of the training population (TP) and of the validation population (VP), the selected trait and the genomic prediction models (frequentist and Bayesian) on the accuracy of GEBVs was investigated in 540 cross validation experiments with 100 replicates. The effect of kinship between the training and validation populations was tested in an additional set of 840 cross validation experiments with a single genomic prediction model. LD was high (average r2 = 0.59 at 25 kb) and decreased slowly, distribution of allele frequencies at individual loci was markedly skewed toward unbalanced frequencies (MAF average value 15.2% and median 9.6%), and differentiation between the four synthetic populations was low (FST ≤0.06). The accuracy of GEBV across all cross validation experiments ranged from 0.12 to 0.54 with an average of 0.30. Significant differences in accuracy were observed among the different levels of each factor investigated. Phenotypic traits had the biggest effect, and the size of the incidence matrix had the smallest. Significant first degree interaction was observed for GEBV accuracy between traits and all the other factors studied, and between prediction models and LD, MAF and composition of the TP. The potential of GS to accelerate genetic gain and breeding options to increase the accuracy of predictions are discussed.

  19. Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding

    PubMed Central

    Ospina, Yolima; Quintero, Constanza; Châtel, Marc Henri; Tohme, Joe; Courtois, Brigitte

    2015-01-01

    Genomic selection (GS) is a promising strategy for enhancing genetic gain. We investigated the accuracy of genomic estimated breeding values (GEBV) in four inter-related synthetic populations that underwent several cycles of recurrent selection in an upland rice-breeding program. A total of 343 S2:4 lines extracted from those populations were phenotyped for flowering time, plant height, grain yield and panicle weight, and genotyped with an average density of one marker per 44.8 kb. The relative effect of the linkage disequilibrium (LD) and minor allele frequency (MAF) thresholds for selecting markers, the relative size of the training population (TP) and of the validation population (VP), the selected trait and the genomic prediction models (frequentist and Bayesian) on the accuracy of GEBVs was investigated in 540 cross validation experiments with 100 replicates. The effect of kinship between the training and validation populations was tested in an additional set of 840 cross validation experiments with a single genomic prediction model. LD was high (average r2 = 0.59 at 25 kb) and decreased slowly, distribution of allele frequencies at individual loci was markedly skewed toward unbalanced frequencies (MAF average value 15.2% and median 9.6%), and differentiation between the four synthetic populations was low (FST ≤0.06). The accuracy of GEBV across all cross validation experiments ranged from 0.12 to 0.54 with an average of 0.30. Significant differences in accuracy were observed among the different levels of each factor investigated. Phenotypic traits had the biggest effect, and the size of the incidence matrix had the smallest. Significant first degree interaction was observed for GEBV accuracy between traits and all the other factors studied, and between prediction models and LD, MAF and composition of the TP. The potential of GS to accelerate genetic gain and breeding options to increase the accuracy of predictions are discussed. PMID:26313446

  20. Orchidstra: An Integrated Orchid Functional Genomics Database

    PubMed Central

    Su, Chun-lin; Chao, Ya-Ting; Yen, Shao-Hua; Chen, Chun-Yi; Chen, Wan-Chieh; Chang, Yao-Chien Alex; Shih, Ming-Che

    2013-01-01

    A specialized orchid database, named Orchidstra (URL: http://orchidstra.abrc.sinica.edu.tw), has been constructed to collect, annotate and share genomic information for orchid functional genomics studies. The Orchidaceae is a large family of Angiosperms that exhibits extraordinary biodiversity in terms of both the number of species and their distribution worldwide. Orchids exhibit many unique biological features; however, investigation of these traits is currently constrained due to the limited availability of genomic information. Transcriptome information for five orchid species and one commercial hybrid has been included in the Orchidstra database. Altogether, these comprise >380,000 non-redundant orchid transcript sequences, of which >110,000 are protein-coding genes. Sequences from the transcriptome shotgun assembly (TSA) were obtained either from output reads from next-generation sequencing technologies assembled into contigs, or from conventional cDNA library approaches. An annotation pipeline using Gene Ontology, KEGG and Pfam was built to assign gene descriptions and functional annotation to protein-coding genes. Deep sequencing of small RNA was also performed for Phalaenopsis aphrodite to search for microRNAs (miRNAs), extending the information archived for this species to miRNA annotation, precursors and putative target genes. The P. aphrodite transcriptome information was further used to design probes for an oligonucleotide microarray, and expression profiling analysis was carried out. The intensities of hybridized probes derived from microarray assays of various tissues were incorporated into the database as part of the functional evidence. In the future, the content of the Orchidstra database will be expanded with transcriptome data and genomic information from more orchid species. PMID:23324169

  1. Gene Networks and Functional Features of Gravitropic response in Rice Shoot Bases

    NASA Astrophysics Data System (ADS)

    Hu, Liwei; Zang, Aiping; Ai, Qianru; Chen, Haiying; Li, Lin; Li, Rui; Su, Feng; Chen, Xijiang; Rong, Hui; Dou, Xianying; Reinhold-Hurek, Barbara; Li, Qi; Cai, Weiming

    To delineate key genes and the corresponding physiological functions as well as the coordina-tion of genes involved in the gravitropism of rice shoot bases, we used whole-genome microarray analysis of upper and lower parts of rice shoot bases at 0.5 h and 6 h after gravistimulation. And bio-information analysis was applied including GO-analysis, expression tendency and net-work analysis. In the lower shoot bases, auxin-mediated signaling pathway and glutathione transferase activity with the biggest enrichment were activated at 0.5 h, while cytokinin stimu-lus and photosynthesis were activated at 6 h. Meanwhile, several processes were suppressed in the lower shoot bases, including: xyloglucan:xyloglucosyl transferase activity, glucan metabolic processes, and ATPase activity at 0.5 h; and tRNA isopentenyltransferase activity, and chiti-nase activity, etc. at 6 h. Gene expression profile responding to gravistimulation suggested that the asymmetrically activation of several phytohormone signaling pathways including auxin, gib-berellin and cytokinin brassinolide ethylene and cytokinin-related genes were involved in the differentially growth between the upper and lower parts of rice shoot bases, and so do cell wall-related genes. Topological analysis of the coexpression networks revealed the core statue of AY177699.1(apetala3-like protein) and AK105103.1 at 0.5 h; AK062612.1 (ethylene response factor) and AK099932.1 (lectin-like receptor kinase 72) at 6 h. All the core factors have the function "response to endogenous stimulus". Additionally, AK108057.1(similar to germin-like protein precursor) was discovered as the most important core gene in the upper shoot bases in 6h after gravistimualtion while AK067424.1(cellulose synthase-like protein), AK120101.1 (Zinc finger, B-box domain containing protein) and CR278698 (ATPase associated with various cel-lular activities cellulose synthase-like protein) contribute equally to gravitropic response in the lower shoot bases.

  2. Immediate Genetic and Epigenetic Changes in F1 Hybrids Parented by Species with Divergent Genomes in the Rice Genus (Oryza)

    PubMed Central

    Sun, Shuai; Wang, Jie; Jiang, Tingting; Cao, Shuai; Josiah, Samuel Manthi; Pang, Jinsong; Lin, Xiuyun; Liu, Bao

    2015-01-01

    Background Inter-specific hybridization occurs frequently in higher plants, and represents a driving force of evolution and speciation. Inter-specific hybridization often induces genetic and epigenetic instabilities in the resultant homoploid hybrids or allopolyploids, a phenomenon known as genome shock. Although genetic and epigenetic consequences of hybridizations between rice subspecies (e.g., japonica and indica) and closely related species sharing the same AA genome have been extensively investigated, those of inter-specific hybridizations between more remote species with different genomes in the rice genus, Oryza, remain largely unknown. Methodology/Principal Findings We investigated the immediate chromosomal and molecular genetic/epigenetic instability of three triploid F1 hybrids produced by inter-specific crossing between species with divergent genomes of Oryza by genomic in situ hybridization (GISH) and molecular marker analysis. Transcriptional and transpositional activity of several transposable elements (TEs) and methylation stability of their flanking regions were also assessed. We made the following principle findings: (i) all three triploid hybrids are stable in both chromosome number and gross structure; (ii) stochastic changes in both DNA sequence and methylation occurred in individual plants of all three triploid hybrids, but in general methylation changes occurred at lower frequencies than genetic changes; (iii) alteration in DNA methylation occurred to a greater extent in genomic loci flanking potentially active TEs than in randomly sampled loci; (iv) transcriptional activation of several TEs commonly occurred in all three hybrids but transpositional events were detected in a genetic context-dependent manner. Conclusions/Significance Artificially constructed inter-specific hybrids of remotely related species with divergent genomes in genus Oryza are chromosomally stable but show immediate and highly stochastic genetic and epigenetic

  3. Heavy metals induce oxidative stress and genome-wide modulation in transcriptome of rice root.

    PubMed

    Dubey, Sonali; Shri, Manju; Misra, Prashant; Lakhwani, Deepika; Bag, Sumit Kumar; Asif, Mehar H; Trivedi, Prabodh Kumar; Tripathi, Rudro Deo; Chakrabarty, Debasis

    2014-06-01

    Industrial growth, ecological disturbances and agricultural practices have contaminated the soil and water with many harmful compounds, including heavy metals. These heavy metals affect growth and development of plants as well as cause severe human health hazards through food chain contamination. In past, studies have been made to identify biochemical and molecular networks associated with heavy metal toxicity and uptake in plants. Studies suggested that most of the physiological and molecular processes affected by different heavy metals are similar to those affected by other abiotic stresses. To identify common and unique responses by different metals, we have studied biochemical and genome-wide modulation in transcriptome of rice (IR-64 cultivar) root after exposure to cadmium (Cd), arsenate [As(V)], lead (Pb) and chromium [Cr(VI)] in hydroponic condition. We observed that root tissue shows variable responses for antioxidant enzyme system for different heavy metals. Genome-wide expression analysis suggests variable number of genes differentially expressed in root in response to As(V), Cd, Pb and Cr(VI) stresses. In addition to unique genes, each heavy metal modulated expression of a large number of common genes. Study also identified cis-acting regions of the promoters which can be determinants for the modulated expression of the genes in response to different heavy metals. Our study advances understanding related to various processes and networks which might be responsible for heavy metal stresses, accumulation and detoxification. PMID:24553786

  4. Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions

    PubMed Central

    Cozzi, Paolo; Casella, Laura; Riccardi, Paolo; Vattari, Alessandra; Orasen, Gabriele; Perrini, Rosaria; Tacconi, Gianni; Tondelli, Alessandro; Biselli, Chiara; Cattivelli, Luigi; Spindel, Jennifer; McCouch, Susan; Abbruscato, Pamela; Valé, Giampiero; Piffanelli, Pietro; Greco, Raffaella

    2016-01-01

    Background In this study we carried out a genome-wide association analysis for plant and grain morphology and root architecture in a unique panel of temperate rice accessions adapted to European pedo-climatic conditions. This is the first study to assess the association of selected phenotypic traits to specific genomic regions in the narrow genetic pool of temperate japonica. A set of 391 rice accessions were GBS-genotyped yielding—after data editing—57000 polymorphic and informative SNPS, among which 54% were in genic regions. Results In total, 42 significant genotype-phenotype associations were detected: 21 for plant morphology traits, 11 for grain quality traits, 10 for root architecture traits. The FDR of detected associations ranged from 3 · 10−7 to 0.92 (median: 0.25). In most cases, the significant detected associations co-localised with QTLs and candidate genes controlling the phenotypic variation of single or multiple traits. The most significant associations were those for flag leaf width on chromosome 4 (FDR = 3 · 10−7) and for plant height on chromosome 6 (FDR = 0.011). Conclusions We demonstrate the effectiveness and resolution of the developed platform for high-throughput phenotyping, genotyping and GWAS in detecting major QTLs for relevant traits in rice. We identified strong associations that may be used for selection in temperate irrigated rice breeding: e.g. associations for flag leaf width, plant height, root volume and length, grain length, grain width and their ratio. Our findings pave the way to successfully exploit the narrow genetic pool of European temperate rice and to pinpoint the most relevant genetic components contributing to the adaptability and high yield of this germplasm. The generated data could be of direct use in genomic-assisted breeding strategies. PMID:27228161

  5. Functional genomics for food fermentation processes.

    PubMed

    Smid, E J; Hugenholtz, J

    2010-01-01

    This review describes recent scientific and technological drivers of food fermentation research. In addition, a number of practical implications of the results of this development will be highlighted. The first part of the manuscript elaborates on the message that genome sequence information gives us an unprecedented view on the biodiversity of microbes in food fermentation. This information can be made applicable for tailoring relevant characteristics of food products through fermentation. The second part deals with the integration of genome sequence data into metabolic models and the use of these models for a number of topics that are relevant for food fermentation processes. The final part will be about metagenomics approaches to reveal the complexity and understand the functionality of undefined complex microbial consortia used in a diverse range of food fermentation processes.

  6. DNA repair and recombination in higher plants: insights from comparative genomics of arabidopsis and rice

    PubMed Central

    2010-01-01

    Background The DNA repair and recombination (DRR) proteins protect organisms against genetic damage, caused by environmental agents and other genotoxic agents, by removal of DNA lesions or helping to abide them. Results We identified genes potentially involved in DRR mechanisms in Arabidopsis and rice using similarity searches and conserved domain analysis against proteins known to be involved in DRR in human, yeast and E. coli. As expected, many of DRR genes are very similar to those found in other eukaryotes. Beside these eukaryotes specific genes, several prokaryotes specific genes were also found to be well conserved in plants. In Arabidopsis, several functionally important DRR gene duplications are present, which do not occur in rice. Among DRR proteins, we found that proteins belonging to the nucleotide excision repair pathway were relatively more conserved than proteins needed for the other DRR pathways. Sub-cellular localization studies of DRR gene suggests that these proteins are mostly reside in nucleus while gene drain in between nucleus and cell organelles were also found in some cases. Conclusions The similarities and dissimilarities in between plants and other organisms' DRR pathways are discussed. The observed differences broaden our knowledge about DRR in the plants world, and raises the potential question of whether differentiated functions have evolved in some cases. These results, altogether, provide a useful framework for further experimental studies in these organisms. PMID:20646326

  7. Genome-Wide Association Mapping of Root Traits in a Japonica Rice Panel

    PubMed Central

    Courtois, Brigitte; Audebert, Alain; Dardou, Audrey; Roques, Sandrine; Ghneim- Herrera, Thaura; Droc, Gaëtan; Frouin, Julien; Rouan, Lauriane; Gozé, Eric; Kilian, Andrzej; Ahmadi, Nourollah; Dingkuhn, Michael

    2013-01-01

    Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r2>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates. PMID:24223758

  8. Tetrahymena functional genomics database (TetraFGD): an integrated resource for Tetrahymena functional genomics.

    PubMed

    Xiong, Jie; Lu, Yuming; Feng, Jinmei; Yuan, Dongxia; Tian, Miao; Chang, Yue; Fu, Chengjie; Wang, Guangying; Zeng, Honghui; Miao, Wei

    2013-01-01

    The ciliated protozoan Tetrahymena thermophila is a useful unicellular model organism for studies of eukaryotic cellular and molecular biology. Researches on T. thermophila have contributed to a series of remarkable basic biological principles. After the macronuclear genome was sequenced, substantial progress has been made in functional genomics research on T. thermophila, including genome-wide microarray analysis of the T. thermophila life cycle, a T. thermophila gene network analysis based on the microarray data and transcriptome analysis by deep RNA sequencing. To meet the growing demands for the Tetrahymena research community, we integrated these data to provide a public access database: Tetrahymena functional genomics database (TetraFGD). TetraFGD contains three major resources, including the RNA-Seq transcriptome, microarray and gene networks. The RNA-Seq data define gene structures and transcriptome, with special emphasis on exon-intron boundaries; the microarray data describe gene expression of 20 time points during three major stages of the T. thermophila life cycle; the gene network data identify potential gene-gene interactions of 15 049 genes. The TetraFGD provides user-friendly search functions that assist researchers in accessing gene models, transcripts, gene expression data and gene-gene relationships. In conclusion, the TetraFGD is an important functional genomic resource for researchers who focus on the Tetrahymena or other ciliates. Database URL: http://tfgd.ihb.ac.cn/

  9. Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice

    PubMed Central

    2014-01-01

    Background Endogenous small (sm) RNAs (primarily si- and miRNAs) are important trans/cis-acting regulators involved in diverse cellular functions. In plants, the RNA-dependent RNA polymerases (RDRs) are essential for smRNA biogenesis. It has been established that RDR2 is involved in the 24 nt siRNA-dependent RNA-directed DNA methylation (RdDM) pathway. Recent studies have suggested that RDR1 is involved in a second RdDM pathway that relies mostly on 21 nt smRNAs and functions to silence a subset of genomic loci that are usually refractory to the normal RdDM pathway in Arabidopsis. Whether and to what extent the homologs of RDR1 may have similar functions in other plants remained unknown. Results We characterized a loss-of-function mutant (Osrdr1) of the OsRDR1 gene in rice (Oryza sativa L.) derived from a retrotransposon Tos17 insertion. Microarray analysis identified 1,175 differentially expressed genes (5.2% of all expressed genes in the shoot-tip tissue of rice) between Osrdr1 and WT, of which 896 and 279 genes were up- and down-regulated, respectively, in Osrdr1. smRNA sequencing revealed regional alterations in smRNA clusters across the rice genome. Some of the regions with altered smRNA clusters were associated with changes in DNA methylation. In addition, altered expression of several miRNAs was detected in Osrdr1, and at least some of which were associated with altered expression of predicted miRNA target genes. Despite these changes, no phenotypic difference was identified in Osrdr1 relative to WT under normal condition; however, ephemeral phenotypic fluctuations occurred under some abiotic stress conditions. Conclusions Our results showed that OsRDR1 plays a role in regulating a substantial number of endogenous genes with diverse functions in rice through smRNA-mediated pathways involving DNA methylation, and which participates in abiotic stress response. PMID:24980094

  10. OsKAT2 is the prevailing functional inward rectifier potassium channels in rice guard cell.

    PubMed

    Hwang, Hyunsik; Yoon, Jin-Young; Cho, Hana; Kim, Beom-Gi

    2013-01-01

    AtKAT1 plays roles as a major channel to uptake K(+) in guard cell when stomata open in dicot model plant Arabidopsis. In a recent publication, we isolated 3 KAT-like potassium channels in rice. We expressed them in CHO cell to identify electrophysiological characteristics of the channels. OsKAT2 showed much bigger inwardly rectifying potassium channel activities among them. The histochemical X-glu staining of transgenic rice leaf blades expressing β-glucuronidase fused with OsKAT2 promoter showed that the OsKAT2 is dominantly expressed in rice guard cell. These findings indicate that OsKAT2 may be a functional ortholog of AtKAT1 in rice. Thus this gene will be the prime target for engineering the guard cell movement to improve drought tolerance in monocot plants, including most major crops.

  11. Retroelements and their impact on genome evolution and functioning.

    PubMed

    Gogvadze, Elena; Buzdin, Anton

    2009-12-01

    Retroelements comprise a considerable fraction of eukaryotic genomes. Since their initial discovery by Barbara McClintock in maize DNA, retroelements have been found in genomes of almost all organisms. First considered as a "junk DNA" or genomic parasites, they were shown to influence genome functioning and to promote genetic innovations. For this reason, they were suggested as an important creative force in the genome evolution and adaptation of an organism to altered environmental conditions. In this review, we summarize the up-to-date knowledge of different ways of retroelement involvement in structural and functional evolution of genes and genomes, as well as the mechanisms generated by cells to control their retrotransposition.

  12. Comparative Genomics in Perennial Ryegrass (Lolium perenne L.): Identification and Characterisation of an Orthologue for the Rice Plant Architecture-Controlling Gene OsABCG5

    PubMed Central

    Shinozuka, Hiroshi; Cogan, Noel O. I.; Spangenberg, German C.; Forster, John W.

    2011-01-01

    Perennial ryegrass is an important pasture grass in temperate regions. As a forage biomass-generating species, plant architecture-related characters provide key objectives for breeding improvement. In silico comparative genomics analysis predicted colocation between a previously identified QTL for plant type (erect versus prostrate growth) and the ortholocus of the rice OsABCG5 gene (LpABCG5), as well as related QTLs in other Poaceae species. Sequencing of an LpABCG5-containing BAC clone identified presence of a paralogue (LpABCG6) in the vicinity of the LpABCG5 locus, in addition to three other gene-like sequences. Comparative genomics involving five other 5 grass species (rice, Brachypodium, sorghum, maize, and foxtail millet) revealed conserved microsynteny in the ABCG5 ortholocus-flanking region. Gene expression profiling and phylogenetic analysis suggested that the two paralogues are functionally distinct. Fourteen additional ABCG5 gene family members, which may interact with the LpABCG5 gene, were identified through sequencing of transcriptomes from perennial ryegrass leaf, anther, and pistils. A larger-scale phylogenetic analysis of the ABCG gene family suggested conservation between major branches of the Poaceae family. This study identified the LpABCG5 gene as a candidate for the plant type determinant, suggesting that manipulation of gene expression may provide valuable phenotypes for perennial ryegrass breeding. PMID:21941532

  13. Description of durum wheat linkage map and comparative sequence analysis of wheat mapped DArT markers with rice and Brachypodium genomes

    PubMed Central

    2013-01-01

    Background The importance of wheat to the world economy, together with progresses in high-throughput next-generation DNA sequencing, have accelerated initiatives of genetic research for wheat improvement. The availability of high density linkage maps is crucial to identify genotype-phenotype associations, but also for anchoring BAC contigs to genetic maps, a strategy followed for sequencing the wheat genome. Results Here we report a genetic linkage map in a durum wheat segregating population and the study of mapped DArT markers. The linkage map consists of 126 gSSR, 31 EST-SSR and 351 DArT markers distributed in 24 linkage groups for a total length of 1,272 cM. Through bioinformatic approaches we have analysed 327 DArT clones to reveal their redundancy, syntenic and functional aspects. The DNA sequences of 174 DArT markers were assembled into a non-redundant set of 60 marker clusters. This explained the generation of clusters in very small chromosome regions across genomes. Of these DArT markers, 61 showed highly significant (Expectation < E-10) BLAST similarity to gene sequences in public databases of model species such as Brachypodium and rice. Based on sequence alignments, the analysis revealed a mosaic gene conservation, with 54 and 72 genes present in rice and Brachypodium species, respectively. Conclusions In the present manuscript we provide a detailed DArT markers characterization and the basis for future efforts in durum wheat map comparing. PMID:24304553

  14. SorghumFDB: sorghum functional genomics database with multidimensional network analysis

    PubMed Central

    Tian, Tian; You, Qi; Zhang, Liwei; Yi, Xin; Yan, Hengyu; Xu, Wenying; Su, Zhen

    2016-01-01

    Sorghum (Sorghum bicolor [L.] Moench) has excellent agronomic traits and biological properties, such as heat and drought-tolerance. It is a C4 grass and potential bioenergy-producing plant, which makes it an important crop worldwide. With the sorghum genome sequence released, it is essential to establish a sorghum functional genomics data mining platform. We collected genomic data and some functional annotations to construct a sorghum functional genomics database (SorghumFDB). SorghumFDB integrated knowledge of sorghum gene family classifications (transcription regulators/factors, carbohydrate-active enzymes, protein kinases, ubiquitins, cytochrome P450, monolignol biosynthesis related enzymes, R-genes and organelle-genes), detailed gene annotations, miRNA and target gene information, orthologous pairs in the model plants Arabidopsis, rice and maize, gene loci conversions and a genome browser. We further constructed a dynamic network of multidimensional biological relationships, comprised of the co-expression data, protein–protein interactions and miRNA-target pairs. We took effective measures to combine the network, gene set enrichment and motif analyses to determine the key regulators that participate in related metabolic pathways, such as the lignin pathway, which is a major biological process in bioenergy-producing plants. Database URL: http://structuralbiology.cau.edu.cn/sorghum/index.html. PMID:27352859

  15. SorghumFDB: sorghum functional genomics database with multidimensional network analysis.

    PubMed

    Tian, Tian; You, Qi; Zhang, Liwei; Yi, Xin; Yan, Hengyu; Xu, Wenying; Su, Zhen

    2016-01-01

    Sorghum (Sorghum bicolor [L.] Moench) has excellent agronomic traits and biological properties, such as heat and drought-tolerance. It is a C4 grass and potential bioenergy-producing plant, which makes it an important crop worldwide. With the sorghum genome sequence released, it is essential to establish a sorghum functional genomics data mining platform. We collected genomic data and some functional annotations to construct a sorghum functional genomics database (SorghumFDB). SorghumFDB integrated knowledge of sorghum gene family classifications (transcription regulators/factors, carbohydrate-active enzymes, protein kinases, ubiquitins, cytochrome P450, monolignol biosynthesis related enzymes, R-genes and organelle-genes), detailed gene annotations, miRNA and target gene information, orthologous pairs in the model plants Arabidopsis, rice and maize, gene loci conversions and a genome browser. We further constructed a dynamic network of multidimensional biological relationships, comprised of the co-expression data, protein-protein interactions and miRNA-target pairs. We took effective measures to combine the network, gene set enrichment and motif analyses to determine the key regulators that participate in related metabolic pathways, such as the lignin pathway, which is a major biological process in bioenergy-producing plants.Database URL: http://structuralbiology.cau.edu.cn/sorghum/index.html. PMID:27352859

  16. Selfish drive can trump function when animal mitochondrial genomes compete.

    PubMed

    Ma, Hansong; O'Farrell, Patrick H

    2016-07-01

    Mitochondrial genomes compete for transmission from mother to progeny. We explored this competition by introducing a second genome into Drosophila melanogaster to follow transmission. Competitions between closely related genomes favored those functional in electron transport, resulting in a host-beneficial purifying selection. In contrast, matchups between distantly related genomes often favored those with negligible, negative or lethal consequences, indicating selfish selection. Exhibiting powerful selfish selection, a genome carrying a detrimental mutation displaced a complementing genome, leading to population death after several generations. In a different pairing, opposing selfish and purifying selection counterbalanced to give stable transmission of two genomes. Sequencing of recombinant mitochondrial genomes showed that the noncoding region, containing origins of replication, governs selfish transmission. Uniparental inheritance prevents encounters between distantly related genomes. Nonetheless, in each maternal lineage, constant competition among sibling genomes selects for super-replicators. We suggest that this relentless competition drives positive selection, promoting change in the sequences influencing transmission. PMID:27270106

  17. Selfish drive can trump function when animal mitochondrial genomes compete.

    PubMed

    Ma, Hansong; O'Farrell, Patrick H

    2016-07-01

    Mitochondrial genomes compete for transmission from mother to progeny. We explored this competition by introducing a second genome into Drosophila melanogaster to follow transmission. Competitions between closely related genomes favored those functional in electron transport, resulting in a host-beneficial purifying selection. In contrast, matchups between distantly related genomes often favored those with negligible, negative or lethal consequences, indicating selfish selection. Exhibiting powerful selfish selection, a genome carrying a detrimental mutation displaced a complementing genome, leading to population death after several generations. In a different pairing, opposing selfish and purifying selection counterbalanced to give stable transmission of two genomes. Sequencing of recombinant mitochondrial genomes showed that the noncoding region, containing origins of replication, governs selfish transmission. Uniparental inheritance prevents encounters between distantly related genomes. Nonetheless, in each maternal lineage, constant competition among sibling genomes selects for super-replicators. We suggest that this relentless competition drives positive selection, promoting change in the sequences influencing transmission.

  18. Genome-wide Association Mapping of Polyphenol Contents and Antioxidant Capacity in Whole-Grain Rice.

    PubMed

    Xu, Feifei; Bao, Jinsong; Kim, Tae-Sung; Park, Yong-Jin

    2016-06-01

    Whole grains contain various bioactive phytochemicals including phenolic acids, and consumption of whole grains may provide desirable health benefits and reduce the risks of chronic diseases due to their antioxidant activities. In this study, we qualified and quantified 9 bound phenolic compounds in 32 red and 88 white pericarp accessions of rice. A genome-wide association study (GWAS) was conducted for free (FP) and bound (BP) phenolic compounds and their antioxidant capacities with high-quality single-nucleotide polymorphisms (SNPs) in two colored grain panels and the whole panel. Rc was detected for all FP and antioxidant capacities in the whole panel. Three loci (chr.1:30970095, chr.6:24392269, and chr.9:6670223) for more than five phenolic-related traits, two loci (chr.4:34120529 and chr.11:28947480) for more than two FP-related traits, and one locus (chr.11:23220681) for ferulic acid detected in two panels were potentially new genes that are valuable for further gene cloning. Overall, this study increases our understanding on the genetics of phenolic acid biosynthesis in the phenylpropanoid pathway. PMID:27163766

  19. Genome-wide association mapping focusing on a rice population derived from rice breeding programs in a region.

    PubMed

    Fujino, Kenji; Obara, Mari; Shimizu, Toshiaki; Koyanagi, Kanako O; Ikegaya, Tomohito

    2015-12-01

    Plant breeding programs in local regions may generate genetic variations that are desirable to local populations and shape adaptability during the establishment of local populations. To elucidate genetic bases for this process, we proposed a new approach for identifying the genetic bases for the traits improved during rice breeding programs; association mapping focusing on a local population. In the present study, we performed association mapping focusing on a local rice population, consisting of 63 varieties, in Hokkaido, the northernmost region of Japan and one of the northern limits of rice cultivation worldwide. Six and seventeen QTLs were identified for heading date and low temperature germinability, respectively. Of these, 13 were novel QTLs in this population and 10 corresponded to the QTLs previously reported based on QTL mapping. The identification of QTLs for traits in local populations including elite varieties may lead to a better understanding of the genetic bases of elite traits. This is of direct relevance for plant breeding programs in local regions.

  20. Flux balance analysis of genome-scale metabolic model of rice (Oryza sativa): aiming to increase biomass.

    PubMed

    Shaw, Rahul; Kundu, Sudip

    2015-10-01

    Due to socio-economic reasons, it is essential to design efficient stress-tolerant, more nutritious, high yielding rice varieties. A systematic understanding of the rice cellular metabolism is essential for this purpose. Here, we analyse a genome-scale metabolic model of rice leaf using Flux Balance Analysis to investigate whether it has potential metabolic flexibility to increase the biosynthesis of any of the biomass components. We initially simulate the metabolic responses under an objective to maximize the biomass components. Using the estimated maximum value of biomass synthesis as a constraint, we further simulate the metabolic responses optimizing the cellular economy. Depending on the physiological conditions of a cell, the transport capacities of intracellular transporters (ICTs) can vary. To mimic this physiological state, we randomly vary the ICTs' transport capacities and investigate their effects. The results show that the rice leaf has the potential to increase glycine and starch in a wide range depending on the ICTs' transport capacities. The predicted biosynthesis pathways vary slightly at the two different optimization conditions. With the constraint of biomass composition, the cell also has the metabolic plasticity to fix a wide range of carbon-nitrogen ratio.

  1. Functional analysis of OsPGIP1 in rice sheath blight resistance.

    PubMed

    Wang, Rui; Lu, Liaoxun; Pan, Xuebiao; Hu, Zongliang; Ling, Fei; Yan, Yan; Liu, Yemao; Lin, Yongjun

    2015-01-01

    As one of the most devastating diseases of rice, sheath blight causes severe rice yield loss. However, little progress has been made in rice breeding for sheath blight resistance. It has been reported that polygalacturonase inhibiting proteins can inhibit the degradation of the plant cell wall by polygalacturonases from pathogens. Here, we prokaryotically expressed and purified OsPGIP1 protein, which was verified by Western blot analysis. Activity assay confirmed the inhibitory activity of OsPGIP1 against the PGase from Rhizoctonia solani. In addition, the location of OsPGIP1 was determined by subcellular localization. Subsequently, we overexpressed OsPGIP1 in Zhonghua 11 (Oryza sativa L. ssp. japonica), and applied PCR and Southern blot analysis to identify the positive T0 transgenic plants with single-copy insertions. Germination assay of the seeds from T1 transgenic plants was carried out to select homozygous OsPGIP1 transgenic lines, and the expression levels of OsPGIP1 in these lines were analyzed by quantitative real-time PCR. Field testing of R. solani inoculation showed that the sheath blight resistance of the transgenic rice was significantly improved. Furthermore, the levels of sheath blight resistance were in accordance with the expression levels of OsPGIP1 in the transgenic lines. Our results reveal the functions of OsPGIP1 and its resistance mechanism to rice sheath blight, which will facilitate rice breeding for sheath blight resistance.

  2. The functional effectiveness of reprocessed rice bran as an ingredient in bakery products.

    PubMed

    Lima, Isabel; Guraya, Harmeet; Champagne, Elaine

    2002-04-01

    Rice bran, as a coproduct of the rice milling industry, is yet to be efficiently utilized for human consumption. Despite its excellent nutrition, its hypoallergenicity and recently claimed nutraceutical properties, it is mainly utilized for animal feed or simply discharged. It is of interest to incorporate this healthy ingredient back into our diet. In these studies, rice bran was processed by drum-drying and pin-milling. This processing step increased hydration capacity and removed grittiness by decreasing mean particle size from 444 to 72 microns and producing a desirable monomodal size distribution. There are no reported studies addressing differences in rice bran composition in food applications and specifically their effect on bread quality. Thus, we were interested in examining the functional properties of bread made with processed full-fat (FFRB) and defatted (DFRB) bran from three cultivars (long, medium and short grain rice) and to compare them to a control. For 10% and 20% replacements of wheat flour, respectively, loaf volume increased 2% for FFRB and decreased 6% for DFRB and decreased by 6% for FFRB and 17% for DFRB. Loaf volume was highest with medium rice bran and this was attributed to its lowest fiber content and highest starch content among three varieties. Texture profile analysis showed no significant differences as far as cohesiveness and springiness, but bread hardness, gumminess and chewiness increased with increased levels of rice bran and was higher for DFRB bread than for FFRB. Measurements of texture determined that there was no detrimental effect in adding 10% FFRB to the bread and a very slight hardening of the loaves with the 20% FFRB, when compared to the control. It was found that FFRB gave better textural characteristics than DFRB overall and differences amongst different rice bran varieties were not significant.

  3. The function of genomes in bioenergetic organelles.

    PubMed Central

    Allen, John F

    2003-01-01

    Mitochondria and chloroplasts are energy-transducing organelles of the cytoplasm of eukaryotic cells. They originated as bacterial symbionts whose host cells acquired respiration from the precursor of the mitochondrion, and oxygenic photosynthesis from the precursor of the chloroplast. The host cells also acquired genetic information from their symbionts, eventually incorporating much of it into their own genomes. Genes of the eukaryotic cell nucleus now encode most mitochondrial and chloroplast proteins. Genes are copied and moved between cellular compartments with relative ease, and there is no obvious obstacle to successful import of any protein precursor from the cytosol. So why are any genes at all retained in cytoplasmic organelles? One proposal is that these small but functional genomes provide a location for genes that is close to, and in the same compartment as, their gene products. This co-location facilitates rapid and direct regulatory coupling. Redox control of synthesis de novo is put forward as the common property of those proteins that must be encoded and synthesized within mitochondria and chloroplasts. This testable hypothesis is termed CORR, for co-location for redox regulation. Principles, predictions and consequences of CORR are examined in the context of competing hypotheses and current evidence. PMID:12594916

  4. Comparison of space flight and heavy ion radiation induced genomic/epigenomic mutations in rice (Oryza sativa)

    NASA Astrophysics Data System (ADS)

    Shi, Jinming; Lu, Weihong; Sun, Yeqing

    2014-04-01

    Rice seeds, after space flight and low dose heavy ion radiation treatment were cultured on ground. Leaves of the mature plants were obtained for examination of genomic/epigenomic mutations by using amplified fragment length polymorphism (AFLP) and methylation sensitive amplification polymorphism (MSAP) method, respectively. The mutation sites were identified by fragment recovery and sequencing. The heritability of the mutations was detected in the next generation. Results showed that both space flight and low dose heavy ion radiation can induce significant alterations on rice genome and epigenome (P < 0.05). For both genetic and epigenetic assays, while there was no significant difference in mutation rates and their ability to be inherited to the next generation, the site of mutations differed between the space flight and radiation treated groups. More than 50% of the mutation sites were shared by two radiation treated groups, radiated with different LET value and dose, while only about 20% of the mutation sites were shared by space flight group and radiation treated group. Moreover, in space flight group, we found that DNA methylation changes were more prone to occur on CNG sequence than CG sequence. Sequencing results proved that both space flight and heavy ion radiation induced mutations were widely spread on rice genome including coding region and repeated region. Our study described and compared the characters of space flight and low dose heavy ion radiation induced genomic/epigenomic mutations. Our data revealed the mechanisms of application of space environment for mutagenesis and crop breeding. Furthermore, this work implicated that the nature of mutations induced under space flight conditions may involve factors beyond ion radiation.

  5. Recurrent parent genome recovery analysis in a marker-assisted backcrossing program of rice (Oryza sativa L.).

    PubMed

    Miah, Gous; Rafii, Mohd Y; Ismail, Mohd R; Puteh, Adam B; Rahim, Harun A; Latif, Mohammad A

    2015-02-01

    Backcross breeding is the most commonly used method for incorporating a blast resistance gene into a rice cultivar. Linkage between the resistance gene and undesirable units can persist for many generations of backcrossing. Marker-assisted backcrossing (MABC) along with marker-assisted selection (MAS) contributes immensely to overcome the main limitation of the conventional breeding and accelerates recurrent parent genome (RPG) recovery. The MABC approach was employed to incorporate (a) blast resistance gene(s) from the donor parent Pongsu Seribu 1, the blast-resistant local variety in Malaysia, into the genetic background of MR219, a popular high-yielding rice variety that is blast susceptible, to develop a blast-resistant MR219 improved variety. In this perspective, the recurrent parent genome recovery was analyzed in early generations of backcrossing using simple sequence repeat (SSR) markers. Out of 375 SSR markers, 70 markers were found polymorphic between the parents, and these markers were used to evaluate the plants in subsequent generations. Background analysis revealed that the extent of RPG recovery ranged from 75.40% to 91.3% and from 80.40% to 96.70% in BC1F1 and BC2F1 generations, respectively. In this study, the recurrent parent genome content in the selected BC2F2 lines ranged from 92.7% to 97.7%. The average proportion of the recurrent parent in the selected improved line was 95.98%. MAS allowed identification of the plants that are more similar to the recurrent parent for the loci evaluated in backcross generations. The application of MAS with the MABC breeding program accelerated the recovery of the RP genome, reducing the number of generations and the time for incorporating resistance against rice blast. PMID:25553855

  6. Comparison of space flight and heavy ion radiation induced genomic/epigenomic mutations in rice (Oryza sativa).

    PubMed

    Shi, Jinming; Lu, Weihong; Sun, Yeqing

    2014-04-01

    Rice seeds, after space flight and low dose heavy ion radiation treatment were cultured on ground. Leaves of the mature plants were obtained for examination of genomic/epigenomic mutations by using amplified fragment length polymorphism (AFLP) and methylation sensitive amplification polymorphism (MSAP) method, respectively. The mutation sites were identified by fragment recovery and sequencing. The heritability of the mutations was detected in the next generation. Results showed that both space flight and low dose heavy ion radiation can induce significant alterations on rice genome and epigenome (P<0.05). For both genetic and epigenetic assays, while there was no significant difference in mutation rates and their ability to be inherited to the next generation, the site of mutations differed between the space flight and radiation treated groups. More than 50% of the mutation sites were shared by two radiation treated groups, radiated with different LET value and dose, while only about 20% of the mutation sites were shared by space flight group and radiation treated group. Moreover, in space flight group, we found that DNA methylation changes were more prone to occur on CNG sequence than CG sequence. Sequencing results proved that both space flight and heavy ion radiation induced mutations were widely spread on rice genome including coding region and repeated region. Our study described and compared the characters of space flight and low dose heavy ion radiation induced genomic/epigenomic mutations. Our data revealed the mechanisms of application of space environment for mutagenesis and crop breeding. Furthermore, this work implicated that the nature of mutations induced under space flight conditions may involve factors beyond ion radiation.

  7. The personal genome browser: visualizing functions of genetic variants.

    PubMed

    Juan, Liran; Teng, Mingxiang; Zang, Tianyi; Hao, Yafeng; Wang, Zhenxing; Yan, Chengwu; Liu, Yongzhuang; Li, Jie; Zhang, Tianjiao; Wang, Yadong

    2014-07-01

    Advances in high-throughput sequencing technologies have brought us into the individual genome era. Projects such as the 1000 Genomes Project have led the individual genome sequencing to become more and more popular. How to visualize, analyse and annotate individual genomes with knowledge bases to support genome studies and personalized healthcare is still a big challenge. The Personal Genome Browser (PGB) is developed to provide comprehensive functional annotation and visualization for individual genomes based on the genetic-molecular-phenotypic model. Investigators can easily view individual genetic variants, such as single nucleotide variants (SNVs), INDELs and structural variations (SVs), as well as genomic features and phenotypes associated to the individual genetic variants. The PGB especially highlights potential functional variants using the PGB built-in method or SIFT/PolyPhen2 scores. Moreover, the functional risks of genes could be evaluated by scanning individual genetic variants on the whole genome, a chromosome, or a cytoband based on functional implications of the variants. Investigators can then navigate to high risk genes on the scanned individual genome. The PGB accepts Variant Call Format (VCF) and Genetic Variation Format (GVF) files as the input. The functional annotation of input individual genome variants can be visualized in real time by well-defined symbols and shapes. The PGB is available at http://www.pgbrowser.org/. PMID:24799434

  8. Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism.

    PubMed

    Matsuda, Fumio; Nakabayashi, Ryo; Yang, Zhigang; Okazaki, Yozo; Yonemaru, Jun-ichi; Ebana, Kaworu; Yano, Masahiro; Saito, Kazuki

    2015-01-01

    Plants produce structurally diverse secondary (specialized) metabolites to increase their fitness for survival under adverse environments. Several bioactive compounds for new drugs have been identified through screening of plant extracts. In this study, genome-wide association studies (GWAS) were conducted to investigate the genetic architecture behind the natural variation of rice secondary metabolites. GWAS using the metabolome data of 175 rice accessions successfully identified 323 associations among 143 single nucleotide polymorphisms (SNPs) and 89 metabolites. The data analysis highlighted that levels of many metabolites are tightly associated with a small number of strong quantitative trait loci (QTLs). The tight association may be a mechanism generating strains with distinct metabolic composition through the crossing of two different strains. The results indicate that one plant species produces more diverse phytochemicals than previously expected, and plants still contain many useful compounds for human applications.

  9. Loss-of-function mutation of rice SLAC7 decreases chloroplast stability and induces a photoprotection mechanism in rice.

    PubMed

    Fan, Xiaolei; Wu, Jiemin; Chen, Taiyu; Tie, Weiwei; Chen, Hao; Zhou, Fei; Lin, Yongjun

    2015-12-01

    Plants absorb sunlight to power the photochemical reactions of photosynthesis, which can potentially damage the photosynthetic machinery. However, the mechanism that protects chloroplasts from the damage remains unclear. In this work, we demonstrated that rice (Oryza sativa L.) SLAC7 is a generally expressed membrane protein. Loss-of-function of SLAC7 caused continuous damage to the chloroplasts of mutant leaves under normal light conditions. Ion leakage indicators related to leaf damage such as H2 O2 and abscisic acid levels were significantly higher in slac7-1 than in the wild type. Consistently, the photosynthesis efficiency and Fv/Fm ratio of slac7-1 were significantly decreased (similar to photoinhibition). In response to chloroplast damage, slac7-1 altered its leaf morphology (curled or fused leaf) by the synergy between plant hormones and transcriptional factors to decrease the absorption of light, suggesting that a photoprotection mechanism for chloroplast damage was activated in slac7-1. When grown in dark conditions, slac7-1 displayed a normal phenotype. SLAC7 under the control of the AtSLAC1 promoter could partially complement the phenotypes of Arabidopsis slac1 mutants, indicating a partial conservation of SLAC protein functions. These results suggest that SLAC7 is essential for maintaining the chloroplast stability in rice. PMID:25739330

  10. Loss‐of‐function mutation of rice SLAC7 decreases chloroplast stability and induces a photoprotection mechanism in rice

    PubMed Central

    Fan, Xiaolei; Wu, Jiemin; Chen, Taiyu; Tie, Weiwei; Chen, Hao; Zhou, Fei

    2015-01-01

    Abstract Plants absorb sunlight to power the photochemical reactions of photosynthesis, which can potentially damage the photosynthetic machinery. However, the mechanism that protects chloroplasts from the damage remains unclear. In this work, we demonstrated that rice (Oryza sativa L.) SLAC7 is a generally expressed membrane protein. Loss‐of‐function of SLAC7 caused continuous damage to the chloroplasts of mutant leaves under normal light conditions. Ion leakage indicators related to leaf damage such as H2O2 and abscisic acid levels were significantly higher in slac7‐1 than in the wild type. Consistently, the photosynthesis efficiency and Fv/Fm ratio of slac7‐1 were significantly decreased (similar to photoinhibition). In response to chloroplast damage, slac7‐1 altered its leaf morphology (curled or fused leaf) by the synergy between plant hormones and transcriptional factors to decrease the absorption of light, suggesting that a photoprotection mechanism for chloroplast damage was activated in slac7‐1. When grown in dark conditions, slac7‐1 displayed a normal phenotype. SLAC7 under the control of the AtSLAC1 promoter could partially complement the phenotypes of Arabidopsis slac1 mutants, indicating a partial conservation of SLAC protein functions. These results suggest that SLAC7 is essential for maintaining the chloroplast stability in rice. PMID:25739330

  11. Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae

    PubMed Central

    Oh, Yeonyee; Donofrio, Nicole; Pan, Huaqin; Coughlan, Sean; Brown, Douglas E; Meng, Shaowu; Mitchell, Thomas; Dean, Ralph A

    2008-01-01

    Background Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processes regulating appressorium formation are incompletely understood. Results We analyzed genome-wide gene expression changes during spore germination and appressorium formation on a hydrophobic surface compared to induction by cAMP. During spore germination, 2,154 (approximately 21%) genes showed differential expression, with the majority being up-regulated. During appressorium formation, 357 genes were differentially expressed in response to both stimuli. These genes, which we refer to as appressorium consensus genes, were functionally grouped into Gene Ontology categories. Overall, we found a significant decrease in expression of genes involved in protein synthesis. Conversely, expression of genes associated with protein and amino acid degradation, lipid metabolism, secondary metabolism and cellular transportation exhibited a dramatic increase. We functionally characterized several differentially regulated genes, including a subtilisin protease (SPM1) and a NAD specific glutamate dehydrogenase (Mgd1), by targeted gene disruption. These studies revealed hitherto unknown findings that protein degradation and amino acid metabolism are essential for appressorium formation and subsequent infection. Conclusion We present the first comprehensive genome-wide transcript profile study and functional analysis of infection structure formation by a fungal plant pathogen. Our data provide novel insight into the underlying molecular mechanisms that will directly benefit efforts to identify fungal pathogenicity factors and aid the development of new disease management strategies. PMID:18492280

  12. Genetic and genomic dissection of resistance genes to the rice sheath blight pathogen

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice sheath blight disease caused by the anastomosis group AG1-IA of the fungal pathogen Rhizoctonia solani is one of the most serious rice diseases in the southern US and the world. The use of fungicides is a popular but costly method to control this disease worldwide. Genetic analysis of host re...

  13. Functional annotations in bacterial genomes based on small RNA signatures.

    PubMed

    Sridhar, Jayavel; Rafi, Ziauddin Ahamed

    2008-04-04

    One of the key challenges in computational genomics is annotating coding genes and identification of regulatory RNAs in complete genomes. An attempt is made in this study which uses the regulatory RNA locations and their conserved flanking genes identified within the genomic backbone of template genome to search for similar RNA locations in query genomes. The search is based on recently reported coexistence of small RNAs and their conserved flanking genes in related genomes. Based on our study, 54 additional sRNA locations and functions of 96 uncharacterized genes are predicted in two draft genomes viz., Serratia marcesens Db1 and Yersinia enterocolitica 8081. Although most of the identified additional small RNA regions and their corresponding flanking genes are homologous in nature, the proposed anchoring technique could successfully identify four non-homologous small RNA regions in Y. enterocolitica genome also. The KEGG Orthology (KO) based automated functional predictions confirms the predicted functions of 65 flanking genes having defined KO numbers, out of the total 96 predictions made by this method. This coexistence based method shows more sensitivity than controlled vocabularies in locating orthologous gene pairs even in the absence of defined Orthology numbers. All functional predictions made by this study in Y. enterocolitica 8081 were confirmed by the recently published complete genome sequence and annotations. This study also reports the possible regions of gene rearrangements in these two genomes and further characterization of such RNA regions could shed more light on their possible role in genome evolution.

  14. Functional annotations in bacterial genomes based on small RNA signatures

    PubMed Central

    Sridhar, Jayavel; Rafi, Ziauddin Ahamed

    2008-01-01

    One of the key challenges in computational genomics is annotating coding genes and identification of regulatory RNAs in complete genomes. An attempt is made in this study which uses the regulatory RNA locations and their conserved flanking genes identified within the genomic backbone of template genome to search for similar RNA locations in query genomes. The search is based on recently reported coexistence of small RNAs and their conserved flanking genes in related genomes. Based on our study, 54 additional sRNA locations and functions of 96 uncharacterized genes are predicted in two draft genomes viz., Serratia marcesens Db1 and Yersinia enterocolitica 8081. Although most of the identified additional small RNA regions and their corresponding flanking genes are homologous in nature, the proposed anchoring technique could successfully identify four non-homologous small RNA regions in Y. enterocolitica genome also. The KEGG Orthology (KO) based automated functional predictions confirms the predicted functions of 65 flanking genes having defined KO numbers, out of the total 96 predictions made by this method. This coexistence based method shows more sensitivity than controlled vocabularies in locating orthologous gene pairs even in the absence of defined Orthology numbers. All functional predictions made by this study in Y. enterocolitica 8081 were confirmed by the recently published complete genome sequence and annotations. This study also reports the possible regions of gene rearrangements in these two genomes and further characterization of such RNA regions could shed more light on their possible role in genome evolution. PMID:18478081

  15. CYP99A3: Functional identification of a diterpene oxidase from the momilactone biosynthetic gene cluster in rice

    PubMed Central

    Wang, Qiang; Hillwig, Matthew L.; Peters, Reuben J.

    2013-01-01

    SUMMARY Rice (Oryza sativa) produces momilactone diterpenoids as both phytoalexins and allelochemicals. Strikingly, the rice genome contains a biosynthetic gene cluster for momilactone production, located on rice chromosome 4, which contains two cytochromes P450 mono-oxygenases, CYP99A2 and CYP99A3, with undefined roles; although it has been previously shown that RNAi double knock-down of this pair of closely related CYP reduced momilactone accumulation. Here we attempted biochemical characterization of CYP99A2 and CYP99A3, which ultimately was achieved by complete gene recoding, enabling functional recombinant expression in bacteria. With these synthetic gene constructs it was possible to demonstrate that, while CYP99A2 does not exhibit significant activity with diterpene substrates, CYP99A3 catalyzes consecutive oxidations of the C19 methyl group of the momilactone precursor syn-pimara-7,15-diene to form, sequentially, syn-pimaradien-19-ol, syn-pimaradien-19-al and syn-pimaradien-19-oic acid. These are presumably intermediates in momilactone biosynthesis, as a C19 carboxylic acid moiety is required for formation of the core 19,6-γ-lactone ring structure. We further were able to detect syn-pimaradien-19-oic acid in rice plants, which indicates physiological relevance for the observed activity of CYP99A3. In addition, we found that CYP99A3 also oxidized syn-stemod-13(17)-ene at C19 to produce, sequentially, syn-stemoden-19-ol, syn-stemoden-19-al and syn-stemoden-19-oic acid, albeit with lower catalytic efficiency than with syn-pimaradiene. Although the CYP99A3 syn-stemodene derived products were not detected in planta, these results nevertheless provide a hint at the currently unknown metabolic fate of this diterpene in rice. Regardless of any wider role, our results strongly indicate that CYP99A3 acts as a multifunctional diterpene oxidase in momilactone biosynthesis. PMID:21175892

  16. Functional profiling of the Saccharomyces cerevisiae genome.

    PubMed

    Giaever, Guri; Chu, Angela M; Ni, Li; Connelly, Carla; Riles, Linda; Véronneau, Steeve; Dow, Sally; Lucau-Danila, Ankuta; Anderson, Keith; André, Bruno; Arkin, Adam P; Astromoff, Anna; El-Bakkoury, Mohamed; Bangham, Rhonda; Benito, Rocio; Brachat, Sophie; Campanaro, Stefano; Curtiss, Matt; Davis, Karen; Deutschbauer, Adam; Entian, Karl-Dieter; Flaherty, Patrick; Foury, Francoise; Garfinkel, David J; Gerstein, Mark; Gotte, Deanna; Güldener, Ulrich; Hegemann, Johannes H; Hempel, Svenja; Herman, Zelek; Jaramillo, Daniel F; Kelly, Diane E; Kelly, Steven L; Kötter, Peter; LaBonte, Darlene; Lamb, David C; Lan, Ning; Liang, Hong; Liao, Hong; Liu, Lucy; Luo, Chuanyun; Lussier, Marc; Mao, Rong; Menard, Patrice; Ooi, Siew Loon; Revuelta, Jose L; Roberts, Christopher J; Rose, Matthias; Ross-Macdonald, Petra; Scherens, Bart; Schimmack, Greg; Shafer, Brenda; Shoemaker, Daniel D; Sookhai-Mahadeo, Sharon; Storms, Reginald K; Strathern, Jeffrey N; Valle, Giorgio; Voet, Marleen; Volckaert, Guido; Wang, Ching-yun; Ward, Teresa R; Wilhelmy, Julie; Winzeler, Elizabeth A; Yang, Yonghong; Yen, Grace; Youngman, Elaine; Yu, Kexin; Bussey, Howard; Boeke, Jef D; Snyder, Michael; Philippsen, Peter; Davis, Ronald W; Johnston, Mark

    2002-07-25

    Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics.

  17. Functional genomics: Probing plant gene function and expression with transposons

    PubMed Central

    Martienssen, Robert A.

    1998-01-01

    Transposable elements provide a convenient and flexible means to disrupt plant genes, so allowing their function to be assessed. By engineering transposons to carry reporter genes and regulatory signals, the expression of target genes can be monitored and to some extent manipulated. Two strategies for using transposons to assess gene function are outlined here: First, the PCR can be used to identify plants that carry insertions into specific genes from among pools of heavily mutagenized individuals (site-selected transposon mutagenesis). This method requires that high copy transposons be used and that a relatively large number of reactions be performed to identify insertions into genes of interest. Second, a large library of plants, each carrying a unique insertion, can be generated. Each insertion site then can be amplified and sequenced systematically. These two methods have been demonstrated in maize, Arabidopsis, and other plant species, and the relative merits of each are discussed in the context of plant genome research. PMID:9482828

  18. An analysis of the complete sequence of a sugarcane bacilliform virus genome infectious to banana and rice.

    PubMed

    Bouhida, M; Lockhart, B E; Olszewski, N E

    1993-01-01

    The genome of sugarcane bacilliform virus (ScBV), a badnavirus, consists of a circular dsDNA. The complete sequence of a cloned infective ScBV genome is reported here. The genome is 7568 bp in size and possesses a number of features suggesting that ScBV is a pararetrovirus. A tRNA(Met)-binding site that may serve as a primer for minus-strand synthesis is present. The plus-strand of the ScBV genome contains three open reading frames (ORFs) which are capable of encoding proteins with calculated M(r) values of 22K, 13K and 215K. The 215K protein has regions with similarity to the RNA-binding domains, aspartic proteases and replicases of retro-elements. In addition, the 215K protein also has a region with restricted similarity to the intercellular transport proteins of plant viruses. Comparisons with the other sequenced badnaviruses, Commelina yellow mottle (CoYMV) and rice tungro bacilliform (RTBV) viruses, indicate that the arrangement of the ORFs in these viruses is conserved. Located next to the putative RNA-binding domain is a cysteine-rich region that is unique to the badnaviruses. When the molecular relationships of a portion of the reverse transcriptases of plant pararetroviruses were determined, two badnaviruses, CoYMV and ScBV, form one distinct cluster, whereas three caulimoviruses, cauliflower mosaic virus, carnation etched ring virus and figwort mosaic virus, form a second cluster. The badnavirus RTBV and the caulimovirus soybean chlorotic mottle virus occupy intermediate positions between the clusters. When introduced by Agrobacterium-mediated inoculation, a construct containing 1.1 copies of the cloned ScBV genome is infectious to both rice and banana.

  19. Loss of floral repressor function adapts rice to higher latitudes in Europe

    PubMed Central

    Gómez-Ariza, Jorge; Galbiati, Francesca; Goretti, Daniela; Brambilla, Vittoria; Shrestha, Roshi; Pappolla, Andrea; Courtois, Brigitte; Fornara, Fabio

    2015-01-01

    The capacity to discriminate variations in day length allows plants to align flowering with the most favourable season of the year. This capacity has been altered by artificial selection when cultivated varieties became adapted to environments different from those of initial domestication. Rice flowering is promoted by short days when HEADING DATE 1 (Hd1) and EARLY HEADING DATE 1 (Ehd1) induce the expression of florigenic proteins encoded by HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1). Repressors of flowering antagonize such induction under long days, maintaining vegetative growth and delaying flowering. To what extent artificial selection of long day repressor loci has contributed to expand rice cultivation to Europe is currently unclear. This study demonstrates that European varieties activate both Hd3a and RFT1 expression regardless of day length and their induction is caused by loss-of-function mutations at major long day floral repressors. However, their contribution to flowering time control varies between locations. Pyramiding of mutations is frequently observed in European germplasm, but single mutations are sufficient to adapt rice to flower at higher latitudes. Expression of Ehd1 is increased in varieties showing reduced or null Hd1 expression under natural long days, as well as in single hd1 mutants in isogenic backgrounds. These data indicate that loss of repressor genes has been a key strategy to expand rice cultivation to Europe, and that Ehd1 is a central node integrating floral repressive signals. PMID:25732533

  20. Functional architecture of two exclusively late stage pollen-specific promoters in rice (Oryza sativa L.).

    PubMed

    Yan, Shuo; Wang, Zhongni; Liu, Yuan; Li, Wei; Wu, Feng; Lin, Xuelei; Meng, Zheng

    2015-07-01

    Late stage pollen-specific promoters are important tools in crop molecular breeding. Several such promoters, and their functional motifs, have been well characterized in dicotyledonous plants such as tomato and tobacco. However, knowledge about the functional architecture of such promoters is limited in the monocotyledonous plant rice. Here, pollen-late-stage-promoter 1 (PLP1) and pollen-late-stage-promoter 2 (PLP2) were characterized using a stable transformation system in rice. Histochemical staining showed that the two promoters exclusively drive GUS expression in late-stage pollen grains in rice. 5' deletion analysis revealed that four regions, including the -1159 to -720 and the -352 to -156 regions of PLP1 and the -740 to -557 and the -557 to -339 regions of PLP2, are important in maintaining the activity and specificity of these promoters. Motif mutation analysis indicated that 'AGAAA' and 'CAAT' motifs in the -740 to -557 region of PLP2 act as enhancers in the promoter. Gain of function experiments indicated that the novel TA-rich motif 'TACATAA' and 'TATTCAT' in the core region of the PLP1 and PLP2 promoters is necessary, but not sufficient, for pollen-specific expression in rice. Our results provide evidence that the enhancer motif 'AGAAA' is conserved in the pollen-specific promoters of both monocots and eudicots, but that some functional architecture characteristics are different.

  1. Genome-wide association study of rice (Oryza sativa L.) leaf traits with a high-throughput leaf scorer.

    PubMed

    Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Wang, Ke; Jiang, Ni; Feng, Hui; Chen, Guoxing; Liu, Qian; Xiong, Lizhong

    2015-09-01

    Leaves are the plant's solar panel and food factory, and leaf traits are always key issues to investigate in plant research. Traditional methods for leaf trait measurement are time-consuming. In this work, an engineering prototype has been established for high-throughput leaf scoring (HLS) of a large number of Oryza sativa accessions. The mean absolute per cent of errors in traditional measurements versus HLS were below 5% for leaf number, area, shape, and colour. Moreover, HLS can measure up to 30 leaves per minute. To demonstrate the usefulness of HLS in dissecting the genetic bases of leaf traits, a genome-wide association study (GWAS) was performed for 29 leaf traits related to leaf size, shape, and colour at three growth stages using HLS on a panel of 533 rice accessions. Nine associated loci contained known leaf-related genes, such as Nal1 for controlling the leaf width. In addition, a total of 73, 123, and 177 new loci were detected for traits associated with leaf size, colour, and shape, respectively. In summary, after evaluating the performance with a large number of rice accessions, the combination of GWAS and high-throughput leaf phenotyping (HLS) has proven a valuable strategy to identify the genetic loci controlling rice leaf traits. PMID:25796084

  2. Genome-wide association study of rice (Oryza sativa L.) leaf traits with a high-throughput leaf scorer

    PubMed Central

    Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Wang, Ke; Jiang, Ni; Feng, Hui; Chen, Guoxing; Liu, Qian; Xiong, Lizhong

    2015-01-01

    Leaves are the plant’s solar panel and food factory, and leaf traits are always key issues to investigate in plant research. Traditional methods for leaf trait measurement are time-consuming. In this work, an engineering prototype has been established for high-throughput leaf scoring (HLS) of a large number of Oryza sativa accessions. The mean absolute per cent of errors in traditional measurements versus HLS were below 5% for leaf number, area, shape, and colour. Moreover, HLS can measure up to 30 leaves per minute. To demonstrate the usefulness of HLS in dissecting the genetic bases of leaf traits, a genome-wide association study (GWAS) was performed for 29 leaf traits related to leaf size, shape, and colour at three growth stages using HLS on a panel of 533 rice accessions. Nine associated loci contained known leaf-related genes, such as Nal1 for controlling the leaf width. In addition, a total of 73, 123, and 177 new loci were detected for traits associated with leaf size, colour, and shape, respectively. In summary, after evaluating the performance with a large number of rice accessions, the combination of GWAS and high-throughput leaf phenotyping (HLS) has proven a valuable strategy to identify the genetic loci controlling rice leaf traits. PMID:25796084

  3. Genome-wide association study of rice (Oryza sativa L.) leaf traits with a high-throughput leaf scorer.

    PubMed

    Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Wang, Ke; Jiang, Ni; Feng, Hui; Chen, Guoxing; Liu, Qian; Xiong, Lizhong

    2015-09-01

    Leaves are the plant's solar panel and food factory, and leaf traits are always key issues to investigate in plant research. Traditional methods for leaf trait measurement are time-consuming. In this work, an engineering prototype has been established for high-throughput leaf scoring (HLS) of a large number of Oryza sativa accessions. The mean absolute per cent of errors in traditional measurements versus HLS were below 5% for leaf number, area, shape, and colour. Moreover, HLS can measure up to 30 leaves per minute. To demonstrate the usefulness of HLS in dissecting the genetic bases of leaf traits, a genome-wide association study (GWAS) was performed for 29 leaf traits related to leaf size, shape, and colour at three growth stages using HLS on a panel of 533 rice accessions. Nine associated loci contained known leaf-related genes, such as Nal1 for controlling the leaf width. In addition, a total of 73, 123, and 177 new loci were detected for traits associated with leaf size, colour, and shape, respectively. In summary, after evaluating the performance with a large number of rice accessions, the combination of GWAS and high-throughput leaf phenotyping (HLS) has proven a valuable strategy to identify the genetic loci controlling rice leaf traits.

  4. Genomic Analysis of an Ascomycete Fungus from the Rice Planthopper Reveals How It Adapts to an Endosymbiotic Lifestyle.

    PubMed

    Fan, Hai-Wei; Noda, Hiroaki; Xie, Hong-Qing; Suetsugu, Yoshitaka; Zhu, Qian-Hua; Zhang, Chuan-Xi

    2015-09-02

    A number of sap-sucking insects harbor endosymbionts, which are thought to play an important role in the development of their hosts. One of the most important rice pests, the brown planthopper (BPH), Nilaparvata lugens (Stål), harbors an obligatory yeast-like symbiont (YLS) that cannot be cultured in vitro. Genomic information on this YLS would be useful to better understand its evolution. In this study, we performed genome sequencing of the YLS using both 454 and Illumina approaches, generating a draft genome that shows a slightly smaller genome size and relatively higher GC content than most ascomycete fungi. A phylogenomic analysis of the YLS supported its close relationship with insect pathogens. We analyzed YLS-specific genes and the categories of genes that are likely to have changed in the YLS during its evolution. The loss of mating type locus demonstrated in the YLS sheds light on the evolution of eukaryotic symbionts. This information about the YLS genome provides a helpful guide for further understanding endosymbiotic associations in hemiptera and the symbiotic replacement of ancient bacteria with a multifunctional YLS seems to have been a successful change.

  5. Genomic Analysis of an Ascomycete Fungus from the Rice Planthopper Reveals How It Adapts to an Endosymbiotic Lifestyle

    PubMed Central

    Fan, Hai-Wei; Noda, Hiroaki; Xie, Hong-Qing; Suetsugu, Yoshitaka; Zhu, Qian-Hua; Zhang, Chuan-Xi

    2015-01-01

    A number of sap-sucking insects harbor endosymbionts, which are thought to play an important role in the development of their hosts. One of the most important rice pests, the brown planthopper (BPH), Nilaparvata lugens (Stål), harbors an obligatory yeast-like symbiont (YLS) that cannot be cultured in vitro. Genomic information on this YLS would be useful to better understand its evolution. In this study, we performed genome sequencing of the YLS using both 454 and Illumina approaches, generating a draft genome that shows a slightly smaller genome size and relatively higher GC content than most ascomycete fungi. A phylogenomic analysis of the YLS supported its close relationship with insect pathogens. We analyzed YLS-specific genes and the categories of genes that are likely to have changed in the YLS during its evolution. The loss of mating type locus demonstrated in the YLS sheds light on the evolution of eukaryotic symbionts. This information about the YLS genome provides a helpful guide for further understanding endosymbiotic associations in hemiptera and the symbiotic replacement of ancient bacteria with a multifunctional YLS seems to have been a successful change. PMID:26338189

  6. OsABCB14 functions in auxin transport and iron homeostasis in rice (Oryza sativa L.).

    PubMed

    Xu, Yanxia; Zhang, Saina; Guo, Haipeng; Wang, Suikang; Xu, Ligen; Li, Chuanyou; Qian, Qian; Chen, Fan; Geisler, Markus; Qi, Yanhua; Jiang, De An

    2014-07-01

    Members of the ATP Binding Cassette B/Multidrug-Resistance/P-glyco-protein (ABCB/MDR/PGP) subfamily were shown to function primarily in Oryza sativa (rice) auxin transport; however, none of the rice ABCB transporters have been functionally characterized. Here, we describe that a knock-down of OsABCB14 confers decreased auxin concentrations and polar auxin transport rates, conferring insensitivity to 2,4-dichlorophenoxyacetic acid (2,4-D) and indole-3-acetic acid (IAA). OsABCB14 displays enhanced specific auxin influx activity in yeast and protoplasts prepared from rice knock-down alleles. OsABCB14 is localized at the plasma membrane, pointing to an important directionality under physiological conditions. osabcb14 mutants were surprisingly found to be insensitive to iron deficiency treatment (-Fe). Their Fe concentration is higher and upregulation of Fe deficiency-responsive genes is lower in osabcb14 mutants than in wild-type rice (Nipponbare, NIP). Taken together, our results strongly support the role of OsABCB14 as an auxin influx transporter involved in Fe homeostasis. The functional characterization of OsABCB14 provides insights in monocot auxin transport and its relationship to Fe nutrition.

  7. Genome-Wide Analysis of 24-nt siRNAs Dynamic Variations during Rice Superior and Inferior Grain Filling

    PubMed Central

    Peng, Ting; Du, Yanxiu; Zhang, Jing; Li, Junzhou; Liu, Yanxia; Zhao, Yafan; Sun, Hongzheng; Zhao, Quanzhi

    2013-01-01

    24 nt-siRNAs are the most abundant small interfering RNAs in rice grains aside from microRNAs. To investigate the roles that 24 nt-siRNAs played in the poor grain filling of rice inferior grains, dynamic variations of 24 nt-siRNAs in inferior grains were compared with those of superior grains by using small RNA deep sequencing technology. The results showed that 24 nt-siRNAs derived from multiple regions of rice genome, and the maintenance of the two strands of 24 nt-siRNA duplex was a non-random process. The amounts of 24 nt-siRNAs declined with the process of grain filling in both superior and inferior grains, but 24 nt-siRNAs in inferior grains was much higher than that of superior grains in each period we sampled. Bioinformatics prediction indicated that 24 nt-siRNAs targeted on more genes involved in most of the known KEGG rice pathways, such as the starch and sucrose biosynthesis pathway. Combined with digital gene expression profiling of target genes, 24 nt-siRNAs mapped on the antisense strands of exons were specifically investigated, but the abundance of 24 nt-siRNAs did not show negative correlations with their corresponding target genes. The results indicated that 24 nt-siRNAs were not involved in down-regulation of target genes. The potential biological meanings for this inconsistency were probably the results of methylation directed gene expression activation, or competition for small RNA stability methylation. PMID:23593380

  8. REVIEW: Zebrafish: A Renewed Model System For Functional Genomics

    NASA Astrophysics Data System (ADS)

    Wen, Xiao-Yan

    2008-01-01

    In the post genome era, a major goal in molecular biology is to determine the function of the many thousands of genes present in the vertebrate genome. The zebrafish (Danio rerio) provides an almost ideal genetic model to identify the biological roles of these novel genes, in part because their embryos are transparent and develop rapidly. The zebrafish has many advantages over mouse for genome-wide mutagenesis studies, allowing for easier, cheaper and faster functional characterization of novel genes in the vertebrate genome. Many molecular research tools such as chemical mutagenesis, transgenesis, gene trapping, gene knockdown, TILLING, gene targeting, RNAi and chemical genetic screen are now available in zebrafish. Combining all the forward, reverse, and chemical genetic tools, it is expected that zebrafish will make invaluable contribution to vertebrate functional genomics in functional annotation of the genes, modeling human diseases and drug discoveries.

  9. SUMO-conjugating enzyme (Sce) and FK506-binding protein (FKBP) encoding rice (Oryza sativa L.) genes: genome-wide analysis, expression studies and evidence for their involvement in abiotic stress response.

    PubMed

    Nigam, Neha; Singh, Amanjot; Sahi, Chandan; Chandramouli, Anupama; Grover, Anil

    2008-04-01

    We report an in-depth characterization of two major stress proteins namely SUMO-conjugating enzyme (Sce) and peptidyl prolyl cis-trans isomerase (PPIase) in rice (Oryza sativa L.). Sce mediates addition of SUMO group to various cell proteins, through process referred to as SUMOylation. Rice nuclear genome has two putative genes encoding the Sce protein (OsSce1 and OsSce2). PCR-amplified full-length OsSce1 cDNA functionally complemented the growth defect in yeast cells lacking the equivalent Ubc9 protein (ScDeltaubc9). RT-PCR analysis showed that transcript levels of OsSce1 and OsSce2 in rice seedlings were regulated by temperature stress. OsSce1 protein was localized to the nucleus in onion epidermal cells as evidenced by the transient GFP expression analysis following micro-projectile gun-based shooting of an OsSce1-GFP fusion construct. PPIase proteins assist molecular chaperones in reactions associated with protein folding and protein transport across membrane. There are 23 putative genes encoding for FK506-binding proteins (FKBPs; specific class of PPIase) in rice genome. OsFKBP20 cDNA was isolated as a stress-inducible EST clone. Largest ORF of 561 bases in OsFKBP20 showed characteristic FK506-binding domain at N-terminus and a coiled-coil motif at C-terminus. RNA expression analysis indicated that OsFKBP20 transcript is heat-inducible. OsFKBP20 over-expression in yeast endowed capacity of high temperature tolerance to yeast cells. Yeast two-hybrid analysis showed that OsSce1 protein physically interacts with the OsFKBP20 protein. It is thus proposed that OsSce1 and OsFKBP20 proteins in concert mediate the stress response of rice plants. PMID:18219493

  10. Retroelements and their impact on genome evolution and functioning.

    PubMed

    Gogvadze, Elena; Buzdin, Anton

    2009-12-01

    Retroelements comprise a considerable fraction of eukaryotic genomes. Since their initial discovery by Barbara McClintock in maize DNA, retroelements have been found in genomes of almost all organisms. First considered as a "junk DNA" or genomic parasites, they were shown to influence genome functioning and to promote genetic innovations. For this reason, they were suggested as an important creative force in the genome evolution and adaptation of an organism to altered environmental conditions. In this review, we summarize the up-to-date knowledge of different ways of retroelement involvement in structural and functional evolution of genes and genomes, as well as the mechanisms generated by cells to control their retrotransposition. PMID:19649766

  11. Molecular characterization of the genome segments S4, S6 and S7 of rice gall dwarf virus.

    PubMed

    Zhang, H M; Yang, J; Xin, X; Chen, J P; Adams, M J

    2007-01-01

    Rice gall dwarf virus (RGDV) is a member of the genus Phytoreovirus within the family Reovirdae. Its genome has 12 segments of double-stranded RNA (dsRNA), of which the nucleotide sequences of segments S4, S6, and S7 were determined, providing the first complete genome sequence of RGDV. Each of the segments S4, S6, and S7 contained conserved terminal sequences conforming to the RGDV consensus, 5'-GGXA ... UGAU-3' (X = U or C). Each segment had a single predicted open reading frame encoding proteins with calculated molecular weights of 79.8, 58.6, and 53.3 kDa. These proteins appeared to be homologous to those encoded by the corresponding segments of rice dwarf virus and wound tumor virus, the other known members of the same genus, having about 20-30% amino acid identity to them. It is therefore likely that RGDV S4 and S6 encode non-structural proteins and S7 an inner core protein. Probable homologies between the segments of all known phytoreoviruses are summarized. Beyond these similarities, the RGDV proteins displayed no significant similarity to any other reported viral proteins.

  12. Characterizing genomic alterations in cancer by complementary functional associations

    PubMed Central

    Kim, J. W.; Botvinnik, O. B.; Abudayyeh, O.; Birger, C.; Rosenbluh, J.; Shrestha, Y.; Abazeed, M. E.; Hammerman, P. S.; DiCara, D.; Konieczkowski, D. J.; Johannessen, C. M.; Liberzon, A.; Alizad-Rahvar, A. R.; Alexe, G.; Aguirre, A.; Ghandi, M.; Greulich, H.; Vazquez, F.; Weir, B. A.; Van Allen, E. M.; Tsherniak, A.; Shao, D. D.; Zack, T. I.; Noble, M.; Getz, G.; Beroukhim, R.; Garraway, L. A.; Ardakani, M.; Romualdi, C.; Sales, G.; Barbie, D. A.; Boehm, J. S.; Hahn, W. C.; Mesirov, J. P.; Tamayo, P.

    2016-01-01

    Systematic efforts to sequence the cancer genome have identified large numbers of relevant mutations and copy number alterations in human cancers; however, elucidating their functional consequences, and their interactions to drive or maintain oncogenic states, is still a significant challenge. Here we introduce REVEALER, a computational method that identifies combinations of mutually exclusive genomic alterations correlated with functional phenotypes, such as the activation or gene-dependency of oncogenic pathways or the sensitivity to a drug treatment. We use REVEALER to uncover complementary genomic alterations associated with the transcriptional activation of β-catenin and NRF2, MEK-inhibitor sensitivity, and KRAS dependency. REVEALER successfully identified both known and new associations demonstrating the power of combining functional profiles with extensive characterization of genomic alterations in cancer genomes. PMID:27088724

  13. Genome-wide DNA polymorphism in the indica rice varieties RGD-7S and Taifeng B as revealed by whole genome re-sequencing.

    PubMed

    Fu, Chong-Yun; Liu, Wu-Ge; Liu, Di-Lin; Li, Ji-Hua; Zhu, Man-Shan; Liao, Yi-Long; Liu, Zhen-Rong; Zeng, Xue-Qin; Wang, Feng

    2016-03-01

    Next-generation sequencing technologies provide opportunities to further understand genetic variation, even within closely related cultivars. We performed whole genome resequencing of two elite indica rice varieties, RGD-7S and Taifeng B, whose F1 progeny showed hybrid weakness and hybrid vigor when grown in the early- and late-cropping seasons, respectively. Approximately 150 million 100-bp pair-end reads were generated, which covered ∼86% of the rice (Oryza sativa L. japonica 'Nipponbare') reference genome. A total of 2,758,740 polymorphic sites including 2,408,845 SNPs and 349,895 InDels were detected in RGD-7S and Taifeng B, respectively. Applying stringent parameters, we identified 961,791 SNPs and 46,640 InDels between RGD-7S and Taifeng B (RGD-7S/Taifeng B). The density of DNA polymorphisms was 256.8 SNPs and 12.5 InDels per 100 kb for RGD-7S/Taifeng B. Copy number variations (CNVs) were also investigated. In RGD-7S, 1989 of 2727 CNVs were overlapped in 218 genes, and 1231 of 2010 CNVs were annotated in 175 genes in Taifeng B. In addition, we verified a subset of InDels in the interval of hybrid weakness genes, Hw3 and Hw4, and obtained some polymorphic InDel markers, which will provide a sound foundation for cloning hybrid weakness genes. Analysis of genomic variations will also contribute to understanding the genetic basis of hybrid weakness and heterosis.

  14. Genome-Wide Dissection of the MicroRNA Expression Profile in Rice Embryo during Early Stages of Seed Germination

    PubMed Central

    He, Dongli; Wang, Qiong; Wang, Kun; Yang, Pingfang

    2015-01-01

    The first 24 hours after imbibition (HAI) is pivotal for rice seed germination, during which embryo cells switch from a quiescent state to a metabolically active state rapidly. MicroRNAs (miRNAs) have increasingly been shown to play important roles in rice development. Nevertheless, limited knowledge about miRNA regulation has been obtained in the early stages of rice seed germination. In this study, the small RNAs (sRNAs) from embryos of 0, 12, and 24 HAI rice seeds were sequenced to investigate the composition and expression patterns of miRNAs. The bioinformatics analysis identified 289 miRNA loci, including 59 known and 230 novel miRNAs, and 35 selected miRNAs were confirmed by stem-loop real-time RT-PCR. Expression analysis revealed that the dry and imbibed seeds have unique miRNA expression patterns compared with other tissues, particularly for the dry seeds. Using three methods, Mireap, psRNATarget and degradome analyses, 1197 potential target genes of identified miRNAs involved in various molecular functions were predicted. Among these target genes, 39 had significantly negative correlations with their corresponding miRNAs as inferred from published transcriptome data, and 6 inversely expressed miRNA-target pairs were confirmed by 5ʹ-RACE assay. Our work provides an inventory of miRNA expression profiles and miRNA-target interactions in rice embryos, and lays a foundation for further studies of miRNA-mediated regulation in initial seed germination. PMID:26681181

  15. Partnering for functional genomics research conference: Abstracts of poster presentations

    SciTech Connect

    1998-06-01

    This reports contains abstracts of poster presentations presented at the Functional Genomics Research Conference held April 16--17, 1998 in Oak Ridge, Tennessee. Attention is focused on the following areas: mouse mutagenesis and genomics; phenotype screening; gene expression analysis; DNA analysis technology development; bioinformatics; comparative analyses of mouse, human, and yeast sequences; and pilot projects to evaluate methodologies.

  16. [Major domestication traits in Asian rice].

    PubMed

    Ou, Shu-Jun; Wang, Hong-Ru; Chu, Cheng-Cai

    2012-11-01

    Rice (Oryza sativa L.) is an excellent model plant in elucidation of cereal domestication. Loss of seed shattering, weakened dormancy, and changes in plant architecture were thought to be three key events in the rice domestication and creating the high-yield, uniform-germinating, and densely-planting modern rice. Loss of shattering is considered to be the direct morphological evidence for identifying domesticated rice. Two major shattering QTLs, Sh4 and qSH1, have displayed different domestication histories. Weakened seed dormancy is essential for synchronous germination in agricultural production. Genes Sdr4, qSD7-1, and qSD12 impose a global and complementary adaptation strategies in controlling seed dormancy. The prostate growth habit of wild rice is an adaptation to disturbed habitats, while the erect growth habit of rice cultivars meet the needs of compact planting, and such a plant architecture is mainly controlled by PROG1. The outcrossing habit of wild rice promotes propagation of domestication genes among different populations, while the self-pollinating habit of cultivated rice facilitates fixation of domestication genes. Currently, the researches on rice domestication mainly focus on individual genes or multiple neutral markers, and much less attention has been paid to the evolution of network controlling domestication traits. With the progress in functional genomics research, the molecular mechanism of domestication traits is emerging. Rice domestication researches based on network will be more comprehensive and better reflect rice domestica-tion process. Here, we reviewed most progresses in molecular mechanisms of rice domestication traits, in order to provide the new insights for rice domestication and molecular breeding.

  17. Effects of Germinated Brown Rice Addition on the Flavor and Functionality of Yogurt

    PubMed Central

    2016-01-01

    This study aimed to investigate the functional and physicochemical properties of yogurt, supplemented with germinated brown rice (GBR) containing γ-aminobutyric acid (GABA), during storage. GBR was produced by soaking brown rice at 30℃, and saccharified germinated brown rice (SGBR) was produced by treating brown rice with α- and β-amylase for 1 h, at 80℃ and 60℃, respectively. Yogurt was manufactured using a commercial starter (YC-X11, CHR. Hansen, Denmark) at 37℃ for 12 h. The fatty acids and GABA contents were analyzed using GC and HPLC, respectively. The fatty acids in the cereal samples consisted of oleic, linoleic, and palmitic acid. The portion of oleic acid was the highest, at 35.65% in GBR, and 32.16% in SGBR. During germination, the oleic acid content increased, whereas linolenic and palmitic acid contents from GBR tended to decrease. Although the portion of saturated fatty acids, such as stearic and myristic acid, decreased significantly (p<0.05), that of unsaturated fatty acids, such as oleic and linoleic acid, increased with an increase in supplementation of BR, GBR, or SGBR in the yogurt. The yogurt, supplemented with cereal samples, showed a tendency of an increase in the concentration of GABA with an increase in the supplementation of the cereal samples. However, yogurt supplemented with GBR showed the highest concentration of GABA, regardless of the supplementation of the cereal samples. These results indicated that yogurt supplemented with BR, GBR, or SGBR could be a promising dairy product.

  18. Diverged copies of the seed regulatory Opaque-2 gene by a segmental duplication in the progenitor genome of rice, sorghum, and maize.

    PubMed

    Xu, Jian-Hong; Messing, Joachim

    2008-09-01

    Comparative analyses of the sequence of entire genomes have shown that gene duplications, chromosomal segmental duplications, or even whole genome duplications (WGD) have played prominent roles in the evolution of many eukaryotic species. Here, we used the ancient duplication of a well known transcription factor in maize, encoded by the Opaque-2 (O2) locus, to examine the general features of divergences of chromosomal segmental duplications in a lineage-specific manner. We took advantage of contiguous chromosomal sequence information in rice (Oryza sativa, Nipponbare), sorghum (Sorghum bicolor, Btx623), and maize (Zea mays, B73) that were aligned by conserved gene order (synteny). This analysis showed that the maize O2 locus is contained within a 1.25 million base-pair (Mb) segment on chromosome 7, which was duplicated approximately 56 million years ago (mya) before the split of rice and maize 50 mya. The duplicated region on chromosome 1 is only half the size and contains the maize OHP gene, which does not restore the o2 mutation although it encodes a protein with the same DNA and protein binding properties in endosperm. The segmental duplication is not only found in rice, but also in sorghum, which split from maize 11.9 mya. A detailed analysis of the duplicated regions provided examples for complex rearrangements including deletions, duplications, conversions, inversions, and translocations. Furthermore, the rice and sorghum genomes appeared to be more stable than the maize genome, probably because maize underwent allotetraploidization and then diploidization. PMID:19825579

  19. The Functional Genomics Initiative at Oak Ridge National Laboratory

    SciTech Connect

    Johnson, Dabney; Justice, Monica; Beattle, Ken; Buchanan, Michelle; Ramsey, Michael; Ramsey, Rose; Paulus, Michael; Ericson, Nance; Allison, David; Kress, Reid; Mural, Richard; Uberbacher, Ed; Mann, Reinhold

    1997-12-31

    The Functional Genomics Initiative at the Oak Ridge National Laboratory integrates outstanding capabilities in mouse genetics, bioinformatics, and instrumentation. The 50 year investment by the DOE in mouse genetics/mutagenesis has created a one-of-a-kind resource for generating mutations and understanding their biological consequences. It is generally accepted that, through the mouse as a surrogate for human biology, we will come to understand the function of human genes. In addition to this world class program in mammalian genetics, ORNL has also been a world leader in developing bioinformatics tools for the analysis, management and visualization of genomic data. Combining this expertise with new instrumentation technologies will provide a unique capability to understand the consequences of mutations in the mouse at both the organism and molecular levels. The goal of the Functional Genomics Initiative is to develop the technology and methodology necessary to understand gene function on a genomic scale and apply these technologies to megabase regions of the human genome. The effort is scoped so as to create an effective and powerful resource for functional genomics. ORNL is partnering with the Joint Genome Institute and other large scale sequencing centers to sequence several multimegabase regions of both human and mouse genomic DNA, to identify all the genes in these regions, and to conduct fundamental surveys to examine gene function at the molecular and organism level. The Initiative is designed to be a pilot for larger scale deployment in the post-genome era. Technologies will be applied to the examination of gene expression and regulation, metabolism, gene networks, physiology and development.

  20. From Loci to Biology: Functional Genomics of Genome-Wide Association for Coronary Disease.

    PubMed

    Nurnberg, Sylvia T; Zhang, Hanrui; Hand, Nicholas J; Bauer, Robert C; Saleheen, Danish; Reilly, Muredach P; Rader, Daniel J

    2016-02-19

    Genome-wide association studies have provided a rich collection of ≈ 58 coronary artery disease (CAD) loci that suggest the existence of previously unsuspected new biology relevant to atherosclerosis. However, these studies only identify genomic loci associated with CAD, and many questions remain even after a genomic locus is definitively implicated, including the nature of the causal variant(s) and the causal gene(s), as well as the directionality of effect. There are several tools that can be used for investigation of the functional genomics of these loci, and progress has been made on a limited number of novel CAD loci. New biology regarding atherosclerosis and CAD will be learned through the functional genomics of these loci, and the hope is that at least some of these new pathways relevant to CAD pathogenesis will yield new therapeutic targets for the prevention and treatment of CAD.

  1. Rice proteomics: A move toward expanded proteome coverage to comparative and functional proteomics uncovers the mysteries of rice and plant biology.

    PubMed

    Agrawal, Ganesh Kumar; Rakwal, Randeep

    2011-05-01

    Growing rice is an important socio-economic activity. Rice proteomics has achieved a tremendous progress in establishing techniques to proteomes of almost all tissues, organs, and organelles during the past one decade (year 2000-2010). We have compiled these progresses time to time over this period. The present compilation discusses proteomics research in rice published between 1st April 2008 and 30th July 2010. Progress continues mainly towards protein cataloging deep into the proteome with high-confident protein assignment and some functional significance than ever before by (i) identifying previously unreported/low-abundance proteins, (ii) quantifying relative/absolute values of proteins, (iii) assigning protein responses to biotic/abiotic stresses, (iv) protein localization into organelles, (v) validating previous proteomes and eliminating false-positive proteins, and (vi) discovering potential biomarkers for tissues, organs, organelles, and for screening transgenic plants and food-safety evaluation. The notable achievements in global mapping of phosphorylation sites and identifying several novel secreted proteins into the extracellular space are worth appreciating. Our ever-increasing knowledge on the rice proteomics is beginning to impact the biology of not only rice, but also crops and plants. These major achievements will be discussed in this review keeping in mind newcomers, young, and established scientists in proteomics and plants.

  2. Nuclear pore proteins and the control of genome functions

    PubMed Central

    Ibarra, Arkaitz

    2015-01-01

    Nuclear pore complexes (NPCs) are composed of several copies of ∼30 different proteins called nucleoporins (Nups). NPCs penetrate the nuclear envelope (NE) and regulate the nucleocytoplasmic trafficking of macromolecules. Beyond this vital role, NPC components influence genome functions in a transport-independent manner. Nups play an evolutionarily conserved role in gene expression regulation that, in metazoans, extends into the nuclear interior. Additionally, in proliferative cells, Nups play a crucial role in genome integrity maintenance and mitotic progression. Here we discuss genome-related functions of Nups and their impact on essential DNA metabolism processes such as transcription, chromosome duplication, and segregation. PMID:25691464

  3. Characterizing genomic alterations in cancer by complementary functional associations | Office of Cancer Genomics

    Cancer.gov

    Systematic efforts to sequence the cancer genome have identified large numbers of mutations and copy number alterations in human cancers. However, elucidating the functional consequences of these variants, and their interactions to drive or maintain oncogenic states, remains a challenge in cancer research. We developed REVEALER, a computational method that identifies combinations of mutually exclusive genomic alterations correlated with functional phenotypes, such as the activation or gene dependency of oncogenic pathways or sensitivity to a drug treatment.

  4. Bacteriophage functional genomics and its role in bacterial pathogen detection.

    PubMed

    Klumpp, Jochen; Fouts, Derrick E; Sozhamannan, Shanmuga

    2013-07-01

    Emerging and reemerging bacterial infectious diseases are a major public health concern worldwide. The role of bacteriophages in the emergence of novel bacterial pathogens by horizontal gene transfer was highlighted by the May 2011 Escherichia coli O104:H4 outbreaks that originated in Germany and spread to other European countries. This outbreak also highlighted the pivotal role played by recent advances in functional genomics in rapidly deciphering the virulence mechanism elicited by this novel pathogen and developing rapid diagnostics and therapeutics. However, despite a steady increase in the number of phage sequences in the public databases, boosted by the next-generation sequencing technologies, few functional genomics studies of bacteriophages have been conducted. Our definition of 'functional genomics' encompasses a range of aspects: phage genome sequencing, annotation and ascribing functions to phage genes, prophage identification in bacterial sequences, elucidating the events in various stages of phage life cycle using genomic, transcriptomic and proteomic approaches, defining the mechanisms of host takeover including specific bacterial-phage protein interactions and identifying virulence and other adaptive features encoded by phages and finally, using prophage genomic information for bacterial detection/diagnostics. Given the breadth and depth of this definition and the fact that some of these aspects (especially phage-encoded virulence/adaptive features) have been treated extensively in other reviews, we restrict our focus only on certain aspects. These include phage genome sequencing and annotation, identification of prophages in bacterial sequences and genetic characterization of phages, functional genomics of the infection process and finally, bacterial identification using genomic information.

  5. Bacteriophage functional genomics and its role in bacterial pathogen detection.

    PubMed

    Klumpp, Jochen; Fouts, Derrick E; Sozhamannan, Shanmuga

    2013-07-01

    Emerging and reemerging bacterial infectious diseases are a major public health concern worldwide. The role of bacteriophages in the emergence of novel bacterial pathogens by horizontal gene transfer was highlighted by the May 2011 Escherichia coli O104:H4 outbreaks that originated in Germany and spread to other European countries. This outbreak also highlighted the pivotal role played by recent advances in functional genomics in rapidly deciphering the virulence mechanism elicited by this novel pathogen and developing rapid diagnostics and therapeutics. However, despite a steady increase in the number of phage sequences in the public databases, boosted by the next-generation sequencing technologies, few functional genomics studies of bacteriophages have been conducted. Our definition of 'functional genomics' encompasses a range of aspects: phage genome sequencing, annotation and ascribing functions to phage genes, prophage identification in bacterial sequences, elucidating the events in various stages of phage life cycle using genomic, transcriptomic and proteomic approaches, defining the mechanisms of host takeover including specific bacterial-phage protein interactions and identifying virulence and other adaptive features encoded by phages and finally, using prophage genomic information for bacterial detection/diagnostics. Given the breadth and depth of this definition and the fact that some of these aspects (especially phage-encoded virulence/adaptive features) have been treated extensively in other reviews, we restrict our focus only on certain aspects. These include phage genome sequencing and annotation, identification of prophages in bacterial sequences and genetic characterization of phages, functional genomics of the infection process and finally, bacterial identification using genomic information. PMID:23520178

  6. TAWAWA1, a regulator of rice inflorescence architecture, functions through the suppression of meristem phase transition.

    PubMed

    Yoshida, Akiko; Sasao, Masafumi; Yasuno, Naoko; Takagi, Kyoko; Daimon, Yasufumi; Chen, Ruihong; Yamazaki, Ryo; Tokunaga, Hiroki; Kitaguchi, Yoshinori; Sato, Yutaka; Nagamura, Yoshiaki; Ushijima, Tomokazu; Kumamaru, Toshihiro; Iida, Shigeru; Maekawa, Masahiko; Kyozuka, Junko

    2013-01-01

    Inflorescence structures result from the activities of meristems, which coordinate both the renewal of stem cells in the center and organ formation at the periphery. The fate of a meristem is specified at its initiation and changes as the plant develops. During rice inflorescence development, newly formed meristems acquire a branch meristem (BM) identity, and can generate further meristems or terminate as spikelets. Thus, the form of rice inflorescence is determined by a reiterative pattern of decisions made at the meristems. In the dominant gain-of-function mutant tawawa1-D, the activity of the inflorescence meristem (IM) is extended and spikelet specification is delayed, resulting in prolonged branch formation and increased numbers of spikelets. In contrast, reductions in TAWAWA1 (TAW1) activity cause precocious IM abortion and spikelet formation, resulting in the generation of small inflorescences. TAW1 encodes a nuclear protein of unknown function and shows high levels of expression in the shoot apical meristem, the IM, and the BMs. TAW1 expression disappears from incipient spikelet meristems (SMs). We also demonstrate that members of the SHORT VEGETATIVE PHASE subfamily of MADS-box genes function downstream of TAW1. We thus propose that TAW1 is a unique regulator of meristem activity in rice and regulates inflorescence development through the promotion of IM activity and suppression of the phase change to SM identity.

  7. Genome-Wide Identification, Classification, and Expression Analysis of Autophagy-Associated Gene Homologues in Rice (Oryza sativa L.)

    PubMed Central

    Xia, Kuaifei; Liu, Tao; Ouyang, Jie; Wang, Ren; Fan, Tian; Zhang, Mingyong

    2011-01-01

    Autophagy is an intracellular degradation process for recycling macromolecules and organelles. It plays important roles in plant development and in response to nutritional demand, stress, and senescence. Organisms from yeast to plants contain many autophagy-associated genes (ATG). In this study, we found that a total of 33 ATG homologues exist in the rice [Oryza sativa L. (Os)] genome, which were classified into 13 ATG subfamilies. Six of them are alternatively spliced genes. Evolutional analysis showed that expansion of 10 OsATG homologues occurred via segmental duplication events and that the occurrence of these OsATG homologues within each subfamily was asynchronous. The Ka/Ks ratios suggested purifying selection for four duplicated OsATG homologues and positive selection for two. Calculating the dates of the duplication events indicated that all duplication events might have occurred after the origin of the grasses, from 21.43 to 66.77 million years ago. Semi-quantitative RT–PCR analysis and mining the digital expression database of rice showed that all 33 OsATG homologues could be detected in at least one cell type of the various tissues under normal or stress growth conditions, but their expression was tightly regulated. The 10 duplicated genes showed expression divergence. The expression of most OsATG homologues was regulated by at least one treatment, including hormones, abiotic and biotic stresses, and nutrient limitation. The identification of OsATG homologues showing constitutive expression or responses to environmental stimuli provides new insights for in-depth characterization of selected genes of importance in rice. PMID:21795261

  8. Comparative evaluation of three different extraction methods for rice (Oryza sativa L.) genomic DNA.

    PubMed

    Sagi, Naoki; Monma, Kimio; Ibe, Akihiro; Kamata, Kunihiro

    2009-04-01

    Recently, more immediate and precise cultivar-identifying methods targeting the specific and/or introduced gene(s) have been put into practical use for various rice cultivars. However trustworthy and innovative the biotechnological analyses may be, DNA purity and quality do have unpredictable influences upon the identification. Extraction methods of rice DNA have hardly ever been compared in a comprehensive manner. In this study, we investigated extraction characteristics of three methods by using 10 rice cultivars and then examined template availability of rice DNAs thereby extracted. An UV spectrophotometric study with a view toward methods revealed three different facts: The Isoplant II kit method with inhibitor absorption yielded the most DNAs, the Takara kit method with magnetic trapping produced the best DNAs free from contaminative proteins, and the enzymatic digestion method exclusively with enzymatic digestions prepared the best DNAs free from contaminative polysaccharides. Moreover, with a view toward cultivars, an insignificant difference in yield was not entirely bore out, and some difference in cultivar might cause significant difference in yield; however, no significant difference in purity was found among the cultivars used. On the other hand, electrophoretic images of the DNAs from the same cultivars showed considerable differences in quality among the methods. Furthermore, the DNA extracts from certain brands of rice proved really available for cultivar identification by using polymerase chain reaction (PCR) related to sequence-tagged sites. Therefore, this study suggested that these extraction methods may be used as the situation demands and that the DNAs thereby extracted might work successfully even in cultivar-identifying PCRs.

  9. The compact Brachypodium genome conserves centromeric regions of a common ancestor with wheat and rice.

    PubMed

    Qi, Lili; Friebe, Bernd; Wu, Jiajie; Gu, Yongqiang; Qian, Chen; Gill, Bikram S

    2010-11-01

    The evolution of five chromosomes of Brachypodium distachyon from a 12-chromosome ancestor of all grasses by dysploidy raises an interesting question about the fate of redundant centromeres. Three independent but complementary approaches were pursued to study centromeric region homologies among the chromosomes of Brachypodium, wheat, and rice. The genes present in pericentromeres of the basic set of seven chromosomes of wheat and the Triticeae, and the 80 rice centromeric genes spanning the CENH3 binding domain of centromeres 3, 4, 5, 7, and 8 were used as "anchor" markers to identify centromere locations in the B. distachyon chromosomes. A total of 53 B. distachyon bacterial artificial chromosome (BAC) clones anchored by wheat pericentromeric expressed sequence tags (ESTs) were used as probes for BAC-fluorescence in situ hybridization (FISH) analysis of B. distachyon mitotic chromosomes. Integrated sequence alignment and BAC-FISH data were used to determine the approximate positions of active and inactive centromeres in the five B. distachyon chromosomes. The following syntenic relationships of the centromeres for Brachypodium (Bd), rice (R), and wheat (W) were evident: Bd1-R6, Bd2-R5-W1, Bd3-R10, Bd4-R11-W4, and Bd5-R4. Six rice centromeres syntenic to five wheat centromeres were inactive in Brachypodium chromosomes. The conservation of centromere gene synteny among several sets of homologous centromeres of three species indicates that active genes can persist in ancient centromeres with more than 40 million years of shared evolutionary history. Annotation of a BAC contig spanning an inactive centromere in chromosome Bd3 which is syntenic to rice Cen8 and W7 pericentromeres, along with BAC FISH data from inactive centromeres revealed that the centromere inactivation was accompanied by the loss of centromeric retrotransposons and turnover of centromere-specific satellites during Bd chromosome evolution.

  10. Genome wide functional genetics in haploid cells.

    PubMed

    Elling, Ulrich; Penninger, Josef M

    2014-08-01

    Some organisms such as yeast or males of social insects are haploid, i.e. they carry a single set of chromosomes, while haploidy in mammals is exclusively restricted to mature germ cells. A single copy of the genome provides the basis for genetic analyses where any recessive mutation of essential genes will show a clear phenotype due to the absence of a second gene copy. Most prominently, haploidy in yeast has been utilized for recessive genetic screens that have markedly contributed to our understanding of development, basic physiology, and disease. Somatic mammalian cells carry two copies of chromosomes (diploidy) that obscure genetic analysis. Near haploid human leukemic cells however have been developed as a high throughput screening tool. Although deemed impossible, we and others have generated mammalian haploid embryonic stem cells from parthenogenetic mouse embryos. Haploid stem cells open the possibility of combining the power of a haploid genome with pluripotency of embryonic stem cells to uncover fundamental biological processes in defined cell types at a genomic scale. Haploid genetics has thus become a powerful alternative to RNAi or CRISPR based screens. PMID:24950427

  11. Determining protein function and interaction from genome analysis

    DOEpatents

    Eisenberg, David; Marcotte, Edward M.; Thompson, Michael J.; Pellegrini, Matteo; Yeates, Todd O.

    2004-08-03

    A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

  12. Assigning protein functions by comparative genome analysis protein phylogenetic profiles

    DOEpatents

    Pellegrini, Matteo; Marcotte, Edward M.; Thompson, Michael J.; Eisenberg, David; Grothe, Robert; Yeates, Todd O.

    2003-05-13

    A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

  13. Application of Functional Genomics for Bovine Respiratory Disease Diagnostics

    PubMed Central

    Rai, Aswathy N.; Epperson, William B.; Nanduri, Bindu

    2015-01-01

    Bovine respiratory disease (BRD) is the most common economically important disease affecting cattle. For developing accurate diagnostics that can predict disease susceptibility/resistance and stratification, it is necessary to identify the molecular mechanisms that underlie BRD. To study the complex interactions among the bovine host and the multitude of viral and bacterial pathogens, as well as the environmental factors associated with BRD etiology, genome-scale high-throughput functional genomics methods such as microarrays, RNA-seq, and proteomics are helpful. In this review, we summarize the progress made in our understanding of BRD using functional genomics approaches. We also discuss some of the available bioinformatics resources for analyzing high-throughput data, in the context of biological pathways and molecular interactions. Although resources for studying host response to infection are avail-able, the corresponding information is lacking for majority of BRD pathogens, impeding progress in identifying diagnostic signatures for BRD using functional genomics approaches. PMID:26526746

  14. Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement.

    PubMed

    Spindel, J E; Begum, H; Akdemir, D; Collard, B; Redoña, E; Jannink, J-L; McCouch, S

    2016-04-01

    To address the multiple challenges to food security posed by global climate change, population growth and rising incomes, plant breeders are developing new crop varieties that can enhance both agricultural productivity and environmental sustainability. Current breeding practices, however, are unable to keep pace with demand. Genomic selection (GS) is a new technique that helps accelerate the rate of genetic gain in breeding by using whole-genome data to predict the breeding value of offspring. Here, we describe a new GS model that combines RR-BLUP with markers fit as fixed effects selected from the results of a genome-wide-association study (GWAS) on the RR-BLUP training data. We term this model GS + de novo GWAS. In a breeding population of tropical rice, GS + de novo GWAS outperformed six other models for a variety of traits and in multiple environments. On the basis of these results, we propose an extended, two-part breeding design that can be used to efficiently integrate novel variation into elite breeding populations, thus expanding genetic diversity and enhancing the potential for sustainable productivity gains. PMID:26860200

  15. Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu.

    PubMed

    Xia, Kai; Li, Yudong; Sun, Jing; Liang, Xinle

    2016-01-01

    Acetobacter pasteurianus, an acetic acid resistant bacterium belonging to alpha-proteobacteria, has been widely used to produce vinegar in the food industry. To understand the mechanism of its high tolerance to acetic acid and robust ability of oxidizing ethanol to acetic acid (> 12%, w/v), we described the 3.1 Mb complete genome sequence (including 0.28 M plasmid sequence) with a G+C content of 52.4% of A. pasteurianus Ab3, which was isolated from the traditional Chinese rice vinegar (Meiguichu) fermentation process. Automatic annotation of the complete genome revealed 2,786 protein-coding genes and 73 RNA genes. The comparative genome analysis among A. pasteurianus strains revealed that A. pasteurianus Ab3 possesses many unique genes potentially involved in acetic acid resistance mechanisms. In particular, two-component systems or toxin-antitoxin systems may be the signal pathway and modulatory network in A. pasteurianus to cope with acid stress. In addition, the large numbers of unique transport systems may also be related to its acid resistance capacity and cell fitness. Our results provide new clues to understanding the underlying mechanisms of acetic acid resistance in Acetobacter species and guiding industrial strain breeding for vinegar fermentation processes.

  16. Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement

    PubMed Central

    Spindel, J E; Begum, H; Akdemir, D; Collard, B; Redoña, E; Jannink, J-L; McCouch, S

    2016-01-01

    To address the multiple challenges to food security posed by global climate change, population growth and rising incomes, plant breeders are developing new crop varieties that can enhance both agricultural productivity and environmental sustainability. Current breeding practices, however, are unable to keep pace with demand. Genomic selection (GS) is a new technique that helps accelerate the rate of genetic gain in breeding by using whole-genome data to predict the breeding value of offspring. Here, we describe a new GS model that combines RR-BLUP with markers fit as fixed effects selected from the results of a genome-wide-association study (GWAS) on the RR-BLUP training data. We term this model GS + de novo GWAS. In a breeding population of tropical rice, GS + de novo GWAS outperformed six other models for a variety of traits and in multiple environments. On the basis of these results, we propose an extended, two-part breeding design that can be used to efficiently integrate novel variation into elite breeding populations, thus expanding genetic diversity and enhancing the potential for sustainable productivity gains. PMID:26860200

  17. Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu

    PubMed Central

    Xia, Kai; Li, Yudong; Sun, Jing; Liang, Xinle

    2016-01-01

    Acetobacter pasteurianus, an acetic acid resistant bacterium belonging to alpha-proteobacteria, has been widely used to produce vinegar in the food industry. To understand the mechanism of its high tolerance to acetic acid and robust ability of oxidizing ethanol to acetic acid (> 12%, w/v), we described the 3.1 Mb complete genome sequence (including 0.28 M plasmid sequence) with a G+C content of 52.4% of A. pasteurianus Ab3, which was isolated from the traditional Chinese rice vinegar (Meiguichu) fermentation process. Automatic annotation of the complete genome revealed 2,786 protein-coding genes and 73 RNA genes. The comparative genome analysis among A. pasteurianus strains revealed that A. pasteurianus Ab3 possesses many unique genes potentially involved in acetic acid resistance mechanisms. In particular, two-component systems or toxin-antitoxin systems may be the signal pathway and modulatory network in A. pasteurianus to cope with acid stress. In addition, the large numbers of unique transport systems may also be related to its acid resistance capacity and cell fitness. Our results provide new clues to understanding the underlying mechanisms of acetic acid resistance in Acetobacter species and guiding industrial strain breeding for vinegar fermentation processes. PMID:27611790

  18. Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement.

    PubMed

    Spindel, J E; Begum, H; Akdemir, D; Collard, B; Redoña, E; Jannink, J-L; McCouch, S

    2016-04-01

    To address the multiple challenges to food security posed by global climate change, population growth and rising incomes, plant breeders are developing new crop varieties that can enhance both agricultural productivity and environmental sustainability. Current breeding practices, however, are unable to keep pace with demand. Genomic selection (GS) is a new technique that helps accelerate the rate of genetic gain in breeding by using whole-genome data to predict the breeding value of offspring. Here, we describe a new GS model that combines RR-BLUP with markers fit as fixed effects selected from the results of a genome-wide-association study (GWAS) on the RR-BLUP training data. We term this model GS + de novo GWAS. In a breeding population of tropical rice, GS + de novo GWAS outperformed six other models for a variety of traits and in multiple environments. On the basis of these results, we propose an extended, two-part breeding design that can be used to efficiently integrate novel variation into elite breeding populations, thus expanding genetic diversity and enhancing the potential for sustainable productivity gains.

  19. Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu.

    PubMed

    Xia, Kai; Li, Yudong; Sun, Jing; Liang, Xinle

    2016-01-01

    Acetobacter pasteurianus, an acetic acid resistant bacterium belonging to alpha-proteobacteria, has been widely used to produce vinegar in the food industry. To understand the mechanism of its high tolerance to acetic acid and robust ability of oxidizing ethanol to acetic acid (> 12%, w/v), we described the 3.1 Mb complete genome sequence (including 0.28 M plasmid sequence) with a G+C content of 52.4% of A. pasteurianus Ab3, which was isolated from the traditional Chinese rice vinegar (Meiguichu) fermentation process. Automatic annotation of the complete genome revealed 2,786 protein-coding genes and 73 RNA genes. The comparative genome analysis among A. pasteurianus strains revealed that A. pasteurianus Ab3 possesses many unique genes potentially involved in acetic acid resistance mechanisms. In particular, two-component systems or toxin-antitoxin systems may be the signal pathway and modulatory network in A. pasteurianus to cope with acid stress. In addition, the large numbers of unique transport systems may also be related to its acid resistance capacity and cell fitness. Our results provide new clues to understanding the underlying mechanisms of acetic acid resistance in Acetobacter species and guiding industrial strain breeding for vinegar fermentation processes. PMID:27611790

  20. Coordinated international action to accelerate genome-to-phenome with FAANG, The Functional Annotation of Animal Genomes project

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We describe the organization of a nascent international effort - the "Functional Annotation of ANimal Genomes" project - whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species....

  1. Molecular progress on the mapping and cloning of functional genes for blast disease in rice (Oryza sativa L.): current status and future considerations.

    PubMed

    Ashkani, S; Rafii, M Y; Shabanimofrad, M; Ghasemzadeh, A; Ravanfar, S A; Latif, M A

    2016-01-01

    Rice blast disease, which is caused by the fungal pathogen Magnaporthe oryzae, is a recurring problem in all rice-growing regions of the world. The use of resistance (R) genes in rice improvement breeding programmes has been considered to be one of the best options for crop protection and blast management. Alternatively, quantitative resistance conferred by quantitative trait loci (QTLs) is also a valuable resource for the improvement of rice disease resistance. In the past, intensive efforts have been made to identify major R-genes as well as QTLs for blast disease using molecular techniques. A review of bibliographic references shows over 100 blast resistance genes and a larger number of QTLs (∼500) that were mapped to the rice genome. Of the blast resistance genes, identified in different genotypes of rice, ∼22 have been cloned and characterized at the molecular level. In this review, we have summarized the reported rice blast resistance genes and QTLs for utilization in future molecular breeding programmes to introgress high-degree resistance or to pyramid R-genes in commercial cultivars that are susceptible to M. oryzae. The goal of this review is to provide an overview of the significant studies in order to update our understanding of the molecular progress on rice and M. oryzae. This information will assist rice breeders to improve the resistance to rice blast using marker-assisted selection which continues to be a priority for rice-breeding programmes.

  2. Structural characteristics and phylogenetic analysis of the mitochondrial genome of the rice leafroller, Cnaphalocrocis medinalis (Lepidoptera: Crambidae).

    PubMed

    Yin, Yonghua; Qu, Fujuan; Yang, Zhongwu; Zhang, Xiuyue; Yue, Bisong

    2014-02-01

    The rice leafroller, Cnaphalocrocis medinalis, is one of the most important pests on rice and possesses striking flight ability. We have determined the nucleotide sequence of the 15,377 bp of a C. medinalis mitochondrial genome (mtDNA). The mtDNA encodes 37 genes and shows a unique lepidopteran CR-M-I-Q arrangement. Three possible substructures were detected in C. medinalis and some other lepidopteran insects' control region. The findings might be relevant to the regulation of mtDNA replication and transcription. Phylogenetic relationships were reconstructed among 19 families in Lepidoptera so far. Cnaphalocrocis medinalis forms a reciprocal monophyletic group with Ostrinia in clade Crambidae instead of Pyralidae. The topology between Papilionoidea and other superfamilies showed an apparent contradiction with traditional Lepidopteran classification. As a well-known migratory insect, the molecular information contained in C. medinalis mtDNA may provide a further insight into the evolution of mitochondria genes and insect species, and may help to better understanding the energy metabolism of invertebrates.

  3. Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae

    PubMed Central

    Gowda, Malali; Nunes, Cristiano C.; Sailsbery, Joshua; Xue, Minfeng; Chen, Feng; Nelson, Cassie A.; Brown, Douglas E.; Oh, Yeonyee; Meng, Shaowu; Mitchell, Thomas; Hagedorn, Curt H.; Dean, Ralph A.

    2010-01-01

    Small RNAs are well described in higher eukaryotes such as mammals and plants; however, knowledge in simple eukaryotes such as filamentous fungi is limited. In this study, we discovered and characterized methylguanosine-capped and polyadenylated small RNAs (CPA-sRNAs) by using differential RNA selection, full-length cDNA cloning and 454 transcriptome sequencing of the rice blast fungus Magnaporthe oryzae. This fungus causes blast, a devastating disease on rice, the principle food staple for over half the world’s population. CPA-sRNAs mapped primarily to the transcription initiation and termination sites of protein-coding genes and were positively correlated with gene expression, particularly for highly expressed genes including those encoding ribosomal proteins. Numerous CPA-sRNAs also mapped to rRNAs, tRNAs, snRNAs, transposable elements and intergenic regions. Many other 454 sequence reads could not be mapped to the genome; however, inspection revealed evidence for non-template additions and chimeric sequences. CPA-sRNAs were independently confirmed using a high affinity variant of eIF-4E to capture 5′-methylguanosine-capped RNA followed by 3′-RACE sequencing. These results expand the repertoire of small RNAs in filamentous fungi. PMID:20660015

  4. Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study.

    PubMed

    Wang, Quanxiu; Xie, Weibo; Xing, Hongkun; Yan, Ju; Meng, Xiangzhou; Li, Xinglei; Fu, Xiangkui; Xu, Jiuyue; Lian, Xingming; Yu, Sibin; Xing, Yongzhong; Wang, Gongwei

    2015-06-01

    Chlorophyll content is one of the most important physiological traits as it is closely related to leaf photosynthesis and crop yield potential. So far, few genes have been reported to be involved in natural variation of chlorophyll content in rice (Oryza sativa) and the extent of variations explored is very limited. We conducted a genome-wide association study (GWAS) using a diverse worldwide collection of 529 O. sativa accessions. A total of 46 significant association loci were identified. Three F2 mapping populations with parents selected from the association panel were tested for validation of GWAS signals. We clearly demonstrated that Grain number, plant height, and heading date7 (Ghd7) was a major locus for natural variation of chlorophyll content at the heading stage by combining evidence from near-isogenic lines and transgenic plants. The enhanced expression of Ghd7 decreased the chlorophyll content, mainly through down-regulating the expression of genes involved in the biosynthesis of chlorophyll and chloroplast. In addition, Narrow leaf1 (NAL1) corresponded to one significant association region repeatedly detected over two years. We revealed a high degree of polymorphism in the 5' UTR and four non-synonymous SNPs in the coding region of NAL1, and observed diverse effects of the major haplotypes. The loci or candidate genes identified would help to fine-tune and optimize the antenna size of canopies in rice breeding.

  5. Genetic dissection of ozone tolerance in rice (Oryza sativa L.) by a genome-wide association study.

    PubMed

    Ueda, Yoshiaki; Frimpong, Felix; Qi, Yitao; Matthus, Elsa; Wu, Linbo; Höller, Stefanie; Kraska, Thorsten; Frei, Michael

    2015-01-01

    Tropospheric ozone causes various negative effects on plants and affects the yield and quality of agricultural crops. Here, we report a genome-wide association study (GWAS) in rice (Oryza sativa L.) to determine candidate loci associated with ozone tolerance. A diversity panel consisting of 328 accessions representing all subgroups of O. sativa was exposed to ozone stress at 60 nl l(-1) for 7h every day throughout the growth season, or to control conditions. Averaged over all genotypes, ozone significantly affected biomass-related traits (plant height -1.0%, shoot dry weight -15.9%, tiller number -8.3%, grain weight -9.3%, total panicle weight -19.7%, single panicle weight -5.5%) and biochemical/physiological traits (symptom formation, SPAD value -4.4%, foliar lignin content +3.4%). A wide range of genotypic variance in response to ozone stress were observed in all phenotypes. Association mapping based on more than 30 000 single-nucleotide polymorphism (SNP) markers yielded 16 significant markers throughout the genome by applying a significance threshold of P<0.0001. Furthermore, by determining linkage disequilibrium blocks associated with significant SNPs, we gained a total of 195 candidate genes for these traits. The following sequence analysis revealed a number of novel polymorphisms in two candidate genes for the formation of visible leaf symptoms, a RING and an EREBP gene, both of which are involved in cell death and stress defence reactions. This study demonstrated substantial natural variation of responses to ozone in rice and the possibility of using GWAS in elucidating the genetic factors underlying ozone tolerance.

  6. Genetic dissection of ozone tolerance in rice (Oryza sativa L.) by a genome-wide association study

    PubMed Central

    Ueda, Yoshiaki; Frimpong, Felix; Qi, Yitao; Matthus, Elsa; Wu, Linbo; Höller, Stefanie; Kraska, Thorsten; Frei, Michael

    2015-01-01

    Tropospheric ozone causes various negative effects on plants and affects the yield and quality of agricultural crops. Here, we report a genome-wide association study (GWAS) in rice (Oryza sativa L.) to determine candidate loci associated with ozone tolerance. A diversity panel consisting of 328 accessions representing all subgroups of O. sativa was exposed to ozone stress at 60 nl l–1 for 7h every day throughout the growth season, or to control conditions. Averaged over all genotypes, ozone significantly affected biomass-related traits (plant height –1.0%, shoot dry weight –15.9%, tiller number –8.3%, grain weight –9.3%, total panicle weight –19.7%, single panicle weight –5.5%) and biochemical/physiological traits (symptom formation, SPAD value –4.4%, foliar lignin content +3.4%). A wide range of genotypic variance in response to ozone stress were observed in all phenotypes. Association mapping based on more than 30 000 single-nucleotide polymorphism (SNP) markers yielded 16 significant markers throughout the genome by applying a significance threshold of P<0.0001. Furthermore, by determining linkage disequilibrium blocks associated with significant SNPs, we gained a total of 195 candidate genes for these traits. The following sequence analysis revealed a number of novel polymorphisms in two candidate genes for the formation of visible leaf symptoms, a RING and an EREBP gene, both of which are involved in cell death and stress defence reactions. This study demonstrated substantial natural variation of responses to ozone in rice and the possibility of using GWAS in elucidating the genetic factors underlying ozone tolerance. PMID:25371505

  7. Mapping genomic features to functional traits through microbial whole genome sequences.

    PubMed

    Zhang, Wei; Zeng, Erliang; Liu, Dan; Jones, Stuart E; Emrich, Scott

    2014-01-01

    Recently, the utility of trait-based approaches for microbial communities has been identified. Increasing availability of whole genome sequences provide the opportunity to explore the genetic foundations of a variety of functional traits. We proposed a machine learning framework to quantitatively link the genomic features with functional traits. Genes from bacteria genomes belonging to different functional traits were grouped to Cluster of Orthologs (COGs), and were used as features. Then, TF-IDF technique from the text mining domain was applied to transform the data to accommodate the abundance and importance of each COG. After TF-IDF processing, COGs were ranked using feature selection methods to identify their relevance to the functional trait of interest. Extensive experimental results demonstrated that functional trait related genes can be detected using our method. Further, the method has the potential to provide novel biological insights.

  8. Contribution of genomics to the understanding of physiological functions.

    PubMed

    Hocquette, J F; Cassar-Malek, I; Scalbert, A; Guillou, F

    2009-10-01

    Genomics has brought with it a true biological revolution and can be applied to all areas of life sciences. The advent of genomics is thus linked to the development of high-throughput techniques which allows the genome of organisms as a whole to be studied. The first high-throughput techniques to be developed were sequencing methods. These advances will allow new approaches to a variety of problems in biology. For instance, the emerging fields of genomic medicine in humans and genomic selection in livestock are promising. After the sequencing of genomes, genomics has shifted to the study of gene expression and function. This is called the "post-genomic area" by some authors or "functional genomics" by others. The most recent "omics" to be developed are associated with the study of the metabolism (e.g. metabolomics). Integrative "omics" approaches (e.g. nutrigenomics) are based on the association of the omics tools at different levels (DNA, RNA, proteins, metabolites) for a specific objective (here nutrition). In terms of perspectives, it is likely that methods for collecting data will outstrip our capacity to adequately analyse these data. So scientists must develop bioinformatic tools and methods to overcome this difficulty. In addition, high-throughput techniques need to be developed in physiology in order to match the increasing amount of genomic information with true biological data. Finally, there is no doubt that all these new approaches will allow important new genes and novel biological mechanisms to be discovered. Physiological models with invalidated or over-expressed genes will be precious tools to check these new biological discoveries.

  9. Advances in functional genomics for investigating salinity stress tolerance mechanisms in cereals.

    PubMed

    Shelden, Megan C; Roessner, Ute

    2013-01-01

    Abiotic stresses such as low water availability and high salinity are major causes of cereal crop yield losses and significantly impact on sustainability. Wheat and barley are two of the most important cereal crops (after maize and rice) and are grown in increasingly hostile environments with soil salinity and drought both expected to increase this century, reducing the availability of arable land. Barley and wheat are classified as glycophytes (salt-sensitive), yet they are more salt-tolerant than other cereal crops such as rice and so are good models for studying salt tolerance in cereals. The exploitation of genetic variation of phenotypic traits through plant breeding could significantly improve growth of cereals in salinity-affected regions, thus leading to improved crop yields. Genetic variation in phenotypic traits for abiotic stress tolerance have been identified in land races and wild germplasm but the molecular basis of these differences is often difficult to determine due to the complex genetic nature of these species. High-throughput functional genomics technologies, such as transcriptomics, metabolomics, proteomics, and ionomics are powerful tools for investigating the molecular responses of plants to abiotic stress. The advancement of these technologies has allowed for the identification and quantification of transcript/metabolites in specific cell types and/or tissues. Using these new technologies on plants will provide a powerful tool to uncovering genetic traits in more complex species such as wheat and barley and provide novel insights into the molecular mechanisms of salinity stress tolerance. PMID:23717314

  10. Functional genomics of lactic acid bacteria: from food to health.

    PubMed

    Douillard, François P; de Vos, Willem M

    2014-08-29

    Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health.

  11. Functional genomics of lactic acid bacteria: from food to health

    PubMed Central

    2014-01-01

    Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health. PMID:25186768

  12. Functional Analysis of the Human Genome:. Study of Genetic Disease

    NASA Astrophysics Data System (ADS)

    Tsui, Lap-Chee

    2003-04-01

    I will divide my remarks into 3 parts. First, I will give a brief summary of the Human Genome Project. Second, I will describe our work on human chromosome 7 to illustrate how we could contribute to the Project and disease research. Third, I would like to bring across the argument that study of genetic disease is an integral component of the Human Genome Project. In particular, I will use cystic fibrosis as an example to elaborate why I consider disease study is a part of functional genomics.

  13. Exploring the post-genomic world: differing explanatory and manipulatory functions of post-genomic sciences

    PubMed Central

    Holmes, Christina; Carlson, Siobhan M.; McDonald, Fiona; Jones, Mavis; Graham, Janice

    2016-01-01

    Richard Lewontin proposed that the ability of a scientific field to create a narrative for public understanding garners it social relevance. This article applies Lewontin's conceptual framework of the functions of science (manipulatory and explanatory) to compare and explain the current differences in perceived societal relevance of genetics/genomics and proteomics. We provide three examples to illustrate the social relevance and strong cultural narrative of genetics/genomics for which no counterpart exists for proteomics. We argue that the major difference between genetics/genomics and proteomics is that genomics has a strong explanatory function, due to the strong cultural narrative of heredity. Based on qualitative interviews and observations of proteomics conferences, we suggest that the nature of proteins, lack of public understanding, and theoretical complexity exacerbates this difference for proteomics. Lewontin's framework suggests that social scientists may find that omics sciences affect social relations in different ways than past analyses of genetics. PMID:27134568

  14. Colibri: a functional data base for the Escherichia coli genome.

    PubMed Central

    Médigue, C; Viari, A; Hénaut, A; Danchin, A

    1993-01-01

    Several data libraries have been created to organize all the data obtained worldwide about the Escherichia coli genome. Because the known data now amount to more than 40% of the whole genome sequence, it has become necessary to organize the data in such a way that appropriate procedures can associate knowledge produced by experiments about each gene to its position on the chromosome and its relation to other relevant genes, for example. In addition, global properties of genes, affected by the introduction of new entries, should be present as appropriate description fields. A data base, implemented on Macintosh by using the data base management system 4th Dimension, is described. It is constructed around a core constituted by known contigs of E. coli sequences and links data collected in general libraries (unmodified) to data associated with evolving knowledge (with modifiable fields). Biologically significant results obtained through the coupling of appropriate procedures (learning or statistical data analysis) are presented. The data base is available through a 4th Dimension runtime and through FTP on Internet. It has been regularly updated and will be systematically linked to other E. coli data bases (M. Kroger, R. Wahl, G. Schachtel, and P. Rice, Nucleic Acids Res. 20(Suppl.):2119-2144, 1992; K. E. Rudd, W. Miller, C. Werner, J. Ostell, C. Tolstoshev, and S. G. Satterfield, Nucleic Acids Res. 19:637-647, 1991) in the near future. Images PMID:8246843

  15. Genome-wide Association Mapping of Quantitative Trait Loci (QTLs) for Contents of Eight Elements in Brown Rice (Oryza sativa L.).

    PubMed

    Nawaz, Zarqa; Kakar, Kaleem U; Li, Xiao-bai; Li, Shan; Zhang, Bin; Shou, Hui-xia; Shu, Qing-yao

    2015-09-16

    An association mapping of quantitative trait loci (QTLs) regulating the concentrations of eight elements in brown rice (Oryza sativa L.) was performed using USDA mini-core subset cultivated in two different environments. In addition, correlation between the grain elemental concentrations was also studied. A total of 60 marker loci associated with 8 grain elemental concentrations were identified, and these loci were clustered into 37 genomic regions. Twenty new QTLs were found to be associated with important elements such as Zn, Fe, and P, along with others. Fe concentration was associated with the greatest number of markers in two environments. In addition, several important elemental/metal transporter genes were identified in a few mapped regions. Positive correlation was observed within all grain elemental concentrations. In summary, the results provide insight into the genetic basis of rice grain element accumulation and may help in the identification of genes associated with the accumulation of Zn, Fe, and other essential elements in rice.

  16. Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice.

    PubMed

    Bessho-Uehara, Kanako; Wang, Diane R; Furuta, Tomoyuki; Minami, Anzu; Nagai, Keisuke; Gamuyao, Rico; Asano, Kenji; Angeles-Shim, Rosalyn B; Shimizu, Yoshihiro; Ayano, Madoka; Komeda, Norio; Doi, Kazuyuki; Miura, Kotaro; Toda, Yosuke; Kinoshita, Toshinori; Okuda, Satohiro; Higashiyama, Tetsuya; Nomoto, Mika; Tada, Yasuomi; Shinohara, Hidefumi; Matsubayashi, Yoshikatsu; Greenberg, Anthony; Wu, Jianzhong; Yasui, Hideshi; Yoshimura, Atsushi; Mori, Hitoshi; McCouch, Susan R; Ashikari, Motoyuki

    2016-08-01

    Domestication of crops based on artificial selection has contributed numerous beneficial traits for agriculture. Wild characteristics such as red pericarp and seed shattering were lost in both Asian (Oryza sativa) and African (Oryza glaberrima) cultivated rice species as a result of human selection on common genes. Awnedness, in contrast, is a trait that has been lost in both cultivated species due to selection on different sets of genes. In a previous report, we revealed that at least three loci regulate awn development in rice; however, the molecular mechanism underlying awnlessness remains unknown. Here we isolate and characterize a previously unidentified EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family member named REGULATOR OF AWN ELONGATION 2 (RAE2) and identify one of its requisite processing enzymes, SUBTILISIN-LIKE PROTEASE 1 (SLP1). The RAE2 precursor is specifically cleaved by SLP1 in the rice spikelet, where the mature RAE2 peptide subsequently induces awn elongation. Analysis of RAE2 sequence diversity identified a highly variable GC-rich region harboring multiple independent mutations underlying protein-length variation that disrupt the function of the RAE2 protein and condition the awnless phenotype in Asian rice. Cultivated African rice, on the other hand, retained the functional RAE2 allele despite its awnless phenotype. Our findings illuminate the molecular function of RAE2 in awn development and shed light on the independent domestication histories of Asian and African cultivated rice. PMID:27466405

  17. Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice

    PubMed Central

    Bessho-Uehara, Kanako; Wang, Diane R.; Furuta, Tomoyuki; Minami, Anzu; Nagai, Keisuke; Gamuyao, Rico; Asano, Kenji; Angeles-Shim, Rosalyn B.; Shimizu, Yoshihiro; Ayano, Madoka; Komeda, Norio; Doi, Kazuyuki; Miura, Kotaro; Toda, Yosuke; Kinoshita, Toshinori; Okuda, Satohiro; Higashiyama, Tetsuya; Nomoto, Mika; Tada, Yasuomi; Shinohara, Hidefumi; Matsubayashi, Yoshikatsu; Greenberg, Anthony; Wu, Jianzhong; Yasui, Hideshi; Yoshimura, Atsushi; Mori, Hitoshi; McCouch, Susan R.; Ashikari, Motoyuki

    2016-01-01

    Domestication of crops based on artificial selection has contributed numerous beneficial traits for agriculture. Wild characteristics such as red pericarp and seed shattering were lost in both Asian (Oryza sativa) and African (Oryza glaberrima) cultivated rice species as a result of human selection on common genes. Awnedness, in contrast, is a trait that has been lost in both cultivated species due to selection on different sets of genes. In a previous report, we revealed that at least three loci regulate awn development in rice; however, the molecular mechanism underlying awnlessness remains unknown. Here we isolate and characterize a previously unidentified EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family member named REGULATOR OF AWN ELONGATION 2 (RAE2) and identify one of its requisite processing enzymes, SUBTILISIN-LIKE PROTEASE 1 (SLP1). The RAE2 precursor is specifically cleaved by SLP1 in the rice spikelet, where the mature RAE2 peptide subsequently induces awn elongation. Analysis of RAE2 sequence diversity identified a highly variable GC-rich region harboring multiple independent mutations underlying protein-length variation that disrupt the function of the RAE2 protein and condition the awnless phenotype in Asian rice. Cultivated African rice, on the other hand, retained the functional RAE2 allele despite its awnless phenotype. Our findings illuminate the molecular function of RAE2 in awn development and shed light on the independent domestication histories of Asian and African cultivated rice. PMID:27466405

  18. Genomic selection & association mapping in rice: effect of trait genetic architecture, training population composition, marker number & statistical model on accuracy of rice genomic selection in elite, tropical rice breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its ef...

  19. Effects of Germinated Brown Rice Addition on the Flavor and Functionality of Yogurt.

    PubMed

    Kim, Mi-Hye; Ahn, Sung-Il; Lim, Chan-Mook; Jhoo, Jin-Woo; Kim, Gur-Yoo

    2016-01-01

    This study aimed to investigate the functional and physicochemical properties of yogurt, supplemented with germinated brown rice (GBR) containing γ-aminobutyric acid (GABA), during storage. GBR was produced by soaking brown rice at 30℃, and saccharified germinated brown rice (SGBR) was produced by treating brown rice with α- and β-amylase for 1 h, at 80℃ and 60℃, respectively. Yogurt was manufactured using a commercial starter (YC-X11, CHR. Hansen, Denmark) at 37℃ for 12 h. The fatty acids and GABA contents were analyzed using GC and HPLC, respectively. The fatty acids in the cereal samples consisted of oleic, linoleic, and palmitic acid. The portion of oleic acid was the highest, at 35.65% in GBR, and 32.16% in SGBR. During germination, the oleic acid content increased, whereas linolenic and palmitic acid contents from GBR tended to decrease. Although the portion of saturated fatty acids, such as stearic and myristic acid, decreased significantly (p<0.05), that of unsaturated fatty acids, such as oleic and linoleic acid, increased with an increase in supplementation of BR, GBR, or SGBR in the yogurt. The yogurt, supplemented with cereal samples, showed a tendency of an increase in the concentration of GABA with an increase in the supplementation of the cereal samples. However, yogurt supplemented with GBR showed the highest concentration of GABA, regardless of the supplementation of the cereal samples. These results indicated that yogurt supplemented with BR, GBR, or SGBR could be a promising dairy product. PMID:27621692

  20. Effects of Germinated Brown Rice Addition on the Flavor and Functionality of Yogurt

    PubMed Central

    2016-01-01

    This study aimed to investigate the functional and physicochemical properties of yogurt, supplemented with germinated brown rice (GBR) containing γ-aminobutyric acid (GABA), during storage. GBR was produced by soaking brown rice at 30℃, and saccharified germinated brown rice (SGBR) was produced by treating brown rice with α- and β-amylase for 1 h, at 80℃ and 60℃, respectively. Yogurt was manufactured using a commercial starter (YC-X11, CHR. Hansen, Denmark) at 37℃ for 12 h. The fatty acids and GABA contents were analyzed using GC and HPLC, respectively. The fatty acids in the cereal samples consisted of oleic, linoleic, and palmitic acid. The portion of oleic acid was the highest, at 35.65% in GBR, and 32.16% in SGBR. During germination, the oleic acid content increased, whereas linolenic and palmitic acid contents from GBR tended to decrease. Although the portion of saturated fatty acids, such as stearic and myristic acid, decreased significantly (p<0.05), that of unsaturated fatty acids, such as oleic and linoleic acid, increased with an increase in supplementation of BR, GBR, or SGBR in the yogurt. The yogurt, supplemented with cereal samples, showed a tendency of an increase in the concentration of GABA with an increase in the supplementation of the cereal samples. However, yogurt supplemented with GBR showed the highest concentration of GABA, regardless of the supplementation of the cereal samples. These results indicated that yogurt supplemented with BR, GBR, or SGBR could be a promising dairy product. PMID:27621692

  1. Human-Mediated Emergence as a Weed and Invasive Radiation in the Wild of the CD Genome Allotetraploid Rice Species (Oryza, Poaceae) in the Neotropics

    PubMed Central

    Second, Gérard; Rouhan, Germinal

    2008-01-01

    Background The genus Oryza is being used as a model in plant genomic studies although there are several issues still to be resolved regarding the spatio-temporal evolution of this ancient genus. Particularly contentious is whether undated transoceanic natural dispersal or recent human interference has been the principal agent determining its present distribution and differentiation. In this context, we studied the origin and distribution history of the allotetraploid CD rice genome. It is endemic to the Neotropics but the genus is thought to have originated in the Paleotropics, and there is relatively little genetic divergence between some orthologous sequences of the C genome component and their Old World counterparts. Methodology/Principal Findings Because of its allotetraploidy, there are several potential pitfalls in trying to date the formation of the CD genome using molecular data and this could lead to erroneous estimates. Therefore, we rather chose to rely on historical evidence to determine whether or not the CD genome was present in the Neotropics before the arrival of Columbus. We searched early collections of herbarium specimens and studied the reports of explorers of the tropical Americas for references to rice. In spite of numerous collectors traveling inland and collecting Oryza, plants determined as CD genome species were not observed away from cultivated rice fields until 1869. Various arguments suggest that they only consisted of weedy forms until that time. Conclusions/Significance The spatio-temporal distribution of herbarium collections fits a simple biogeographical scenario for the emergence in cultivated rice fields followed by radiation in the wild of the CD genome in the Neotropics during the last four centuries. This probably occurred from species introduced to the Americas by humans and we found no evidence that the CD genome pre-existed in the Old World. We therefore propose a new evolutionary hypothesis for such a recent origin of the

  2. A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Functional annotations of large plant genome projects mostly provide information on gene function and gene families based on the presence of protein domains and gene homology, but not necessarily in association with gene expression or metabolic and regulatory networks. These additional annotations a...

  3. Genome of Cnaphalocrocis medinalis Granulovirus, the First Crambidae-Infecting Betabaculovirus Isolated from Rice Leaffolder to Sequenced

    PubMed Central

    Han, Guangjie; Xu, Jian; Liu, Qin; Li, Chuanming; Xu, Hongxing; Lu, Zhongxian

    2016-01-01

    Cnaphalocrocis medinalis is a major pest of rice in South and South-East Asia. Insecticides are the major means farmers use for management. A naturally occurring baculovirus, C. medinalis granulovirus (CnmeGV), has been isolated from the larvae and this has the potential for use as microbial agent. Here, we described the complete genome sequence of CnmeGV and compared it to other baculovirus genomes. The genome of CnmeGV is 112,060 base pairs in length, has a G+C content of 35.2%. It contains 133 putative open reading frames (ORFs) of at least 150 nucleotides. A hundred and one (101) of these ORFs are homologous to other baculovirus genes including 37 baculovirus core genes. Thirty-two (32) ORFs are unique to CnmeGV with no homologues detected in the GeneBank and 53 tandem repeats (TRs) with sequence length from 25 to 551 nt intersperse throughout the genome of CnmeGV. Six (6) homologous regions (hrs) were identified interspersed throughout the genome. Hr2 contains 11 imperfect palindromes and a high content of AT sequence (about 73%). The unique ORF28 contains a coiled-coil region and a zinc finger-like domain of 4–50 residues specialized by two C2C2 zinc finger motifs that putatively bound two atoms of zinc. ORF21 encoding a chit-1 protein suggesting a horizontal gene transfer from alphabaculovirus. The putative protein presents two carbohydrate-binding module family 14 (CBM_14) domains rather than other homologues detected from betabaculovirus that only contains one chit-binding region. Gene synteny maps showed the colinearity of sequenced betabaculovirus. Phylogenetic analysis indicated that CnmeGV grouped in the betabaculovirus, with a close relation to AdorGV. The cladogram obtained in this work grouped the 17 complete GV genomes in one monophyletic clade. CnmeGV represents a new crambidae host-isolated virus species from the genus Betabaculovirus and is most closely relative of AdorGV. The analyses and information derived from this study will provide a

  4. Genome of Cnaphalocrocis medinalis Granulovirus, the First Crambidae-Infecting Betabaculovirus Isolated from Rice Leaffolder to Sequenced.

    PubMed

    Han, Guangjie; Xu, Jian; Liu, Qin; Li, Chuanming; Xu, Hongxing; Lu, Zhongxian

    2016-01-01

    Cnaphalocrocis medinalis is a major pest of rice in South and South-East Asia. Insecticides are the major means farmers use for management. A naturally occurring baculovirus, C. medinalis granulovirus (CnmeGV), has been isolated from the larvae and this has the potential for use as microbial agent. Here, we described the complete genome sequence of CnmeGV and compared it to other baculovirus genomes. The genome of CnmeGV is 112,060 base pairs in length, has a G+C content of 35.2%. It contains 133 putative open reading frames (ORFs) of at least 150 nucleotides. A hundred and one (101) of these ORFs are homologous to other baculovirus genes including 37 baculovirus core genes. Thirty-two (32) ORFs are unique to CnmeGV with no homologues detected in the GeneBank and 53 tandem repeats (TRs) with sequence length from 25 to 551 nt intersperse throughout the genome of CnmeGV. Six (6) homologous regions (hrs) were identified interspersed throughout the genome. Hr2 contains 11 imperfect palindromes and a high content of AT sequence (about 73%). The unique ORF28 contains a coiled-coil region and a zinc finger-like domain of 4-50 residues specialized by two C2C2 zinc finger motifs that putatively bound two atoms of zinc. ORF21 encoding a chit-1 protein suggesting a horizontal gene transfer from alphabaculovirus. The putative protein presents two carbohydrate-binding module family 14 (CBM_14) domains rather than other homologues detected from betabaculovirus that only contains one chit-binding region. Gene synteny maps showed the colinearity of sequenced betabaculovirus. Phylogenetic analysis indicated that CnmeGV grouped in the betabaculovirus, with a close relation to AdorGV. The cladogram obtained in this work grouped the 17 complete GV genomes in one monophyletic clade. CnmeGV represents a new crambidae host-isolated virus species from the genus Betabaculovirus and is most closely relative of AdorGV. The analyses and information derived from this study will provide a

  5. Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function.

    PubMed

    Prunier, Julien; Verta, Jukka-Pekka; MacKay, John J

    2016-01-01

    Conifers have been understudied at the genomic level despite their worldwide ecological and economic importance but the situation is rapidly changing with the development of next generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In just a few years, genomes of 20-24 gigabases have been sequenced for several conifers, with several others expected in the near future. Biological insights have resulted from recent sequencing initiatives as well as genetic mapping, gene expression profiling and gene discovery research over nearly two decades. We review the knowledge arising from conifer genomics research emphasizing genome evolution and the genomic basis of adaptation, and outline emerging questions and knowledge gaps. We discuss future directions in three areas with potential inputs from NGS technologies: the evolutionary impacts of adaptation in conifers based on the adaptation-by-speciation model; the contributions of genetic variability of gene expression in adaptation; and the development of a broader understanding of genetic diversity and its impacts on genome function. These research directions promise to sustain research aimed at addressing the emerging challenges of adaptation that face conifer trees.

  6. Functional genomics identifies drivers of medulloblastoma dissemination.

    PubMed

    Mumert, Michael; Dubuc, Adrian; Wu, Xiaochong; Northcott, Paul A; Chin, Steven S; Pedone, Carolyn A; Taylor, Michael D; Fults, Daniel W

    2012-10-01

    Medulloblastomas are malignant brain tumors that arise in the cerebellum in children and disseminate via the cerebrospinal fluid to the leptomeningeal spaces of the brain and spinal cord. Challenged by the poor prognosis for patients with metastatic dissemination, pediatric oncologists have developed aggressive treatment protocols, combining surgery, craniospinal radiation, and high-dose chemotherapy, that often cause disabling neurotoxic effects in long-term survivors. Insights into the genetic control of medulloblastoma dissemination have come from transposon insertion mutagenesis studies. Mobilizing the Sleeping Beauty transposon in cerebellar neural progenitor cells caused widespread dissemination of typically nonmetastatic medulloblastomas in Patched(+/-) mice, in which Shh signaling is hyperactive. Candidate metastasis genes were identified by sequencing the insertion sites and then mapping these sequences back to the mouse genome. To determine whether genes located at transposon insertion sites directly caused medulloblastomas to disseminate, we overexpressed candidate genes in Nestin(+) neural progenitors in the cerebella of mice by retroviral transfer in combination with Shh. We show here that ectopic expression of Eras, Lhx1, Ccrk, and Akt shifted the in vivo growth characteristics of Shh-induced medulloblastomas from a localized pattern to a disseminated pattern in which tumor cells seeded the leptomeningeal spaces of the brain and spinal cord. PMID:22875024

  7. Recombination between defective tombusvirus RNAs generates functional hybrid genomes

    SciTech Connect

    White, K.A.; Morris, T.J.

    1994-04-26

    The tombusviruses represent a group of small icosahedral plant viruses that contain monopartite positive-sense RNA genomes. Tombusviruses are able to generate small replicating deletion mutants of their genomes (i.e., defective interfering RNAs) during infections via RNA recombination and/or rearrangement. To further study the process of RNA recombination and to determine whether tombusviruses were capable of trans-recombination, protoplasts were coinoculated with in vitro-generated transcripts of a nonreplicating 3{prime}-truncated genomic RNA of cucumber necrosis tombusvirus and either replicative or replication-defective DI RNAs of tomato bushy stunt tombusvirus. After 48-hr incubation, two dominant replicative chimeric recombinant viral RNA populations were detected that contained various large contiguous 5{prime} segments of the cucumber necrosis tombusvirus genomic RNA fused to 3{prime}-terminal regions of the tomato bushy stunt tombusvirus defective interfering RNA. Some of the larger chimeric recombinants formed in protoplasts were able to systemically infect plants and induce wild-type symptoms. In addition, a functional chimeric genome was generated in planta after direct coinoculation of whole plants with the defective RNA components. These results indicate that (i) RNA recombination can occur relatively efficiently in single-cell infections, (ii) trans-recombination can occur with nonreplicating viral RNA components, and (iii) functional chimeric genomes can be generated via recombination. Possible mechanisms for the formation of the recombinants are proposed, and evolutionary implications are discussed.

  8. Chymotrypsin protease inhibitor gene family in rice: Genomic organization and evidence for the presence of a bidirectional promoter shared between two chymotrypsin protease inhibitor genes.

    PubMed

    Singh, Amanjot; Sahi, Chandan; Grover, Anil

    2009-01-01

    Protease inhibitors play important roles in stress and developmental responses of plants. Rice genome contains 17 putative members in chymotrypsin protease inhibitor (ranging in size from 7.21 to 11.9 kDa) gene family with different predicted localization sites. Full-length cDNA encoding for a putative subtilisin-chymotrypsin protease inhibitor (OCPI2) was obtained from Pusa basmati 1 (indica) rice seedlings. 620 bp-long OCPI2 cDNA contained 219 bp-long ORF, coding for 72 amino acid-long 7.7 kDa subtilisin-chymotrypsin protease inhibitor (CPI) cytoplasmic protein. Expression analysis by semi-quantitative RT-PCR analysis showed that OCPI2 transcript is induced by varied stresses including salt, ABA, low temperature and mechanical injury in both root and shoot tissues of the seedlings. Transgenic rice plants produced with OCPI2 promoter-gus reporter gene showed that this promoter directs high salt- and ABA-regulated expression of the GUS gene. Another CPI gene (OCPI1) upstream to OCPI2 (with 1126 bp distance between the transcription initiation sites of the two genes; transcription in the reverse orientation) was noted in genome sequence of rice genome. A vector that had GFP and GUS reporter genes in opposite orientations driven by 1881 bp intergenic sequence between the OCPI2 and OCPI1 (encompassing the region between the translation initiation sites of the two genes) was constructed and shot in onion epidermal cells by particle bombardment. Expression of both GFP and GUS from the same epidermal cell showed that this sequence represents a bidirectional promoter. Examples illustrating gene pairs showing co-expression of two divergent neighboring genes sharing a bidirectional promoter have recently been extensively worked out in yeast and human systems. We provide an example of a gene pair constituted of two homologous genes showing co-expression governed by a bidirectional promoter in rice. PMID:18952157

  9. Whole Mitochondrial Genome Sequencing and Re-Examination of a Cytoplasmic Male Sterility-Associated Gene in Boro-Taichung-Type Cytoplasmic Male Sterile Rice

    PubMed Central

    Kazama, Tomohiko; Toriyama, Kinya

    2016-01-01

    Nuclear genome substitutions between subspecies can lead to cytoplasmic male sterility (CMS) through incompatibility between nuclear and mitochondrial genomes. Boro-Taichung (BT)-type CMS rice was obtained by substituting the nuclear genome of Oryza sativa subsp. indica cultivar Chinsurah Boro II with that of Oryza sativa subsp. japonica cultivar Taichung 65. In BT-type CMS rice, the mitochondrial gene orf79 is associated with male sterility. A complete sequence of the Boro-type mitochondrial genome responsible for BT-type CMS has not been determined to date. Here, we used pyrosequencing to construct the Boro-type mitochondrial genome. The contiguous sequences were assembled into five circular DNA molecules, four of which could be connected into a single circle. The two resulting subgenomic circles were unable to form a reliable master circle, as recombination between them was scarcely detected. We also found an unequal abundance of DNA molecules for the two loci of atp6. These results indicate the presence of multi-partite DNA molecules in the Boro-type mitochondrial genome. Expression patterns were investigated for Boro-type mitochondria-specific orfs, which were not found in the mitochondria from the standard japonica cultivar Nipponbare. Restorer of fertility 1 (RF1)-dependent RNA processing has been observed in orf79-containing RNA but was not detected in other Boro-type mitochondria-specific orfs, supporting the conclusion that orf79 is a unique CMS-associated gene in Boro-type mitochondria. PMID:27414645

  10. Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites.

    PubMed

    Norton, Gareth J; Douglas, Alex; Lahner, Brett; Yakubova, Elena; Guerinot, Mary Lou; Pinson, Shannon R M; Tarpley, Lee; Eizenga, Georgia C; McGrath, Steve P; Zhao, Fang-Jie; Islam, M Rafiqul; Islam, Shofiqul; Duan, Guilan; Zhu, Yongguan; Salt, David E; Meharg, Andrew A; Price, Adam H

    2014-01-01

    The mineral concentrations in cereals are important for human health, especially for individuals who consume a cereal subsistence diet. A number of elements, such as zinc, are required within the diet, while some elements are toxic to humans, for example arsenic. In this study we carry out genome-wide association (GWA) mapping of grain concentrations of arsenic, copper, molybdenum and zinc in brown rice using an established rice diversity panel of ∼ 300 accessions and 36.9 k single nucleotide polymorphisms (SNPs). The study was performed across five environments: one field site in Bangladesh, one in China and two in the US, with one of the US sites repeated over two years. GWA mapping on the whole dataset and on separate subpopulations of rice revealed a large number of loci significantly associated with variation in grain arsenic, copper, molybdenum and zinc. Seventeen of these loci were detected in data obtained from grain cultivated in more than one field location, and six co-localise with previously identified quantitative trait loci. Additionally, a number of candidate genes for the uptake or transport of these elements were located near significantly associated SNPs (within 200 kb, the estimated global linkage disequilibrium previously employed in this rice panel). This analysis highlights a number of genomic regions and candidate genes for further analysis as well as the challenges faced when mapping environmentally-variable traits in a highly genetically structured diversity panel. PMID:24586963

  11. Mobilized retrotransposon Tos17 of rice by alien DNA introgression transposes into genes and causes structural and methylation alterations of a flanking genomic region.

    PubMed

    Han, F P; Liu, Z L; Tan, M; Hao, S; Fedak, G; Liu, B

    2004-01-01

    Tos17 is a copia-like endogenous retrotransposon of rice, which can be activated by various stresses such as tissue culture and alien DNA introgression. To confirm element mobilization by introgression and to study possible structural and epigenetic effects of Tos17 insertion on its target sequences, we isolated all flanking regions of Tos17 in an introgressed rice line (Tong35) that contains minute amount of genomic DNA from wild rice (Zizania latifolia). It was found that there has been apparent but limited mobilization of Tos17 in this introgression line, as being reflected by increased but stable copy number of the element in progeny of the line. Three of the five activated copies of the element have transposed into genes. Based on sequence analysis and Southern blot hybridization with several double-enzyme digests, no structural change in Tos17 could be inferred in the introgression line. Cytosine methylation status at all seven CCGG sites within Tos17 was also identical between the introgression line and its rice parent (Matsumae)-all sites being heavily methylated. In contrast, changes in structure and cytosine methylation patterns were detected in one of the three low-copy genomic regions that flank newly transposed Tos17, and all changes are stably inherited through selfed generations. PMID:15703040

  12. Genome Wide Association Mapping of Grain Arsenic, Copper, Molybdenum and Zinc in Rice (Oryza sativa L.) Grown at Four International Field Sites

    PubMed Central

    Norton, Gareth J.; Douglas, Alex; Lahner, Brett; Yakubova, Elena; Guerinot, Mary Lou; Pinson, Shannon R. M.; Tarpley, Lee; Eizenga, Georgia C.; McGrath, Steve P.; Zhao, Fang-Jie; Islam, M. Rafiqul; Islam, Shofiqul; Duan, Guilan; Zhu, Yongguan; Salt, David E.; Meharg, Andrew A.; Price, Adam H.

    2014-01-01

    The mineral concentrations in cereals are important for human health, especially for individuals who consume a cereal subsistence diet. A number of elements, such as zinc, are required within the diet, while some elements are toxic to humans, for example arsenic. In this study we carry out genome-wide association (GWA) mapping of grain concentrations of arsenic, copper, molybdenum and zinc in brown rice using an established rice diversity panel of ∼300 accessions and 36.9 k single nucleotide polymorphisms (SNPs). The study was performed across five environments: one field site in Bangladesh, one in China and two in the US, with one of the US sites repeated over two years. GWA mapping on the whole dataset and on separate subpopulations of rice revealed a large number of loci significantly associated with variation in grain arsenic, copper, molybdenum and zinc. Seventeen of these loci were detected in data obtained from grain cultivated in more than one field location, and six co-localise with previously identified quantitative trait loci. Additionally, a number of candidate genes for the uptake or transport of these elements were located near significantly associated SNPs (within 200 kb, the estimated global linkage disequilibrium previously employed in this rice panel). This analysis highlights a number of genomic regions and candidate genes for further analysis as well as the challenges faced when mapping environmentally-variable traits in a highly genetically structured diversity panel. PMID:24586963

  13. New insights into the genetic basis of natural chilling and cold shock tolerance in rice by genome-wide association analysis.

    PubMed

    Lv, Yan; Guo, Zilong; Li, Xiaokai; Ye, Haiyan; Li, Xianghua; Xiong, Lizhong

    2016-03-01

    In order to understand cold adaptability and explore additional genetic resources for the cold tolerance improvement of rice, we investigated the genetic variation of 529 rice accessions under natural chilling and cold shock stress conditions at the seedling stage using genome-wide association studies; a total of 132 loci were identified. Among them, 12 loci were common for both chilling and cold shock tolerance, suggesting that rice has a distinct and overlapping genetic response and adaptation to the two stresses. Haplotype analysis of a known gene OsMYB2, which is involved in cold tolerance, revealed indica-japonica differentiation and latitude tendency for the haplotypes of this gene. By checking the subpopulation and geographical distribution of accessions with tolerance or sensitivity under these two stress conditions, we found that the chilling tolerance group, which mainly consisted of japonica accessions, has a wider latitudinal distribution than the chilling sensitivity group. We conclude that the genetic basis of natural chilling stress tolerance in rice is distinct from that of cold shock stress frequently used for low-temperature treatment in the laboratory and the cold adaptability of rice is associated with the subpopulation and latitudinal distribution.

  14. Functional characterization of a rice de novo DNA methyltransferase, OsDRM2, expressed in Escherichia coli and yeast

    SciTech Connect

    Pang, Jinsong; Dong, Mingyue; Li, Ning; Zhao, Yanli; Liu, Bao

    2013-03-01

    Highlights: ► A rice de novo DNA methyltransferase OsDRM2 was cloned. ► In vitro methylation activity of OsDRM2 was characterized with Escherichia coli. ► Assays of OsDRM2 in vivo methylation were done with Saccharomyces cerevisiae. ► OsDRM2 methylation activity is not preferential to any type of cytosine context. ► The activity of OsDRM2 is independent of RdDM pathway. - Abstract: DNA methylation of cytosine nucleotides is an important epigenetic modification that occurs in most eukaryotic organisms and is established and maintained by various DNA methyltransferases together with their co-factors. There are two major categories of DNA methyltransferases: de novo and maintenance. Here, we report the isolation and functional characterization of a de novo methyltransferase, named OsDRM2, from rice (Oryza sativa L.). The full-length coding region of OsDRM2 was cloned and transformed into Escherichia coli and Saccharomyces cerevisiae. Both of these organisms expressed the OsDRM2 protein, which exhibited stochastic de novo methylation activity in vitro at CG, CHG, and CHH di- and tri-nucleotide patterns. Two lines of evidence demonstrated the de novo activity of OsDRM2: (1) a 5′-CCGG-3′ containing DNA fragment that had been pre-treated with OsDRM2 protein expressed in E. coli was protected from digestion by the CG-methylation-sensitive isoschizomer HpaII; (2) methylation-sensitive amplified polymorphism (MSAP) analysis of S. cerevisiae genomic DNA from transformants that had been introduced with OsDRM2 revealed CG and CHG methylation levels of 3.92–9.12%, and 2.88–6.93%, respectively, whereas the mock control S. cerevisiae DNA did not exhibit cytosine methylation. These results were further supported by bisulfite sequencing of the 18S rRNA and EAF5 genes of the transformed S. cerevisiae, which exhibited different DNA methylation patterns, which were observed in the genomic DNA. Our findings establish that OsDRM2 is an active de novo DNA

  15. Unstable transmission of rice chromosomes without functional centromeric repeats in asexual propagation.

    PubMed

    Gong, Zhiyun; Yu, Hengxiu; Huang, Jian; Yi, Chuandeng; Gu, Minghong

    2009-01-01

    During sexual propagation of primary trisomic 8, chromosome 8 breaks in some rice plants, resulting in a telotrisomic (2n+.8S) line. In this study, we observed that the extra short arm of chromosome 8 (.8S) can easily be lost in the telotrisomic, and we determined by fluorescence in-situ hybridization (FISH) analysis that the centromeric region of the extra .8S did not contain the rice centromeric satellite repeat (CentO) and centromere-specific retrotransposon (CRR); however, the extra .8S contained part of the CentO and CRR sequences in the initially preserved telotrisomic line. We confirmed by real-time quantitative PCR (RQ-PCR) analysis that the original functional centromere of the extra .8S was lost. Using both FISH and RQ-PCR, the breakage point of the extra .8S was found within the BAC clone a0070J19 sequence containing the first part of the short arm near the centromere region of chromosome 8 but without any CentO or CRR sequences. However, part of the DNA sequence within the a0070J19 BAC clone played a role in the new functional centromere, contributing to the morphological variations by asexually propagated plants of rice telotrisomics in the field. We conclude that CENH3, a key element in the eukaryotic kinetochore, may not always bind properly with the new functional centromere, resulting in loss of the extra .8S during mitosis and the chromosome numbers returning to diploid levels in subsequent generations.

  16. Functional food red yeast rice (RYR) for metabolic syndrome amelioration: a review on pros and cons.

    PubMed

    Patel, Seema

    2016-05-01

    Red yeast rice (RYR), the fermentation product of mold Monascus purpureus has been an integral part of Oriental food and traditional Chinese medicine, long before the discovery of their medicinal roles. With the identification of bioactive components as polyketide pigments (statins), and unsaturated fatty acids, RYR has gained a nutraceutical status. Hypercholesterolemic effect of this fermented compound has been validated and monacolin K has been recognized as the pivotal component in cholesterol alleviation. Functional similarity with commercial drug lovastatin sans the side effects has catapulted its popularity in other parts of the world as well. Apart from the hypotensive role, ameliorative benefits of RYR as anti-inflammatory, antidiabetic, anticancer and osteogenic agent have emerged, fueling intense research on it. Mechanistic studies have revealed their interaction with functional agents like coenzyme Q10, astaxanthin, vitamin D, folic acid, policosanol, and berberine. On the other hand, concurrence of mycotoxin citrinin and variable content of statin has marred its integration in mainstream medication. In this disputable scenario, evaluation of the scopes and lacunae to overcome seems to contribute to an eminent area of healthcare. Red yeast rice (RYR), the rice-based fermentation product of mold Monascus purpureus is a functional food. Its bioactive component monacolin K acts like synthetic drug lovastatin, without the severe side effects of the latter. RYR has been validated to lower cholesterol, control high blood pressure; confer anti-flammation, hypoglycaemic, anticancer and osteogenic properties. However, dose inconsistency and co-occurrence of toxin citrinin hampers its dietary supplementation prospect. Further research might facilitate development of RYR as a nutraceutical.

  17. Functional food red yeast rice (RYR) for metabolic syndrome amelioration: a review on pros and cons.

    PubMed

    Patel, Seema

    2016-05-01

    Red yeast rice (RYR), the fermentation product of mold Monascus purpureus has been an integral part of Oriental food and traditional Chinese medicine, long before the discovery of their medicinal roles. With the identification of bioactive components as polyketide pigments (statins), and unsaturated fatty acids, RYR has gained a nutraceutical status. Hypercholesterolemic effect of this fermented compound has been validated and monacolin K has been recognized as the pivotal component in cholesterol alleviation. Functional similarity with commercial drug lovastatin sans the side effects has catapulted its popularity in other parts of the world as well. Apart from the hypotensive role, ameliorative benefits of RYR as anti-inflammatory, antidiabetic, anticancer and osteogenic agent have emerged, fueling intense research on it. Mechanistic studies have revealed their interaction with functional agents like coenzyme Q10, astaxanthin, vitamin D, folic acid, policosanol, and berberine. On the other hand, concurrence of mycotoxin citrinin and variable content of statin has marred its integration in mainstream medication. In this disputable scenario, evaluation of the scopes and lacunae to overcome seems to contribute to an eminent area of healthcare. Red yeast rice (RYR), the rice-based fermentation product of mold Monascus purpureus is a functional food. Its bioactive component monacolin K acts like synthetic drug lovastatin, without the severe side effects of the latter. RYR has been validated to lower cholesterol, control high blood pressure; confer anti-flammation, hypoglycaemic, anticancer and osteogenic properties. However, dose inconsistency and co-occurrence of toxin citrinin hampers its dietary supplementation prospect. Further research might facilitate development of RYR as a nutraceutical. PMID:27038957

  18. Functional genomics of tomato: opportunities and challenges in post-genome NGS era.

    PubMed

    Kumar, Rahul; Khurana, Ashima

    2014-12-01

    The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger's and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-a-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other 'omics' tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies.

  19. Functional genomics of tomato: opportunities and challenges in post-genome NGS era.

    PubMed

    Kumar, Rahul; Khurana, Ashima

    2014-12-01

    The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger's and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-a-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other 'omics' tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies. PMID:25431420

  20. Environmental Response and Genomic Regions Correlated with Rice Root Growth and Yield under Drought in the OryzaSNP Panel across Multiple Study Systems.

    PubMed

    Wade, Len J; Bartolome, Violeta; Mauleon, Ramil; Vasant, Vivek Deshmuck; Prabakar, Sumeet Mankar; Chelliah, Muthukumar; Kameoka, Emi; Nagendra, K; Reddy, K R Kamalnath; Varma, C Mohan Kumar; Patil, Kalmeshwar Gouda; Shrestha, Roshi; Al-Shugeairy, Zaniab; Al-Ogaidi, Faez; Munasinghe, Mayuri; Gowda, Veeresh; Semon, Mande; Suralta, Roel R; Shenoy, Vinay; Vadez, Vincent; Serraj, Rachid; Shashidhar, H E; Yamauchi, Akira; Babu, Ranganathan Chandra; Price, Adam; McNally, Kenneth L; Henry, Amelia

    2015-01-01

    The rapid progress in rice genotyping must be matched by advances in phenotyping. A better understanding of genetic variation in rice for drought response, root traits, and practical methods for studying them are needed. In this study, the OryzaSNP set (20 diverse genotypes that have been genotyped for SNP markers) was phenotyped in a range of field and container studies to study the diversity of rice root growth and response to drought. Of the root traits measured across more than 20 root experiments, root dry weight showed the most stable genotypic performance across studies. The environment (E) component had the strongest effect on yield and root traits. We identified genomic regions correlated with root dry weight, percent deep roots, maximum root depth, and grain yield based on a correlation analysis with the phenotypes and aus, indica, or japonica introgression regions using the SNP data. Two genomic regions were identified as hot spots in which root traits and grain yield were co-located; on chromosome 1 (39.7-40.7 Mb) and on chromosome 8 (20.3-21.9 Mb). Across experiments, the soil type/ growth medium showed more correlations with plant growth than the container dimensions. Although the correlations among studies and genetic co-location of root traits from a range of study systems points to their potential utility to represent responses in field studies, the best correlations were observed when the two setups had some similar properties. Due to the co-location of the identified genomic regions (from introgression block analysis) with QTL for a number of previously reported root and drought traits, these regions are good candidates for detailed characterization to contribute to understanding rice improvement for response to drought. This study also highlights the utility of characterizing a small set of 20 genotypes for root growth, drought response, and related genomic regions. PMID:25909711

  1. Environmental Response and Genomic Regions Correlated with Rice Root Growth and Yield under Drought in the OryzaSNP Panel across Multiple Study Systems

    PubMed Central

    Wade, Len J.; Bartolome, Violeta; Mauleon, Ramil; Vasant, Vivek Deshmuck; Prabakar, Sumeet Mankar; Chelliah, Muthukumar; Kameoka, Emi; Nagendra, K.; Reddy, K. R. Kamalnath; Varma, C. Mohan Kumar; Patil, Kalmeshwar Gouda; Shrestha, Roshi; Al-Shugeairy, Zaniab; Al-Ogaidi, Faez; Munasinghe, Mayuri; Gowda, Veeresh; Semon, Mande; Suralta, Roel R.; Shenoy, Vinay; Vadez, Vincent; Serraj, Rachid; Shashidhar, H. E.; Yamauchi, Akira; Babu, Ranganathan Chandra; Price, Adam; McNally, Kenneth L.; Henry, Amelia

    2015-01-01

    The rapid progress in rice genotyping must be matched by advances in phenotyping. A better understanding of genetic variation in rice for drought response, root traits, and practical methods for studying them are needed. In this study, the OryzaSNP set (20 diverse genotypes that have been genotyped for SNP markers) was phenotyped in a range of field and container studies to study the diversity of rice root growth and response to drought. Of the root traits measured across more than 20 root experiments, root dry weight showed the most stable genotypic performance across studies. The environment (E) component had the strongest effect on yield and root traits. We identified genomic regions correlated with root dry weight, percent deep roots, maximum root depth, and grain yield based on a correlation analysis with the phenotypes and aus, indica, or japonica introgression regions using the SNP data. Two genomic regions were identified as hot spots in which root traits and grain yield were co-located; on chromosome 1 (39.7–40.7 Mb) and on chromosome 8 (20.3–21.9 Mb). Across experiments, the soil type/ growth medium showed more correlations with plant growth than the container dimensions. Although the correlations among studies and genetic co-location of root traits from a range of study systems points to their potential utility to represent responses in field studies, the best correlations were observed when the two setups had some similar properties. Due to the co-location of the identified genomic regions (from introgression block analysis) with QTL for a number of previously reported root and drought traits, these regions are good candidates for detailed characterization to contribute to understanding rice improvement for response to drought. This study also highlights the utility of characterizing a small set of 20 genotypes for root growth, drought response, and related genomic regions. PMID:25909711

  2. Environmental Response and Genomic Regions Correlated with Rice Root Growth and Yield under Drought in the OryzaSNP Panel across Multiple Study Systems.

    PubMed

    Wade, Len J; Bartolome, Violeta; Mauleon, Ramil; Vasant, Vivek Deshmuck; Prabakar, Sumeet Mankar; Chelliah, Muthukumar; Kameoka, Emi; Nagendra, K; Reddy, K R Kamalnath; Varma, C Mohan Kumar; Patil, Kalmeshwar Gouda; Shrestha, Roshi; Al-Shugeairy, Zaniab; Al-Ogaidi, Faez; Munasinghe, Mayuri; Gowda, Veeresh; Semon, Mande; Suralta, Roel R; Shenoy, Vinay; Vadez, Vincent; Serraj, Rachid; Shashidhar, H E; Yamauchi, Akira; Babu, Ranganathan Chandra; Price, Adam; McNally, Kenneth L; Henry, Amelia

    2015-01-01

    The rapid progress in rice genotyping must be matched by advances in phenotyping. A better understanding of genetic variation in rice for drought response, root traits, and practical methods for studying them are needed. In this study, the OryzaSNP set (20 diverse genotypes that have been genotyped for SNP markers) was phenotyped in a range of field and container studies to study the diversity of rice root growth and response to drought. Of the root traits measured across more than 20 root experiments, root dry weight showed the most stable genotypic performance across studies. The environment (E) component had the strongest effect on yield and root traits. We identified genomic regions correlated with root dry weight, percent deep roots, maximum root depth, and grain yield based on a correlation analysis with the phenotypes and aus, indica, or japonica introgression regions using the SNP data. Two genomic regions were identified as hot spots in which root traits and grain yield were co-located; on chromosome 1 (39.7-40.7 Mb) and on chromosome 8 (20.3-21.9 Mb). Across experiments, the soil type/ growth medium showed more correlations with plant growth than the container dimensions. Although the correlations among studies and genetic co-location of root traits from a range of study systems points to their potential utility to represent responses in field studies, the best correlations were observed when the two setups had some similar properties. Due to the co-location of the identified genomic regions (from introgression block analysis) with QTL for a number of previously reported root and drought traits, these regions are good candidates for detailed characterization to contribute to understanding rice improvement for response to drought. This study also highlights the utility of characterizing a small set of 20 genotypes for root growth, drought response, and related genomic regions.

  3. Genomic Functionalization: The Next Revolution In Biology

    SciTech Connect

    Anderson, Peter; Schoeniger, Joseph S.; Imbro, Paula M.

    2014-07-01

    We have implemented a ligand-alignment algorithm into our developed computational pipeline for identifying specificity-determining features (SDFs) in protein-ligand complexes. Given a set of protein-ligand complex structures, the algorithm aligns the complexes by ligand rather than by the C -RMSD or standard approach, providing a single reference frame for extracting SDFs. We anticipate that this ligand-alignment capability will be highly useful for protein function prediction. We already have a database containing > 20 K ligand-protein complex crystal structures taken from the Protein Data Bank. By aligning these proteins to single reference frames using ligand alignment, we can submit the complexes to our pipeline for SDF extraction. The SDFs derived from this training procedure can be used as thumbprints that are hallmarks of individual enzyme classes. These SDF thumbprints may then serve as guides to the prediction of function of new unknown proteins.

  4. An Italian functional genomic resource for Medicago truncatula

    PubMed Central

    Porceddu, Andrea; Panara, Francesco; Calderini, Ornella; Molinari, Lorna; Taviani, Paola; Lanfaloni, Luisa; Scotti, Carla; Carelli, Maria; Scaramelli, Laura; Bruschi, Gianluca; Cosson, Viviane; Ratet, Pascal; de Larembergue, Henri; Duc, Gerard; Piano, Efisio; Arcioni, Sergio

    2008-01-01

    Background Medicago truncatula is a model species for legumes. Its functional genomics have been considerably boosted in recent years due to initiatives based both in Europe and US. Collections of mutants are becoming increasingly available and this will help unravel the genetic control of important traits for many species of legumes. Findings Our report is on the production of three complementary mutant collections of the model species Medicago truncatula produced in Italy in the frame of a national genomic initiative. Well established strategies were used: Tnt1 mutagenesis, TILLING and activation tagging. Both forward and reverse genetics screenings proved the efficiency of the mutagenesis approaches adopted, enabling the isolation of interesting mutants which are in course of characterization. We anticipate that the reported collections will be complementary to the recently established functional genomics tools developed for Medicago truncatula both in Europe and in the United States. PMID:19077311

  5. Effect of low temperature plasma on the functional properties of basmati rice flour.

    PubMed

    Thirumdas, Rohit; Deshmukh, R R; Annapure, U S

    2016-06-01

    The present study deals with the application of low temperature plasma on basmati rice flour and its effect on functional properties such as gel hydrations properties, flour hydration properties, gelatinization temperatures and antioxidant properties. The water holding capacity and water binding capacity were observed to be increased with increase in plasma power and time of treatment as the air plasma is known to make the surface more hydrophilic. XRD analysis revealed there is no significance difference in the crystalline structure after the plasma treatment. DSC shows a decrease in peak temperatures (Tp) after the treatment. Hot paste viscosities were observed to be decease from 692 to 591 BU was corresponded to decrease in peak temperature. The total polyphenolic content and reducing power was observed to be increased. The effects of plasma treatment on functional groups of polyphenols were observed by changes in absorption intensities using FTIR. This study demonstrates that the low temperature plasma treatmentis capable of improving the functional properties of basmati rice.

  6. Effect of low temperature plasma on the functional properties of basmati rice flour.

    PubMed

    Thirumdas, Rohit; Deshmukh, R R; Annapure, U S

    2016-06-01

    The present study deals with the application of low temperature plasma on basmati rice flour and its effect on functional properties such as gel hydrations properties, flour hydration properties, gelatinization temperatures and antioxidant properties. The water holding capacity and water binding capacity were observed to be increased with increase in plasma power and time of treatment as the air plasma is known to make the surface more hydrophilic. XRD analysis revealed there is no significance difference in the crystalline structure after the plasma treatment. DSC shows a decrease in peak temperatures (Tp) after the treatment. Hot paste viscosities were observed to be decease from 692 to 591 BU was corresponded to decrease in peak temperature. The total polyphenolic content and reducing power was observed to be increased. The effects of plasma treatment on functional groups of polyphenols were observed by changes in absorption intensities using FTIR. This study demonstrates that the low temperature plasma treatmentis capable of improving the functional properties of basmati rice. PMID:27478230

  7. Structural and functional properties of alkali-treated high-amylose rice starch.

    PubMed

    Cai, Jinwen; Yang, Yang; Man, Jianmin; Huang, Jun; Wang, Zhifeng; Zhang, Changquan; Gu, Minghong; Liu, Qiaoquan; Wei, Cunxu

    2014-02-15

    Native starches were isolated from mature grains of high-amylose transgenic rice TRS and its wild-type rice TQ and treated with 0.1% and 0.4% NaOH for 7 and 14 days at 35 °C. Alkali-treated starches were characterised for structural and functional properties using various physical methods. The 0.1% NaOH treatment had no significant effect on structural and functional properties of starches except that it markedly increased the hydrolysis of starch by amylolytic enzymes. The 0.4% NaOH treatment resulted in some changes in structural and functional properties of starches. The alkali treatment affected granule morphology and decreased the electron density between crystalline and amorphous lamellae of starch. The effect of alkali on the crystalline structure including long- and short-range ordered structure was not pronounced. Compared with control starch, alkali-treated TRS starches had lower amylose content, higher onset and peak gelatinisation temperatures, and faster hydrolysis of starch by HCl and amylolytic enzymes.

  8. Functional genomics of Buchnera and the ecology of aphid hosts.

    PubMed

    Moran, Nancy A; Degnan, Patrick H

    2006-04-01

    In many animal groups, mutualistic bacterial symbionts play a central role in host ecology, by provisioning rare nutrients and thus enabling specialization on restricted diets. Among such symbionts, genomic studies are most advanced for Buchnera, the obligate symbiont of aphids, which feed on phloem sap. The contents of the highly reduced Buchnera genomes have verified its role in aphid nutrition. Comparisons of Buchnera gene sets indicate ongoing, irreversible gene losses that are expected to affect aphid nutritional needs. Furthermore, almost all regulatory genes have been eliminated, raising the question of whether and how gene expression responds to environmental change. Microarray studies on genome-wide expression indicate that Buchnera has evolved some constitutive changes in gene expression: homologues of heat stress genes have elevated transcript levels in Buchnera (relative to other bacteria) even in the absence of stress. Additionally, the microarray results indicate that responses to heat stress and to amino acid availability are both few and modest. Observed responses are consistent with control by the few ancestral regulators retained in the genome. Initial studies on the role of host genes in mediating the symbiosis reveal distinctive expression patterns in host cells harbouring Buchnera. In the near future, a complete genome of pea aphid will accelerate progress in understanding the functional integration of aphid and Buchnera genomes. Although information for other insect symbioses is relatively limited, studies on symbionts of carpenter ants and tsetse flies indicate many similarities to Buchnera. PMID:16626452

  9. Functional properties and structural characterization of rice δ1-pyrroline-5-carboxylate reductase

    DOE PAGES

    Forlani, Giuseppe; Bertazzini, Michele; Zarattini, Marco; Funck, Dietmar; Ruszkowski, Milosz; Nocek, Bogusław

    2015-07-28

    The majority of plant species accumulate high intracellular levels of proline to cope with hyperosmotic stress conditions. Proline synthesis from glutamate is tightly regulated at both the transcriptional and the translational levels, yet little is known about the mechanisms for post-translational regulation of the enzymatic activities involved. The gene coding in rice (Oryza sativa L.) for δ1-pyrroline-5-carboxylate (P5C) reductase, the enzyme that catalyzes the second and final step in this pathway, was isolated and expressed in Escherichia coli. The structural and functional properties of the affinity-purified protein were characterized. As for most species, rice P5C reductase was able to usemore » in vitro either NADH or NADPH as the electron donor. However, strikingly different effects of cations and anions were found depending on the pyridine nucleotide used, namely inhibition of NADH-dependent activity and stimulation of NADPH-dependent activity. Moreover, physiological concentrations of proline and NADP+ were strongly inhibitory for the NADH-dependent reaction, whereas the NADPH-dependent activity was mildly affected. Our results suggest that only NADPH may be used in vivo and that stress-dependent variations in ion homeostasis and NADPH/NADP+ ratio could modulate enzyme activity, being functional in promoting proline accumulation and potentially also adjusting NADPH consumption during the defense against hyperosmotic stress. The apparent molecular weight of the native protein observed in size exclusion chromatography indicated a high oligomerization state. We also report the first crystal structure of a plant P5C reductase at 3.40-Å resolution, showing a decameric quaternary assembly. It was possible to identify dynamic structural differences among rice, human, and bacterial enzymes.« less

  10. Functional properties and structural characterization of rice δ1-pyrroline-5-carboxylate reductase

    PubMed Central

    Forlani, Giuseppe; Bertazzini, Michele; Zarattini, Marco; Funck, Dietmar; Ruszkowski, Milosz; Nocek, Bogusław

    2015-01-01

    The majority of plant species accumulate high intracellular levels of proline to cope with hyperosmotic stress conditions. Proline synthesis from glutamate is tightly regulated at both the transcriptional and the translational levels, yet little is known about the mechanisms for post-translational regulation of the enzymatic activities involved. The gene coding in rice (Oryza sativa L.) for δ1-pyrroline-5-carboxylate (P5C) reductase, the enzyme that catalyzes the second and final step in this pathway, was isolated and expressed in Escherichia coli. The structural and functional properties of the affinity-purified protein were characterized. As for most species, rice P5C reductase was able to use in vitro either NADH or NADPH as the electron donor. However, strikingly different effects of cations and anions were found depending on the pyridine nucleotide used, namely inhibition of NADH-dependent activity and stimulation of NADPH-dependent activity. Moreover, physiological concentrations of proline and NADP+ were strongly inhibitory for the NADH-dependent reaction, whereas the NADPH-dependent activity was mildly affected. Our results suggest that only NADPH may be used in vivo and that stress-dependent variations in ion homeostasis and NADPH/NADP+ ratio could modulate enzyme activity, being functional in promoting proline accumulation and potentially also adjusting NADPH consumption during the defense against hyperosmotic stress. The apparent molecular weight of the native protein observed in size exclusion chromatography indicated a high oligomerization state. We also report the first crystal structure of a plant P5C reductase at 3.40-Å resolution, showing a decameric quaternary assembly. Based on the structure, it was possible to identify dynamic structural differences among rice, human, and bacterial enzymes. PMID:26284087

  11. Comparative proteomic study and functional analysis of translationally controlled tumor protein in rice roots under Hg2+ stress.

    PubMed

    Wang, Feijuan; Shang, Yongshen; Yang, Ling; Zhu, Cheng

    2012-01-01

    So far, very little is known about mercury stress-induced intercellular metabolic changes in rice roots at the proteome level. To investigate the response of rice roots to mercury stress, changes in protein expression in rice roots were analyzed using a comparative proteomics approach. Six-leaf stage rice seedlings were treated with 50 micromol/L HgCl2 for 3 hr; 29 protein spots showed a significant changes in abundance under stress when compared with the Hg2+ -tolerant rice mutant and wild type (Zhonghua 11). Furthermore, all these protein spots were identified by mass spectrometry to match 27 diverse protein species. The identified proteins were involved in several processes, including stress response, redox homeostasis, signal transduction, regulation and metabolism; some were found to be cellular structure proteins and a few were unknown. Among the up-regulated proteins, OsTCTP (translationally controlled tumor protein) was chosen to perform hetereologous expression in yeast which was presumed to participate in the Hg2+ tolerance of rice, providing evidence for its role in alleviating Hg2+ damage. Among the many tests, we found that OsTCTP-overexpressed yeast strains were more resistant to Hg2+ than wild-type yeast. Thus, we propose that OsTCTP contributes to Hg2+ resistance. Here we present, for the first time, the functional characterization of OsTCTP in connection with Hg2+ stress in plants.

  12. Genomic Prediction of Biological Shape: Elliptic Fourier Analysis and Kernel Partial Least Squares (PLS) Regression Applied to Grain Shape Prediction in Rice (Oryza sativa L.)

    PubMed Central

    Iwata, Hiroyoshi; Ebana, Kaworu; Uga, Yusaku; Hayashi, Takeshi

    2015-01-01

    Shape is an important morphological characteristic both in animals and plants. In the present study, we examined a method for predicting biological contour shapes based on genome-wide marker polymorphisms. The method is expected to contribute to the acceleration of genetic improvement of biological shape via genomic selection. Grain shape variation observed in rice (Oryza sativa L.) germplasms was delineated using elliptic Fourier descriptors (EFDs), and was predicted based on genome-wide single nucleotide polymorphism (SNP) genotypes. We applied four methods including kernel PLS (KPLS) regression for building a prediction model of grain shape, and compared the accuracy of the methods via cross-validation. We analyzed multiple datasets that differed in marker density and sample size. Datasets with larger sample size and higher marker density showed higher accuracy. Among the four methods, KPLS showed the highest accuracy. Although KPLS and ridge regression (RR) had equivalent accuracy in a single dataset, the result suggested the potential of KPLS for the prediction of high-dimensional EFDs. Ordinary PLS, however, was less accurate than RR in all datasets, suggesting that the use of a non-linear kernel was necessary for accurate prediction using the PLS method. Rice grain shape can be predicted accurately based on genome-wide SNP genotypes. The proposed method is expected to be useful for genomic selection in biological shape. PMID:25825876

  13. Functional annotation from the genome sequence of the giant panda.

    PubMed

    Huo, Tong; Zhang, Yinjie; Lin, Jianping

    2012-08-01

    The giant panda is one of the most critically endangered species due to the fragmentation and loss of its habitat. Studying the functions of proteins in this animal, especially specific trait-related proteins, is therefore necessary to protect the species. In this work, the functions of these proteins were investigated using the genome sequence of the giant panda. Data on 21,001 proteins and their functions were stored in the Giant Panda Protein Database, in which the proteins were divided into two groups: 20,179 proteins whose functions can be predicted by GeneScan formed the known-function group, whereas 822 proteins whose functions cannot be predicted by GeneScan comprised the unknown-function group. For the known-function group, we further classified the proteins by molecular function, biological process, cellular component, and tissue specificity. For the unknown-function group, we developed a strategy in which the proteins were filtered by cross-Blast to identify panda-specific proteins under the assumption that proteins related to the panda-specific traits in the unknown-function group exist. After this filtering procedure, we identified 32 proteins (2 of which are membrane proteins) specific to the giant panda genome as compared against the dog and horse genomes. Based on their amino acid sequences, these 32 proteins were further analyzed by functional classification using SVM-Prot, motif prediction using MyHits, and interacting protein prediction using the Database of Interacting Proteins. Nineteen proteins were predicted to be zinc-binding proteins, thus affecting the activities of nucleic acids. The 32 panda-specific proteins will be further investigated by structural and functional analysis.

  14. The rice OsSAG12-2 gene codes for a functional protease that negatively regulates stress-induced cell death.

    PubMed

    Singh, Subaran; Singh, Anupriya; Nandi, Ashis Kumar

    2016-09-01

    Senescence is the final stage of plant development. Although expression of most of the genes is suppressed during senescence, a set of genes referred as senescence-associated genes (SAGs) is induced. Arabidopsis thaliana SAG12 (AtSAG12) is one such gene that has been mostly studied for its strict association with senescence. AtSAG12 encodes a papain-like cysteine protease, expressed predominantly in senescence-associated vacuoles. Rice genome contains multiple AtSAG12 homologues (OsSAGs). OsSAG12-1, the closest structural homologue of AtSAG12, is a negative regulator of developmental and stress-induced cell death. Proteolytic activity has not been established for any SAG12 homologues in vitro. Here, we report that OsSAG12-2, the second structural homologue of AtSAG12 from rice, codes for a functional proteolytic enzyme. The recombinant OsSAG12-2 protein produced in Escherichia coli undergoes autolysis to generate a functional protease. The matured OsSAG12-2 protein shows 27 percent trypsin-equivalent proteolytic activity on azocasein substrate. Dark-induced senescence activates OsSAG12-2 expression. Down-regulation of OsSAG12-2 in the transgenic artificial miRNA lines results in enhanced salt- and UV-induced cell death, even though it does not affect cell viability in the stress-free condition. Our results show that OsSAG12-2 codes for a functional protease that negatively regulates stress-induced cell death in rice. PMID:27581936

  15. SRY-related genes in the genome of the rice field eel (Monopterus albus)

    PubMed Central

    Zhou, Rongjia; Cheng, Hanhua; Zhang, Quiyang; Guo, Yiqing; Cooper, Richard K; Tiersch, Terrence R

    2002-01-01

    The mammalian sex determining gene, SRY, is the founding member of the new growing family of Sox (SRY-like HMG-box gene) genes. Sox genes encode transcription factors with diverse roles in development, and a few of them are involved in sex determination and differentiation. We report here the existence of Sox genes in the rice field eel, Monopterus albus, and DNA sequence information of the HMG box region of five Sox genes. The Sox1, Sox4 and Sox14 genes do not have introns in the HMG box region. The Sox9 gene and Sox17 gene, which each have an intron in the conserved region, show strong identity at the amino acid level with the corresponding genes of mammals and chickens. Similar structure and identity of the Sox9 and Sox17 genes among mammals, chickens and fish suggest that these genes have evolutionarily conserved roles, potentially including sex determination and differentiation. PMID:11929629

  16. Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data.

    PubMed

    Lohse, Marc; Nagel, Axel; Herter, Thomas; May, Patrick; Schroda, Michael; Zrenner, Rita; Tohge, Takayuki; Fernie, Alisdair R; Stitt, Mark; Usadel, Björn

    2014-05-01

    Next-generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable to functional genomics analyses. The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences. It uses the MapMan 'BIN' ontology, which is tailored for functional annotation of plant 'omics' data. The classification procedure performs parallel sequence searches against reference databases, compiles the results and computes the most likely MapMan BINs for each query. In the current version, the pipeline relies on manually curated reference classifications originating from the three reference organisms (Arabidopsis, Chlamydomonas, rice), various other plant species that have a reviewed SwissProt annotation, and more than 2000 protein domain and family profiles at InterPro, CDD and KOG. Functional annotations predicted by Mercator achieve accuracies above 90% when benchmarked against manual annotation. In addition to mapping files for direct use in the visualization software MapMan, Mercator provides graphical overview charts, detailed annotation information in a convenient web browser interface and a MapMan-to-GO translation table to export results as GO terms. Mercator is available free of charge via http://mapman.gabipd.org/web/guest/app/Mercator.

  17. Rice ( Oryza) hemoglobins

    PubMed Central

    Arredondo-Peter, Raúl; Moran, Jose F.; Sarath, Gautam

    2014-01-01

    Hemoglobins (Hbs) corresponding to non-symbiotic (nsHb) and truncated (tHb) Hbs have been identified in rice ( Oryza). This review discusses the major findings from the current studies on rice Hbs. At the molecular level, a family of the nshb genes, consisting of hb1, hb2, hb3, hb4 and hb5, and a single copy of the thb gene exist in Oryza sativa var. indica and O. sativa var. japonica, Hb transcripts coexist in rice organs and Hb polypeptides exist in rice embryonic and vegetative organs and in the cytoplasm of differentiating cells. At the structural level, the crystal structure of rice Hb1 has been elucidated, and the structures of the other rice Hbs have been modeled. Kinetic analysis indicated that rice Hb1 and 2, and possibly rice Hb3 and 4, exhibit a very high affinity for O 2, whereas rice Hb5 and tHb possibly exhibit a low to moderate affinity for O 2. Based on the accumulated information on the properties of rice Hbs and data from the analysis of other plant and non-plant Hbs, it is likely that Hbs play a variety of roles in rice organs, including O 2-transport, O 2-sensing, NO-scavenging and redox-signaling. From an evolutionary perspective, an outline for the evolution of rice Hbs is available. Rice nshb and thb genes vertically evolved through different lineages, rice nsHbs evolved into clade I and clade II lineages and rice nshbs and thbs evolved under the effect of neutral selection. This review also reveals lacunae in our ability to completely understand rice Hbs. Primary lacunae are the absence of experimental information about the precise functions of rice Hbs, the properties of modeled rice Hbs and the cis-elements and trans-acting factors that regulate the expression of rice hb genes, and the partial understanding of the evolution of rice Hbs. PMID:25653837

  18. Rice ( Oryza) hemoglobins.

    PubMed

    Arredondo-Peter, Raúl; Moran, Jose F; Sarath, Gautam

    2014-01-01

    Hemoglobins (Hbs) corresponding to non-symbiotic (nsHb) and truncated (tHb) Hbs have been identified in rice ( Oryza). This review discusses the major findings from the current studies on rice Hbs. At the molecular level, a family of the nshb genes, consisting of hb1, hb2, hb3, hb4 and hb5, and a single copy of the thb gene exist in Oryza sativa var. indica and O. sativa var. japonica, Hb transcripts coexist in rice organs and Hb polypeptides exist in rice embryonic and vegetative organs and in the cytoplasm of differentiating cells. At the structural level, the crystal structure of rice Hb1 has been elucidated, and the structures of the other rice Hbs have been modeled. Kinetic analysis indicated that rice Hb1 and 2, and possibly rice Hb3 and 4, exhibit a very high affinity for O 2, whereas rice Hb5 and tHb possibly exhibit a low to moderate affinity for O 2. Based on the accumulated information on the properties of rice Hbs and data from the analysis of other plant and non-plant Hbs, it is likely that Hbs play a variety of roles in rice organs, including O 2-transport, O 2-sensing, NO-scavenging and redox-signaling. From an evolutionary perspective, an outline for the evolution of rice Hbs is available. Rice nshb and thb genes vertically evolved through different lineages, rice nsHbs evolved into clade I and clade II lineages and rice nshbs and thbs evolved under the effect of neutral selection. This review also reveals lacunae in our ability to completely understand rice Hbs. Primary lacunae are the absence of experimental information about the precise functions of rice Hbs, the properties of modeled rice Hbs and the cis-elements and trans-acting factors that regulate the expression of rice hb genes, and the partial understanding of the evolution of rice Hbs.

  19. Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data

    PubMed Central

    Zhang, Jianwei; Chen, Ling-Ling; Sun, Shuai; Kudrna, Dave; Copetti, Dario; Li, Weiming; Mu, Ting; Jiao, Wen-Biao; Xing, Feng; Lee, Seunghee; Talag, Jayson; Song, Jia-Ming; Du, Bogu; Xie, Weibo; Luo, Meizhong; Maldonado, Carlos Ernesto; Goicoechea, Jose Luis; Xiong, Lizhong; Wu, Changyin; Xing, Yongzhong; Zhou, Dao-xiu; Yu, Sibin; Zhao, Yu; Wang, Gongwei; Yu, Yeisoo; Luo, Yijie; Hurtado, Beatriz Elena Padilla; Danowitz, Ann; Wing, Rod A.; Zhang, Qifa

    2016-01-01

    Over the past 30 years, we have performed many fundamental studies on two Oryza sativa subsp. indica varieties, Zhenshan 97 (ZS97) and Minghui 63 (MH63). To improve the resolution of many of these investigations, we generated two reference-quality reference genome assemblies using the most advanced sequencing technologies. Using PacBio SMRT technology, we produced over 108 (ZS97) and 174 (MH63) Gb of raw sequence data from 166 (ZS97) and 209 (MH63) pools of BAC clones, and generated ~97 (ZS97) and ~74 (MH63) Gb of paired-end whole-genome shotgun (WGS) sequence data with Illumina sequencing technology. With these data, we successfully assembled two platinum standard reference genomes that have been publicly released. Here we provide the full sets of raw data used to generate these two reference genome assemblies. These data sets can be used to test new programs for better genome assembly and annotation, aid in the discovery of new insights into genome structure, function, and evolution, and help to provide essential support to biological research in general. PMID:27622467

  20. Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data.

    PubMed

    Zhang, Jianwei; Chen, Ling-Ling; Sun, Shuai; Kudrna, Dave; Copetti, Dario; Li, Weiming; Mu, Ting; Jiao, Wen-Biao; Xing, Feng; Lee, Seunghee; Talag, Jayson; Song, Jia-Ming; Du, Bogu; Xie, Weibo; Luo, Meizhong; Maldonado, Carlos Ernesto; Goicoechea, Jose Luis; Xiong, Lizhong; Wu, Changyin; Xing, Yongzhong; Zhou, Dao-Xiu; Yu, Sibin; Zhao, Yu; Wang, Gongwei; Yu, Yeisoo; Luo, Yijie; Hurtado, Beatriz Elena Padilla; Danowitz, Ann; Wing, Rod A; Zhang, Qifa

    2016-01-01

    Over the past 30 years, we have performed many fundamental studies on two Oryza sativa subsp. indica varieties, Zhenshan 97 (ZS97) and Minghui 63 (MH63). To improve the resolution of many of these investigations, we generated two reference-quality reference genome assemblies using the most advanced sequencing technologies. Using PacBio SMRT technology, we produced over 108 (ZS97) and 174 (MH63) Gb of raw sequence data from 166 (ZS97) and 209 (MH63) pools of BAC clones, and generated ~97 (ZS97) and ~74 (MH63) Gb of paired-end whole-genome shotgun (WGS) sequence data with Illumina sequencing technology. With these data, we successfully assembled two platinum standard reference genomes that have been publicly released. Here we provide the full sets of raw data used to generate these two reference genome assemblies. These data sets can be used to test new programs for better genome assembly and annotation, aid in the discovery of new insights into genome structure, function, and evolution, and help to provide essential support to biological research in general. PMID:27622467

  1. Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data.

    PubMed

    Zhang, Jianwei; Chen, Ling-Ling; Sun, Shuai; Kudrna, Dave; Copetti, Dario; Li, Weiming; Mu, Ting; Jiao, Wen-Biao; Xing, Feng; Lee, Seunghee; Talag, Jayson; Song, Jia-Ming; Du, Bogu; Xie, Weibo; Luo, Meizhong; Maldonado, Carlos Ernesto; Goicoechea, Jose Luis; Xiong, Lizhong; Wu, Changyin; Xing, Yongzhong; Zhou, Dao-Xiu; Yu, Sibin; Zhao, Yu; Wang, Gongwei; Yu, Yeisoo; Luo, Yijie; Hurtado, Beatriz Elena Padilla; Danowitz, Ann; Wing, Rod A; Zhang, Qifa

    2016-09-13

    Over the past 30 years, we have performed many fundamental studies on two Oryza sativa subsp. indica varieties, Zhenshan 97 (ZS97) and Minghui 63 (MH63). To improve the resolution of many of these investigations, we generated two reference-quality reference genome assemblies using the most advanced sequencing technologies. Using PacBio SMRT technology, we produced over 108 (ZS97) and 174 (MH63) Gb of raw sequence data from 166 (ZS97) and 209 (MH63) pools of BAC clones, and generated ~97 (ZS97) and ~74 (MH63) Gb of paired-end whole-genome shotgun (WGS) sequence data with Illumina sequencing technology. With these data, we successfully assembled two platinum standard reference genomes that have been publicly released. Here we provide the full sets of raw data used to generate these two reference genome assemblies. These data sets can be used to test new programs for better genome assembly and annotation, aid in the discovery of new insights into genome structure, function, and evolution, and help to provide essential support to biological research in general.

  2. Functional foods and the biomedicalisation of everyday life: a case of germinated brown rice.

    PubMed

    Kim, Hyomin

    2013-07-01

    Germinated brown rice (GBR) is a functional food, whose benefits for chronic diseases have been demonstrated by scientific research on a single constituent of GBR, gamma aminobutyric acid. This article examines the processes through which the emphasis on biomedical rationality made during the production and consumption of functional foods is embedded in the complicated social contexts of the post-1990s. In the case of GBR, the Korean government, food scientists, mass media and consumers have added cultural accounts to the biomedical understanding of foods. In particular, consumers have transformed their households and online communities into a place for surveillance medicine. Functional foods are embedded in multiple actors' perspectives on what healthy foods mean and how and where the risks of chronic diseases should be managed.

  3. Functional genomics and its implications for molecular medicine.

    PubMed

    Broeckel, Ulrich; Maresso, Karen; Kugathasan, Subra

    2006-10-01

    Technological development in genetics and genomics provides unprecedented possibilities to identify the underlying molecular basic of many common diseases. With the availability of the human genome sequence and growing information on the most frequent DNA variations combined with the molecular analysis on the RNA expression and protein level, diseases might be characterized in the future at the molecular level. Describing gene function anf the specific role of DNA, RNA, and proteins in the disease process provides novel diagnosis tools and treatment. Ultimately how the unique genetic signature of an individual influences the risk and prognosis of disease will be the basis for individualized medicine in the years to come.

  4. Quantitative trait loci associated with functional stay-green SNU-SG1 in rice.

    PubMed

    Yoo, Soo-Cheul; Cho, Sung-Hwan; Zhang, Haitao; Paik, Hyo-Chung; Lee, Chung-Hee; Li, Jinjie; Yoo, Jeong-Hoon; Lee, Byun-Woo; Koh, Hee-Jong; Seo, Hak Soo; Paek, Nam-Chon

    2007-08-31

    During monocarpic senescence in higher plants, functional stay-green delays leaf yellowing, maintaining photosynthetic competence, whereas nonfunctional stay-green retains leaf greenness without sustaining photosynthetic activity. Thus, functional stay-green is considered a beneficial trait that can increase grain yield in cereal crops. A stay-green japonica rice 'SNU-SG1' had a good seed-setting rate and grain yield, indicating the presence of a functional stay-green genotype. SNU-SG1 was crossed with two regular cultivars to determine the inheritance mode and identify major QTLs conferring stay-green in SNU-SG1. For QTL analysis, linkage maps with 100 and 116 DNA marker loci were constructed using selective genotyping with F2 and RIL (recombinant inbred line) populations, respectively. Molecular marker-based QTL analyses with both populations revealed that the functional stay-green phenotype of SNU-SG1 is regulated by several major QTLs accounting for a large portion of the genetic variation. Three main-effect QTLs located on chromosomes 7 and 9 were detected in both populations and a number of epistatic-effect QTLs were also found. The amount of variation explained by several digenic interactions was larger than that explained by main-effect QTLs. Two main-effect QTLs on chromosome 9 can be considered the target loci that most influence the functional stay-green in SNU-SG1. The functional stay-green QTLs may help develop low-input high-yielding rice cultivars by QTL-marker-assisted breeding with SNU-SG1.

  5. Transcriptome and genome sequencing uncovers functional variation in humans

    PubMed Central

    Lappalainen, Tuuli; Sammeth, Michael; Friedländer, Marc R; ‘t Hoen, Peter AC; Monlong, Jean; Rivas, Manuel A; Gonzàlez-Porta, Mar; Kurbatova, Natalja; Griebel, Thasso; Ferreira, Pedro G; Barann, Matthias; Wieland, Thomas; Greger, Liliana; van Iterson, Maarten; Almlöf, Jonas; Ribeca, Paolo; Pulyakhina, Irina; Esser, Daniela; Giger, Thomas; Tikhonov, Andrew; Sultan, Marc; Bertier, Gabrielle; MacArthur, Daniel G; Lek, Monkol; Lizano, Esther; Buermans, Henk PJ; Padioleau, Ismael; Schwarzmayr, Thomas; Karlberg, Olof; Ongen, Halit; Kilpinen, Helena; Beltran, Sergi; Gut, Marta; Kahlem, Katja; Amstislavskiy, Vyacheslav; Stegle, Oliver; Pirinen, Matti; Montgomery, Stephen B; Donnelly, Peter; McCarthy, Mark I; Flicek, Paul; Strom, Tim M; Lehrach, Hans; Schreiber, Stefan; Sudbrak, Ralf; Carracedo, Ángel; Antonarakis, Stylianos E; Häsler, Robert; Syvänen, Ann-Christine; van Ommen, Gert-Jan; Brazma, Alvis; Meitinger, Thomas; Rosenstiel, Philip; Guigó, Roderic; Gut, Ivo G; Estivill, Xavier; Dermitzakis, Emmanouil T

    2013-01-01

    Summary Genome sequencing projects are discovering millions of genetic variants in humans, and interpretation of their functional effects is essential for understanding the genetic basis of variation in human traits. Here we report sequencing and deep analysis of mRNA and miRNA from lymphoblastoid cell lines of 462 individuals from the 1000 Genomes Project – the first uniformly processed RNA-seq data from multiple human populations with high-quality genome sequences. We discovered extremely widespread genetic variation affecting regulation of the majority of genes, with transcript structure and expression level variation being equally common but genetically largely independent. Our characterization of causal regulatory variation sheds light on cellular mechanisms of regulatory and loss-of-function variation, and allowed us to infer putative causal variants for dozens of disease-associated loci. Altogether, this study provides a deep understanding of the cellular mechanisms of transcriptome variation and of the landscape of functional variants in the human genome. PMID:24037378

  6. A Populus EST resource for plant functional genomics.

    PubMed

    Sterky, Fredrik; Bhalerao, Rupali R; Unneberg, Per; Segerman, Bo; Nilsson, Peter; Brunner, Amy M; Charbonnel-Campaa, Laurence; Lindvall, Jenny Jonsson; Tandre, Karolina; Strauss, Steven H; Sundberg, Björn; Gustafsson, Petter; Uhlén, Mathias; Bhalerao, Rishikesh P; Nilsson, Ove; Sandberg, Göran; Karlsson, Jan; Lundeberg, Joakim; Jansson, Stefan

    2004-09-21

    Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide >4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (POPULUSDB) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.

  7. Beyond Drosophila: RNAi in vivo and functional genomics in insects.

    PubMed

    Bellés, Xavier

    2010-01-01

    The increasing availability of insect genomes has revealed a large number of genes with unknown functions and the resulting problem of how to discover these functions. The RNA interference (RNAi) technique, which generates loss-of-function phenotypes by depletion of a chosen transcript, can help to overcome this challenge. RNAi can unveil the functions of new genes, lead to the discovery of new functions for old genes, and find the genes for old functions. Moreover, the possibility of studying the functions of homologous genes in different species can allow comparisons of the genetic networks regulating a given function in different insect groups, thereby facilitating an evolutionary insight into developmental processes. RNAi also has drawbacks and obscure points, however, such as those related to differences in species sensitivity. Disentangling these differences is one of the main challenges in the RNAi field.

  8. Genomic islands predict functional adaptation in marine actinobacteria

    SciTech Connect

    Penn, Kevin; Jenkins, Caroline; Nett, Markus; Udwary, Daniel; Gontang, Erin; McGlinchey, Ryan; Foster, Brian; Lapidus, Alla; Podell, Sheila; Allen, Eric; Moore, Bradley; Jensen, Paul

    2009-04-01

    Linking functional traits to bacterial phylogeny remains a fundamental but elusive goal of microbial ecology 1. Without this information, it becomes impossible to resolve meaningful units of diversity and the mechanisms by which bacteria interact with each other and adapt to environmental change. Ecological adaptations among bacterial populations have been linked to genomic islands, strain-specific regions of DNA that house functionally adaptive traits 2. In the case of environmental bacteria, these traits are largely inferred from bioinformatic or gene expression analyses 2, thus leaving few examples in which the functions of island genes have been experimentally characterized. Here we report the complete genome sequences of Salinispora tropica and S. arenicola, the first cultured, obligate marine Actinobacteria 3. These two species inhabit benthic marine environments and dedicate 8-10percent of their genomes to the biosynthesis of secondary metabolites. Despite a close phylogenetic relationship, 25 of 37 secondary metabolic pathways are species-specific and located within 21 genomic islands, thus providing new evidence linking secondary metabolism to ecological adaptation. Species-specific differences are also observed in CRISPR sequences, suggesting that variations in phage immunity provide fitness advantages that contribute to the cosmopolitan distribution of S. arenicola 4. The two Salinispora genomes have evolved by complex processes that include the duplication and acquisition of secondary metabolite genes, the products of which provide immediate opportunities for molecular diversification and ecological adaptation. Evidence that secondary metabolic pathways are exchanged by Horizontal Gene Transfer (HGT) yet are fixed among globally distributed populations 5 supports a functional role for their products and suggests that pathway acquisition represents a previously unrecognized force driving bacterial diversification

  9. Functional Genomics Using the Saccharomyces cerevisiae Yeast Deletion Collections.

    PubMed

    Nislow, Corey; Wong, Lai Hong; Lee, Amy Huei-Yi; Giaever, Guri

    2016-01-01

    Constructed by a consortium of 16 laboratories, the Saccharomyces genome-wide deletion collections have, for the past decade, provided a powerful, rapid, and inexpensive approach for functional profiling of the yeast genome. Loss-of-function deletion mutants were systematically created using a polymerase chain reaction (PCR)-based gene deletion strategy to generate a start-to-stop codon replacement of each open reading frame by homologous recombination. Each strain carries two molecular barcodes that serve as unique strain identifiers, enabling their growth to be analyzed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays or through the use of next-generation sequencing technologies. Functional profiling of the deletion collections, using either strain-by-strain or parallel assays, provides an unbiased approach to systematically survey the yeast genome. The Saccharomyces yeast deletion collections have proved immensely powerful in contributing to the understanding of gene function, including functional relationships between genes and genetic pathways in response to diverse genetic and environmental perturbations. PMID:27587784

  10. Functional characterisation of OsCPK21, a calcium-dependent protein kinase that confers salt tolerance in rice.

    PubMed

    Asano, Takayuki; Hakata, Makoto; Nakamura, Hidemitsu; Aoki, Naohiro; Komatsu, Setsuko; Ichikawa, Hiroaki; Hirochika, Hirohiko; Ohsugi, Ryu

    2011-01-01

    Calcium acts as a messenger in various signal transduction pathways in plants. Calcium-dependent protein kinases (CDPKs) play important roles in regulating downstream components in calcium signaling pathways. In rice, the CDPKs constitute a large multigene family consisting of 29 genes, but the biological functions and functional divergence or redundancy of most of these genes remain unclear. Using a mini-scale full-length cDNA overexpressor (FOX) gene hunting system, we generated 250 independent transgenic rice plants overexpressing individual rice CDPKs (CDPK FOX-rice lines). These CDPK FOX-rice lines were screened for salt stress tolerance. The survival rate of the OsCPK21-FOX plants was higher than that of wild-type (WT) plants grown under high salinity conditions. The inhibition of seedling growth by abscisic acid (ABA) treatment was greater in the OsCPK21-FOX plants than in WT plants. Several ABA- and high salinity-inducible genes were more highly expressed in the OsCPK21-FOX plants than in WT plants. These results suggest that OsCPK21 is involved in the positive regulation of the signaling pathways that are involved in the response to ABA and salt stress.

  11. [Functional annotation of rice WRKY transcription factors based on their transcriptional features].

    PubMed

    Liyun, Li; Jianan, Shi; Shuo, Yang; Caiqiang, Sun; Guozhen, Liu

    2016-02-01

    Transcription factors regulate alteration of transcription levels. Recently, huge amount of transcriptomic data are accumulated via the application of high throughput sequencing technology, and it is reasonable to postulate that in-depth analysis of transcription data could be used to enhance gene annotation. In this study, we chose the gene family of rice WRKY transcription factors. Based on literature search, the transcriptional data under different biological processes, including biotic and abiotic stress, development, and nutrient absorption and hormone treatments were analyzed systematically. To the end, we summarize the list of differentially expressed WRKY genes. We also expect that such information will enrich their functional annotation and also provide direct clues for subsequent functional studies. PMID:26907776

  12. Analyzing Rice distributed functional magnetic resonance imaging data: a Bayesian approach

    NASA Astrophysics Data System (ADS)

    Lauwers, Lieve; Barbé, Kurt; Van Moer, Wendy; Pintelon, Rik

    2010-11-01

    Analyzing functional MRI data is often a hard task due to the fact that these periodic signals are strongly disturbed with noise. In many cases, the signals are buried under the noise and not visible, such that detection is quite impossible. However, it is well known that the amplitude measurements of such disturbed signals follow a Rice distribution which is characterized by two parameters. In this paper, an alternative Bayesian approach is proposed to tackle this two-parameter estimation problem. By incorporating prior knowledge into a mathematical framework, the drawbacks of the existing methods (i.e. the maximum likelihood approach and the method of moments) can be overcome. The performance of the proposed Bayesian estimator is analyzed theoretically and illustrated through simulations. Finally, the developed approach is successfully applied to measurement data for the analysis of functional MRI.

  13. Cloning of TPS gene from eelgrass species Zostera marina and its functional identification by genetic transformation in rice.

    PubMed

    Zhao, Feng; Li, Qiuying; Weng, Manli; Wang, Xiuliang; Guo, Baotai; Wang, Li; Wang, Wei; Duan, Delin; Wang, Bin

    2013-12-01

    The full-length cDNA sequence (2613 bp) of the trehalose-6-phosphate synthase (TPS) gene of eelgrass Zostera marina (ZmTPS) was identified and cloned. Z. marina is a kind of seed-plant growing in sea water during its whole life history. The open reading frame (ORF) region of ZmTPS gene encodes a protein of 870 amino acid residues and a stop codon. The corresponding genomic DNA sequence is 3770 bp in length, which contains 3 exons and 2 introns. The ZmTPS gene was transformed into rice variety ZH11 via Agrobacterium-mediated transformation method. After antibiotic screening, molecular characterization, salt-tolerance and trehalose content determinations, two transgenic lines resistant to 150 mM NaCL solutions were screened. Our study results indicated that the ZmTPS gene was integrated into the genomic DNA of the two transgenic rice lines and could be expressed well. Moreover, the detection of the transformed ZmTPS gene in the progenies of the two transgenic lines was performed from T1 to T4 generations; and results suggested that the transformed ZmTPS gene can be transmitted from parent to the progeny in transgenic rice.

  14. Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes.

    PubMed

    Wang, Xi-liang; Song, Shu-hui; Wu, Yong-Sheng; Li, Yu-Li; Chen, Ting-ting; Huang, Zhi-yuan; Liu, Shuo; Dunwell, Thomas L; Pfeifer, Gerd P; Dunwell, Jim M; Wamaedeesa, Raheema; Ullah, Ihsan; Wang, Yinsheng; Hu, Song-nian

    2015-11-01

    5-Hydroxymethylcytosine (5hmC), a modified form of cytosine that is considered the sixth nucleobase in DNA, has been detected in mammals and is believed to play an important role in gene regulation. In this study, 5hmC modification was detected in rice by employing a dot-blot assay, and its levels was further quantified in DNA from different rice tissues using liquid chromatography-multistage mass spectrometry (LC-MS/MS/MS). The results showed large intertissue variation in 5hmC levels. The genome-wide profiles of 5hmC modification in three different rice cultivars were also obtained using a sensitive chemical labelling followed by a next-generation sequencing method. Thousands of 5hmC peaks were identified, and a comparison of the distributions of 5hmC among different rice cultivars revealed the specificity and conservation of 5hmC modification. The identified 5hmC peaks were significantly enriched in heterochromatin regions, and mainly located in transposable elements (TEs), especially around retrotransposons. The correlation analysis of 5hmC and gene expression data revealed a close association between 5hmC and silent TEs. These findings provide a resource for plant DNA 5hmC epigenetic studies and expand our knowledge of 5hmC modification. PMID:26272901

  15. A genome-wide association study of a global rice panel reveals resistance in Oryza sativa to root-knot nematodes

    PubMed Central

    Dimkpa, Stanley O. N.; Lahari, Zobaida; Shrestha, Roshi; Douglas, Alex; Gheysen, Godelieve; Price, Adam H.

    2016-01-01

    The root-knot nematode Meloidogyne graminicola is one of the most serious nematode pests worldwide and represents a major constraint on rice production. While variation in the susceptibility of Asian rice (Oryza sativa) exists, so far no strong and reliable resistance has been reported. Quantitative trait loci for partial resistance have been reported but no underlying genes have been tagged or cloned. Here, 332 accessions of the Rice Diversity Panel 1 were assessed for gall formation, revealing large variation across all subpopulations of rice and higher susceptibility in temperate japonica accessions. Accessions Khao Pahk Maw and LD 24 appeared to be resistant, which was confirmed in large pot experiments where no galls were observed. Detailed observations on these two accessions revealed no nematodes inside the roots 2 days after inoculation and very few females after 17 days (5 in Khao Pahk Maw and <1 in LD 24, in comparison with >100 in the susceptible controls). These two cultivars appear ideal donors for breeding root-knot nematode resistance. A genome-wide association study revealed 11 quantitative trait loci, two of which are close to epistatic loci detected in the Bala x Azucena population. The discussion highlights a small number of candidate genes worth exploring further, in particular many genes with lectin domains and genes on chromosome 11 with homology to the Hordeum Mla locus. PMID:26552884

  16. Identification of candidate network hubs involved in metabolic adjustments of rice under drought stress by integrating transcriptome data and genome-scale metabolic network.

    PubMed

    Mohanty, Bijayalaxmi; Kitazumi, Ai; Cheung, C Y Maurice; Lakshmanan, Meiyappan; de los Reyes, Benildo G; Jang, In-Cheol; Lee, Dong-Yup

    2016-01-01

    In this study, we have integrated a rice genome-scale metabolic network and the transcriptome of a drought-tolerant rice line, DK151, to identify the major transcriptional regulators involved in metabolic adjustments necessary for adaptation to drought. This was achieved by examining the differential expressions of transcription factors and metabolic genes in leaf, root and young panicle of rice plants subjected to drought stress during tillering, booting and panicle elongation stages. Critical transcription factors such as AP2/ERF, bZIP, MYB and NAC that control the important nodes in the gene regulatory pathway were identified through correlative analysis of the patterns of spatio-temporal expression and cis-element enrichment. We showed that many of the candidate transcription factors involved in metabolic adjustments were previously linked to phenotypic variation for drought tolerance. This approach represents the first attempt to integrate models of transcriptional regulation and metabolic pathways for the identification of candidate regulatory genes for targeted selection in rice breeding. PMID:26566840

  17. Analysis of Magnaporthe oryzae Genome Reveals a Fungal Effector, Which Is Able to Induce Resistance Response in Transgenic Rice Line Containing Resistance Gene, Pi54

    PubMed Central

    Ray, Soham; Singh, Pankaj K.; Gupta, Deepak K.; Mahato, Ajay K.; Sarkar, Chiranjib; Rathour, Rajeev; Singh, Nagendra K.; Sharma, Tilak R.

    2016-01-01

    Rice blast caused by Magnaporthe oryzae is one of the most important diseases of rice. Pi54, a rice gene that imparts resistance to M. oryzae isolates prevalent in India, was already cloned but its avirulent counterpart in the pathogen was not known. After decoding the whole genome of an avirulent isolate of M. oryzae, we predicted 11440 protein coding genes and then identified four candidate effector proteins which are exclusively expressed in the infectious structure, appresoria. In silico protein modeling followed by interaction analysis between Pi54 protein model and selected four candidate effector proteins models revealed that Mo-01947_9 protein model encoded by a gene located at chromosome 4 of M. oryzae, interacted best at the Leucine Rich Repeat domain of Pi54 protein model. Yeast-two-hybrid analysis showed that Mo-01947_9 protein physically interacts with Pi54 protein. Nicotiana benthamiana leaf infiltration assay confirmed induction of hypersensitive response in the presence of Pi54 gene in a heterologous system. Genetic complementation test also proved that Mo-01947_9 protein induces avirulence response in the pathogen in presence of Pi54 gene. Here, we report identification and cloning of a new fungal effector gene which interacts with blast resistance gene Pi54 in rice. PMID:27551285

  18. Analysis of Magnaporthe oryzae Genome Reveals a Fungal Effector, Which Is Able to Induce Resistance Response in Transgenic Rice Line Containing Resistance Gene, Pi54.

    PubMed

    Ray, Soham; Singh, Pankaj K; Gupta, Deepak K; Mahato, Ajay K; Sarkar, Chiranjib; Rathour, Rajeev; Singh, Nagendra K; Sharma, Tilak R

    2016-01-01

    Rice blast caused by Magnaporthe oryzae is one of the most important diseases of rice. Pi54, a rice gene that imparts resistance to M. oryzae isolates prevalent in India, was already cloned but its avirulent counterpart in the pathogen was not known. After decoding the whole genome of an avirulent isolate of M. oryzae, we predicted 11440 protein coding genes and then identified four candidate effector proteins which are exclusively expressed in the infectious structure, appresoria. In silico protein modeling followed by interaction analysis between Pi54 protein model and selected four candidate effector proteins models revealed that Mo-01947_9 protein model encoded by a gene located at chromosome 4 of M. oryzae, interacted best at the Leucine Rich Repeat domain of Pi54 protein model. Yeast-two-hybrid analysis showed that Mo-01947_9 protein physically interacts with Pi54 protein. Nicotiana benthamiana leaf infiltration assay confirmed induction of hypersensitive response in the presence of Pi54 gene in a heterologous system. Genetic complementation test also proved that Mo-01947_9 protein induces avirulence response in the pathogen in presence of Pi54 gene. Here, we report identification and cloning of a new fungal effector gene which interacts with blast resistance gene Pi54 in rice. PMID:27551285

  19. Functional genomics of Lactobacillus casei establishment in the gut

    PubMed Central

    Licandro-Seraut, Hélène; Scornec, Hélène; Pédron, Thierry; Cavin, Jean-François; Sansonetti, Philippe J.

    2014-01-01

    Although the composition of the gut microbiota and its symbiotic contribution to key host physiological functions are well established, little is known as yet about the bacterial factors that account for this symbiosis. We selected Lactobacillus casei as a model microorganism to proceed to genomewide identification of the functions required for a symbiont to establish colonization in the gut. As a result of our recent development of a transposon-mutagenesis tool that overcomes the barrier that had prevented L. casei random mutagenesis, we developed a signature-tagged mutagenesis approach combining whole-genome reverse genetics using a set of tagged transposons and in vivo screening using the rabbit ligated ileal loop model. After sequencing transposon insertion sites in 9,250 random mutants, we assembled a library of 1,110 independent mutants, all disrupted in a different gene, that provides a representative view of the L. casei genome. By determining the relative quantity of each of the 1,110 mutants before and after the in vivo challenge, we identified a core of 47 L. casei genes necessary for its establishment in the gut. They are involved in housekeeping functions, metabolism (sugar, amino acids), cell wall biogenesis, and adaptation to environment. Hence we provide what is, to our knowledge, the first global functional genomics analysis of L. casei symbiosis. PMID:25024222

  20. Functional genomic analysis of the Drosophila immune response.

    PubMed

    Valanne, Susanna

    2014-01-01

    Drosophila melanogaster has been widely used as a model organism for over a century now, and also as an immunological research model for over 20 years. With the emergence of RNA interference (RNAi) in Drosophila as a robust tool to silence genes of interest, large-scale or genome-wide functional analysis has become a popular way of studying the Drosophila immune response in cell culture. Drosophila immunity is composed of cellular and humoral immunity mechanisms, and especially the systemic, humoral response pathways have been extensively dissected using the functional genomic approach. Although most components of the main immune pathways had already been found using traditional genetic screening techniques, important findings including pathway components, positive and negative regulators and modifiers have been made with RNAi screening. Additionally, RNAi screening has produced new information on host-pathogen interactions related to the pathogenesis of many microbial species. PMID:23707784

  1. Complete genome sequence of Deinococcus soli N5(T), a gamma-radiation- resistant bacterium isolated from rice field in South Korea.

    PubMed

    Joo, Eun Sun; Kim, Eun Bit; Jeon, Seon Hwa; Srinivasan, Sathiyaraj

    2015-10-10

    A Gram-negative, non-motile and short-rod shaped and gamma-radiation-resistant bacterium Deinococcus soli N5(T), isolated from a rice field soil in South Korea. The complete genome of D. soli N5(T) consists of a chromosome (3,236,984bp). The key enzymes for the central DNA repair mechanisms were present in the genome. The enzyme coding genes has been identified which is involving in the nucleotide excision repair (NER) pathway. The gene cluster in the genome sequence suggest that the D. soli N5(T) use (NER) pathways for efficient removal of pyrimidine dimers that are the most abundant type of UV- induced damage.

  2. Functional annotation of introns in mitochondrial genome--a brief review.

    PubMed

    Anandakumar, Shanmugam; Ravindran, Suda Parimala; Shanmughavel, Piramanayagam

    2016-01-01

    The present study is to decipher the non-coding regions present in mitochondrial genomes that cause diseases in humans and predict their functional roles through comparative genomics approach followed by functional annotation of these segments.

  3. Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network

    PubMed Central

    Xu, Xi-Wen; Zhou, Xiong-Hui; Wang, Rui-Ru; Peng, Wen-Lei; An, Yue; Chen, Ling-Ling

    2016-01-01

    Long intergenic non-coding RNAs (lincRNAs) may play widespread roles in gene regulation and other biological processes, however, a systematic examination of the functions of lincRNAs in the biological responses of rice to phosphate (Pi) starvation has not been performed. Here, we used a computational method to predict the functions of lincRNAs in Pi-starved rice. Overall, 3,170 lincRNA loci were identified using RNA sequencing data from the roots and shoots of control and Pi-starved rice. A competing endogenous RNA (ceRNA) network was constructed for each tissue by considering the competing relationships between lincRNAs and genes, and the correlations between the expression levels of RNAs in ceRNA pairs. Enrichment analyses showed that most of the communities in the networks were related to the biological processes of Pi starvation. The lincRNAs in the two tissues were individually functionally annotated based on the ceRNA networks, and the differentially expressed lincRNAs were biologically meaningful. For example, XLOC_026030 was upregulated from 3 days after Pi starvation, and its functional annotation was ‘cellular response to Pi starvation’. In conclusion, we systematically annotated lincRNAs in rice and identified those involved in the biological response to Pi starvation. PMID:26860696

  4. Functional Profiling Using the Saccharomyces Genome Deletion Project Collections.

    PubMed

    Nislow, Corey; Wong, Lai Hong; Lee, Amy Huei-Yi; Giaever, Guri

    2016-01-01

    The ability to measure and quantify the fitness of an entire organism requires considerably more complex approaches than simply using traditional "omic" methods that examine, for example, the abundance of RNA transcripts, proteins, or metabolites. The yeast deletion collections represent the only systematic, comprehensive set of null alleles for any organism in which such fitness measurements can be assayed. Generated by the Saccharomyces Genome Deletion Project, these collections allow the systematic and parallel analysis of gene functions using any measurable phenotype. The unique 20-bp molecular barcodes engineered into the genome of each deletion strain facilitate the massively parallel analysis of individual fitness. Here, we present functional genomic protocols for use with the yeast deletion collections. We describe how to maintain, propagate, and store the deletion collections and how to perform growth fitness assays on single and parallel screening platforms. Phenotypic fitness analyses of the yeast mutants, described in brief here, provide important insights into biological functions, mechanisms of drug action, and response to environmental stresses. It is important to bear in mind that the specific assays described in this protocol represent some of the many ways in which these collections can be assayed, and in this description particular attention is paid to maximizing throughput using growth as the phenotypic measure. PMID:27587776

  5. Resources for Functional Genomics Studies in Drosophila melanogaster

    PubMed Central

    Mohr, Stephanie E.; Hu, Yanhui; Kim, Kevin; Housden, Benjamin E.; Perrimon, Norbert

    2014-01-01

    Drosophila melanogaster has become a system of choice for functional genomic studies. Many resources, including online databases and software tools, are now available to support design or identification of relevant fly stocks and reagents or analysis and mining of existing functional genomic, transcriptomic, proteomic, etc. datasets. These include large community collections of fly stocks and plasmid clones, “meta” information sites like FlyBase and FlyMine, and an increasing number of more specialized reagents, databases, and online tools. Here, we introduce key resources useful to plan large-scale functional genomics studies in Drosophila and to analyze, integrate, and mine the results of those studies in ways that facilitate identification of highest-confidence results and generation of new hypotheses. We also discuss ways in which existing resources can be used and might be improved and suggest a few areas of future development that would further support large- and small-scale studies in Drosophila and facilitate use of Drosophila information by the research community more generally. PMID:24653003

  6. The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae.

    PubMed

    Gibbons, John G; Salichos, Leonidas; Slot, Jason C; Rinker, David C; McGary, Kriston L; King, Jonas G; Klich, Maren A; Tabb, David L; McDonald, W Hayes; Rokas, Antonis

    2012-08-01

    The domestication of animals, plants, and microbes fundamentally transformed the lifestyle and demography of the human species [1]. Although the genetic and functional underpinnings of animal and plant domestication are well understood, little is known about microbe domestication [2-6]. Here, we systematically examined genome-wide sequence and functional variation between the domesticated fungus Aspergillus oryzae, whose saccharification abilities humans have harnessed for thousands of years to produce sake, soy sauce, and miso from starch-rich grains, and its wild relative A. flavus, a potentially toxigenic plant and animal pathogen [7]. We discovered dramatic changes in the sequence variation and abundance profiles of genes and wholesale primary and secondary metabolic pathways between domesticated and wild relative isolates during growth on rice. Our data suggest that, through selection by humans, an atoxigenic lineage of A. flavus gradually evolved into a "cell factory" for enzymes and metabolites involved in the saccharification process. These results suggest that whereas animal and plant domestication was largely driven by Neolithic "genetic tinkering" of developmental pathways, microbe domestication was driven by extensive remodeling of metabolism.

  7. Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome.

    PubMed

    Fonville, Natalie C; Velmurugan, Karthik Raja; Tae, Hongseok; Vaksman, Zalman; McIver, Lauren J; Garner, Harold R

    2016-01-01

    The human genome is 99% complete. This study contributes to filling the 1% gap by enriching previously unknown repeat regions called microsatellites (MST). We devised a Global MST Enrichment (GME) kit to enrich and nextgen sequence 2 colorectal cell lines and 16 normal human samples to illustrate its utility in identifying contigs from reads that do not map to the genome reference. The analysis of these samples yielded 790 novel extra-referential concordant contigs that are observed in more than one sample. We searched for evidence of functional elements in the concordant contigs in two ways: (1) BLAST-ing each contig against normal RNA-Seq samples, (2) Checking for predicted functional elements using GlimmerHMM. Of the 790 concordant contigs, 37 had an exact match to at least one RNA-Seq read; 15 aligned to more than 100 RNA-Seq reads. Of the 249 concordant contigs predicted by GlimmerHMM to have functional elements, 6 had at least one exact RNA-Seq match. BLAST-ing these novel contigs against all publically available sequences confirmed that they were found in human and chimpanzee BAC and FOSMID clones sequenced as part of the original human genome project. These extra-referential contigs predominantly contained pentameric repeats, especially two motifs: AATGG and GTGGA. PMID:27278669

  8. Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome

    PubMed Central

    Fonville, Natalie C.; Velmurugan, Karthik Raja; Tae, Hongseok; Vaksman, Zalman; McIver, Lauren J.; Garner, Harold R.

    2016-01-01

    The human genome is 99% complete. This study contributes to filling the 1% gap by enriching previously unknown repeat regions called microsatellites (MST). We devised a Global MST Enrichment (GME) kit to enrich and nextgen sequence 2 colorectal cell lines and 16 normal human samples to illustrate its utility in identifying contigs from reads that do not map to the genome reference. The analysis of these samples yielded 790 novel extra-referential concordant contigs that are observed in more than one sample. We searched for evidence of functional elements in the concordant contigs in two ways: (1) BLAST-ing each contig against normal RNA-Seq samples, (2) Checking for predicted functional elements using GlimmerHMM. Of the 790 concordant contigs, 37 had an exact match to at least one RNA-Seq read; 15 aligned to more than 100 RNA-Seq reads. Of the 249 concordant contigs predicted by GlimmerHMM to have functional elements, 6 had at least one exact RNA-Seq match. BLAST-ing these novel contigs against all publically available sequences confirmed that they were found in human and chimpanzee BAC and FOSMID clones sequenced as part of the original human genome project. These extra-referential contigs predominantly contained pentameric repeats, especially two motifs: AATGG and GTGGA. PMID:27278669

  9. Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome.

    PubMed

    Fonville, Natalie C; Velmurugan, Karthik Raja; Tae, Hongseok; Vaksman, Zalman; McIver, Lauren J; Garner, Harold R

    2016-06-09

    The human genome is 99% complete. This study contributes to filling the 1% gap by enriching previously unknown repeat regions called microsatellites (MST). We devised a Global MST Enrichment (GME) kit to enrich and nextgen sequence 2 colorectal cell lines and 16 normal human samples to illustrate its utility in identifying contigs from reads that do not map to the genome reference. The analysis of these samples yielded 790 novel extra-referential concordant contigs that are observed in more than one sample. We searched for evidence of functional elements in the concordant contigs in two ways: (1) BLAST-ing each contig against normal RNA-Seq samples, (2) Checking for predicted functional elements using GlimmerHMM. Of the 790 concordant contigs, 37 had an exact match to at least one RNA-Seq read; 15 aligned to more than 100 RNA-Seq reads. Of the 249 concordant contigs predicted by GlimmerHMM to have functional elements, 6 had at least one exact RNA-Seq match. BLAST-ing these novel contigs against all publically available sequences confirmed that they were found in human and chimpanzee BAC and FOSMID clones sequenced as part of the original human genome project. These extra-referential contigs predominantly contained pentameric repeats, especially two motifs: AATGG and GTGGA.

  10. Functional Genomics of Drought Tolerance in Bioenergy Crops

    SciTech Connect

    Yin, Hengfu; Chen, Rick; Yang, Jun; Weston, David; Chen, Jay; Muchero, Wellington; Ye, Ning; Tschaplinski, Timothy J; Wullschleger, Stan D; Cheng, Zong-Ming; Tuskan, Gerald A; Yang, Xiaohan

    2014-01-01

    With the predicted trends in climate change, drought will increasingly impose a grand challenge to biomass production. Most of the bioenergy crops have some degree of drought susceptibility with low water-use efficiency (WUE). It is imperative to improve drought tolerance and WUE in bioenergy crops for sustainable biomass production in arid and semi-arid regions with minimal water input. Genetics and functional genomics can play a critical role in generating knowledge to inform and aid genetic improvement of drought tolerance in bioenergy crops. The molecular aspect of drought response has been extensively investigated in model plants like Arabidopsis, yet our understanding of the molecular mechanisms underlying drought tolerance in bioenergy crops are limited. Crops exhibit various responses to drought stress depending on species and genotype. A rational strategy for studying drought tolerance in bioenergy crops is to translate the knowledge from model plants and pinpoint the unique features associated with individual species and genotypes. In this review, we summarize the general knowledge about drought responsive pathways in plants, with a focus on the identification of commonality and specialty in drought responsive mechanisms among different species and/or genotypes. We describe the genomic resources developed for bioenergy crops and discuss genetic and epigenetic regulation of drought responses. We also examine comparative and evolutionary genomics to leverage the ever-increasing genomics resources and provide new insights beyond what has been known from studies on individual species. Finally, we outline future exploration of drought tolerance using the emerging new technologies.

  11. Insect genome content phylogeny and functional annotation of core insect genomes.

    PubMed

    Rosenfeld, Jeffrey A; Foox, Jonathan; DeSalle, Rob

    2016-04-01

    Twenty-one fully sequenced and well annotated insect genomes were examined for genome content in a phylogenetic context. Gene presence/absence matrices and phylogenetic trees were constructed using several phylogenetic criteria. The role of e-value on phylogenetic analysis and genome content characterization is examined using scaled e-value cutoffs and a single linkage clustering approach to orthology determination. Previous studies have focused on the role of gene loss in terminals in the insect tree of life. The present study examines several common ancestral nodes in the insect tree. We suggest that the common ancestors of major insect groups like Diptera, Hymenoptera, Hemiptera and Holometabola experience more gene gain than gene loss. This suggests that as major insect groups arose, their genomic repertoire expanded through gene duplication (segmental duplications), followed by contraction by gene loss in specific terminal lineages. In addition, we examine the functional significance of the loss and gain of genes in the divergence of some of the major insect groups. PMID:26549428

  12. Functional genomic studies of aldo-keto reductases.

    PubMed

    Petrash, J M; Murthy, B S; Young, M; Morris, K; Rikimaru, L; Griest, T A; Harter, T

    2001-01-30

    Aldose reductase (AR) is considered a potential mediator of diabetic complications and is a drug target for inhibitors of diabetic retinopathy and neuropathy in clinical trials. However, the physiological role of this enzyme still has not been established. Since effective inhibition of diabetic complications will require early intervention, it is important to delineate whether AR fulfills a physiological role that cannot be compensated by an alternate aldo-keto reductase. Functional genomics provides a variety of powerful new tools to probe the physiological roles of individual genes, especially those comprising gene families. Several eucaryotic genomes have been sequenced and annotated, including yeast, nematode and fly. To probe the function of AR, we have chosen to utilize the budding yeast Saccharomyces cerevisiae as a potential model system. Unlike Caenorhabditis elegans and D. melanogaster, yeast provides a more desirable system for our studies because its genome is manipulated more readily and is able to sustain multiple gene deletions in the presence of either drug or auxotrophic selectable markers. Using BLAST searches against the human AR gene sequence, we identified six genes in the complete S. cerevisiae genome with strong homology to AR. In all cases, amino acids thought to play important catalytic roles in human AR are conserved in the yeast AR-like genes. All six yeast AR-like open reading frames (ORFs) have been cloned into plasmid expression vectors. Substrate and AR inhibitor specificities have been surveyed on four of the enzyme forms to identify, which are the most functionally similar to human AR. Our data reveal that two of the enzymes (YDR368Wp and YHR104Wp) are notable for their similarity to human AR in terms of activity with aldoses and substituted aromatic aldehydes. Ongoing studies are aimed at characterizing the phenotypes of yeast strains containing single and multiple knockouts of the AR-like genes. PMID:11306085

  13. Genome Engineering Using Targeted Oligonucleotide Libraries and Functional Selection

    PubMed Central

    Diner, Elie J.; Garza-Sánchez, Fernando; Hayes, Christopher S.

    2011-01-01

    The λ phage Red proteins greatly enhance homologous recombination in Escherichia coli. Red-mediated recombination or “recombineering” can be used to construct targeted gene deletions as well as to introduce point mutations into the genome. Here, we describe our method for scanning mutagenesis using recombineered oligonucleotide libraries. This approach entails randomization of specific codons within a target gene, followed by functional selection to isolate mutants. Oligonucleotide library mutagenesis has generated hundreds of novel antibiotic resistance mutations in genes encoding ribosomal proteins, and should be applicable to other systems for which functional selections exist. PMID:21815087

  14. Genetic architecture of cold tolerance in rice at the seedling stage and heading determined through genome-wide association studies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cold stress at the seedling stage limits rice (Oryza sativa L.) production in temperate regions or at high elevations in the tropics due to poor plant stand establishment and delayed maturity. At the heading stage, cold temperature causes sterility, thus decreasing grain yield. Initially, the Rice D...

  15. Functional Conservation of MIKC*-Type MADS Box Genes in Arabidopsis and Rice Pollen Maturation[C][W

    PubMed Central

    Liu, Yuan; Cui, Shaojie; Wu, Feng; Yan, Shuo; Lin, Xuelei; Du, Xiaoqiu; Chong, Kang; Schilling, Susanne; Theißen, Günter; Meng, Zheng

    2013-01-01

    There are two groups of MADS intervening keratin-like and C-terminal (MIKC)-type MADS box genes, MIKCC type and MIKC* type. In seed plants, the MIKCC type shows considerable diversity, but the MIKC* type has only two subgroups, P- and S-clade, which show conserved expression in the gametophyte. To examine the functional conservation of MIKC*-type genes, we characterized all three rice (Oryza sativa) MIKC*-type genes. All three genes are specifically expressed late in pollen development. The single knockdown or knockout lines, respectively, of the S-clade MADS62 and MADS63 did not show a mutant phenotype, but lines in which both S-clade genes were affected showed severe defects in pollen maturation and germination, as did knockdown lines of MADS68, the only P-clade gene in rice. The rice MIKC*-type proteins form strong heterodimeric complexes solely with partners from the other subclade; these complexes specifically bind to N10-type C-A-rich-G-boxes in vitro and regulate downstream gene expression by binding to N10-type promoter motifs. The rice MIKC* genes have a much lower degree of functional redundancy than the Arabidopsis thaliana MIKC* genes. Nevertheless, our data indicate that the function of heterodimeric MIKC*-type protein complexes in pollen development has been conserved since the divergence of monocots and eudicots, roughly 150 million years ago. PMID:23613199

  16. Functions of OsBZR1 and 14-3-3 proteins in brassinosteroid signaling in rice

    PubMed Central

    Bai, Ming-Yi; Zhang, Li-Ying; Gampala, Srinivas S.; Zhu, Sheng-Wei; Song, Wen-Yuan; Chong, Kang; Wang, Zhi-Yong

    2007-01-01

    Brassinosteroids (BR) are essential growth hormones found throughout the plant kingdom. BR bind to the receptor kinase BRI1 on the cell surface to activate a signal transduction pathway that regulates nuclear gene expression and plant growth. To understand the downstream BR signaling mechanism in rice, we studied the function of OsBZR1 using reverse genetic approaches and identified OsBZR1-interacting proteins. Suppressing OsBZR1 expression by RNAi resulted in dwarfism, erect leaves, reduced BR sensitivity, and altered BR-responsive gene expression in transgenic rice plants, demonstrating an essential role of OsBZR1 in BR responses in rice. Moreover, a yeast two-hybrid screen identified 14-3-3 proteins as OsBZR1-interacting proteins. Mutation of a putative 14-3-3-binding site of OsBZR1 abolished its interaction with the 14-3-3 proteins in yeast and in vivo. Such mutant OsBZR1 proteins suppressed the phenotypes of the Arabidopsis bri1–5 mutant and showed an increased nuclear distribution compared with the wild-type protein, suggesting that 14-3-3 proteins directly inhibit OsBZR1 function at least in part by reducing its nuclear localization. These results demonstrate a conserved function of OsBZR1 and an important role of 14-3-3 proteins in brassinosteroid signal transduction in rice. PMID:17699623

  17. Event-based text mining for biology and functional genomics.

    PubMed

    Ananiadou, Sophia; Thompson, Paul; Nawaz, Raheel; McNaught, John; Kell, Douglas B

    2015-05-01

    The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of 'events', i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research.

  18. A functional isopenicillin N synthase in an animal genome.

    PubMed

    Roelofs, Dick; Timmermans, Martijn J T N; Hensbergen, Paul; van Leeuwen, Hans; Koopman, Jessica; Faddeeva, Anna; Suring, Wouter; de Boer, Tjalf E; Mariën, Janine; Boer, Remon; Bovenberg, Roel; van Straalen, Nico M

    2013-03-01

    Horizontal transfer of genes is widespread among prokaryotes, but is less common between microorganisms and animals. Here, we present evidence for the presence of a gene encoding functional isopenicillin N synthase, an enzyme in the β-lactam antibiotics biosynthesis pathway, in the genome of the soil-living collembolan species, Folsomia candida (FcIPNS). At present, this gene is only known from bacteria and fungi, as is the capacity to produce β-lactam antibiotics. The FcIPNS gene was located on two genomic contigs, was physically linked to a predicted insect ATP-binding cassette transporter gene, and contained three introns each flanked by eukaryotic splicing recognition sites (GT/AG). Homology searches revealed no similarity between these introns and the FcIPNS regions of bacteria or fungi. All amino acids conserved across bacteria and fungi were also conserved in F. candida. Recombinant FcIPNS was able to convert its substrate amino δ-(l-α-aminoadipyl)-l-cysteinyl-d-valine into isopenicillin N, providing strong evidence that FcIPNS is functional. Phylogenetic analysis clustered FcIPNS outside the bacterial IPNS clade, and also outside the fungal IPNS clade, suggesting an ancient gene transfer followed by divergence in the F. candida genome. In conclusion, the data suggest that the soil-living collembolan F. candida has assimilated the capacity for antibacterial activity by horizontal gene transfer, which may be an important adaptive trait in the microbe-dominated soil ecosystem. PMID:23204388

  19. Whole-genome sequence-based analysis of thyroid function.

    PubMed

    Taylor, Peter N; Porcu, Eleonora; Chew, Shelby; Campbell, Purdey J; Traglia, Michela; Brown, Suzanne J; Mullin, Benjamin H; Shihab, Hashem A; Min, Josine; Walter, Klaudia; Memari, Yasin; Huang, Jie; Barnes, Michael R; Beilby, John P; Charoen, Pimphen; Danecek, Petr; Dudbridge, Frank; Forgetta, Vincenzo; Greenwood, Celia; Grundberg, Elin; Johnson, Andrew D; Hui, Jennie; Lim, Ee M; McCarthy, Shane; Muddyman, Dawn; Panicker, Vijay; Perry, John R B; Bell, Jordana T; Yuan, Wei; Relton, Caroline; Gaunt, Tom; Schlessinger, David; Abecasis, Goncalo; Cucca, Francesco; Surdulescu, Gabriela L; Woltersdorf, Wolfram; Zeggini, Eleftheria; Zheng, Hou-Feng; Toniolo, Daniela; Dayan, Colin M; Naitza, Silvia; Walsh, John P; Spector, Tim; Davey Smith, George; Durbin, Richard; Richards, J Brent; Sanna, Serena; Soranzo, Nicole; Timpson, Nicholas J; Wilson, Scott G

    2015-01-01

    Normal thyroid function is essential for health, but its genetic architecture remains poorly understood. Here, for the heritable thyroid traits thyrotropin (TSH) and free thyroxine (FT4), we analyse whole-genome sequence data from the UK10K project (N=2,287). Using additional whole-genome sequence and deeply imputed data sets, we report meta-analysis results for common variants (MAF≥1%) associated with TSH and FT4 (N=16,335). For TSH, we identify a novel variant in SYN2 (MAF=23.5%, P=6.15 × 10(-9)) and a new independent variant in PDE8B (MAF=10.4%, P=5.94 × 10(-14)). For FT4, we report a low-frequency variant near B4GALT6/SLC25A52 (MAF=3.2%, P=1.27 × 10(-9)) tagging a rare TTR variant (MAF=0.4%, P=2.14 × 10(-11)). All common variants explain ≥20% of the variance in TSH and FT4. Analysis of rare variants (MAF<1%) using sequence kernel association testing reveals a novel association with FT4 in NRG1. Our results demonstrate that increased coverage in whole-genome sequence association studies identifies novel variants associated with thyroid function. PMID:25743335

  20. Whole-genome sequence-based analysis of thyroid function.

    PubMed

    Taylor, Peter N; Porcu, Eleonora; Chew, Shelby; Campbell, Purdey J; Traglia, Michela; Brown, Suzanne J; Mullin, Benjamin H; Shihab, Hashem A; Min, Josine; Walter, Klaudia; Memari, Yasin; Huang, Jie; Barnes, Michael R; Beilby, John P; Charoen, Pimphen; Danecek, Petr; Dudbridge, Frank; Forgetta, Vincenzo; Greenwood, Celia; Grundberg, Elin; Johnson, Andrew D; Hui, Jennie; Lim, Ee M; McCarthy, Shane; Muddyman, Dawn; Panicker, Vijay; Perry, John R B; Bell, Jordana T; Yuan, Wei; Relton, Caroline; Gaunt, Tom; Schlessinger, David; Abecasis, Goncalo; Cucca, Francesco; Surdulescu, Gabriela L; Woltersdorf, Wolfram; Zeggini, Eleftheria; Zheng, Hou-Feng; Toniolo, Daniela; Dayan, Colin M; Naitza, Silvia; Walsh, John P; Spector, Tim; Davey Smith, George; Durbin, Richard; Richards, J Brent; Sanna, Serena; Soranzo, Nicole; Timpson, Nicholas J; Wilson, Scott G

    2015-03-06

    Normal thyroid function is essential for health, but its genetic architecture remains poorly understood. Here, for the heritable thyroid traits thyrotropin (TSH) and free thyroxine (FT4), we analyse whole-genome sequence data from the UK10K project (N=2,287). Using additional whole-genome sequence and deeply imputed data sets, we report meta-analysis results for common variants (MAF≥1%) associated with TSH and FT4 (N=16,335). For TSH, we identify a novel variant in SYN2 (MAF=23.5%, P=6.15 × 10(-9)) and a new independent variant in PDE8B (MAF=10.4%, P=5.94 × 10(-14)). For FT4, we report a low-frequency variant near B4GALT6/SLC25A52 (MAF=3.2%, P=1.27 × 10(-9)) tagging a rare TTR variant (MAF=0.4%, P=2.14 × 10(-11)). All common variants explain ≥20% of the variance in TSH and FT4. Analysis of rare variants (MAF<1%) using sequence kernel association testing reveals a novel association with FT4 in NRG1. Our results demonstrate that increased coverage in whole-genome sequence association studies identifies novel variants associated with thyroid function.

  1. The complete genome sequence of a south Indian isolate of Rice tungro spherical virus reveals evidence of genetic recombination between distinct isolates.

    PubMed

    Sailaja, B; Anjum, Najreen; Patil, Yogesh K; Agarwal, Surekha; Malathi, P; Krishnaveni, D; Balachandran, S M; Viraktamath, B C; Mangrauthia, Satendra K

    2013-12-01

    In this study, complete genome of a south Indian isolate of Rice tungro spherical virus (RTSV) from Andhra Pradesh (AP) was sequenced, and the predicted amino acid sequence was analysed. The RTSV RNA genome consists of 12,171 nt without the poly(A) tail, encoding a putative typical polyprotein of 3,470 amino acids. Furthermore, cleavage sites and sequence motifs of the polyprotein were predicted. Multiple alignment with other RTSV isolates showed a nucleotide sequence identity of 95% to east Indian isolates and 90% to Philippines isolates. A phylogenetic tree based on complete genome sequence showed that Indian isolates clustered together, while Vt6 and PhilA isolates of Philippines formed two separate clusters. Twelve recombination events were detected in RNA genome of RTSV using the Recombination Detection Program version 3. Recombination analysis suggested significant role of 5' end and central region of genome in virus evolution. Further, AP and Odisha isolates appeared as important RTSV isolates involved in diversification of this virus in India through recombination phenomenon. The new addition of complete genome of first south Indian isolate provided an opportunity to establish the molecular evolution of RTSV through recombination analysis and phylogenetic relationship.

  2. Bordetella pertussis evolution in the (functional) genomics era.

    PubMed

    Belcher, Thomas; Preston, Andrew

    2015-11-01

    The incidence of whooping cough caused by Bordetella pertussis in many developed countries has risen dramatically in recent years. This has been linked to the use of an acellular pertussis vaccine. In addition, it is thought that B. pertussis is adapting under acellular vaccine mediated immune selection pressure, towards vaccine escape. Genomics-based approaches have revolutionized the ability to resolve the fine structure of the global B. pertussis population and its evolution during the era of vaccination. Here, we discuss the current picture of B. pertussis evolution and diversity in the light of the current resurgence, highlight import questions raised by recent studies in this area and discuss the role that functional genomics can play in addressing current knowledge gaps.

  3. Adapting CRISPR/Cas9 for functional genomics screens.

    PubMed

    Malina, Abba; Katigbak, Alexandra; Cencic, Regina; Maïga, Rayelle Itoua; Robert, Francis; Miura, Hisashi; Pelletier, Jerry

    2014-01-01

    The use of CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) for targeted genome editing has been widely adopted and is considered a "game changing" technology. The ease and rapidity by which this approach can be used to modify endogenous loci in a wide spectrum of cell types and organisms makes it a powerful tool for customizable genetic modifications as well as for large-scale functional genomics. The development of retrovirus-based expression platforms to simultaneously deliver the Cas9 nuclease and single guide (sg) RNAs provides unique opportunities by which to ensure stable and reproducible expression of the editing tools and a broad cell targeting spectrum, while remaining compatible with in vivo genetic screens. Here, we describe methods and highlight considerations for designing and generating sgRNA libraries in all-in-one retroviral vectors for such applications.

  4. Syntenic relationships between the U and M genomes of Aegilops, wheat and the model species Brachypodium and rice as revealed by COS markers.

    PubMed

    Molnár, István; Šimková, Hana; Leverington-Waite, Michelle; Goram, Richard; Cseh, András; Vrána, Jan; Farkas, András; Doležel, Jaroslav; Molnár-Láng, Márta; Griffiths, Simon

    2013-01-01

    Diploid Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata are important wild gene sources for wheat. With the aim of assisting in alien gene transfer, this study provides gene-based conserved orthologous set (COS) markers for the U and M genome chromosomes. Out of the 140 markers tested on a series of wheat-Aegilops chromosome introgression lines and flow-sorted subgenomic chromosome fractions, 100 were assigned to Aegilops chromosomes and six and seven duplications were identified in the U and M genomes, respectively. The marker-specific EST sequences were BLAST-ed to Brachypodium and rice genomic sequences to investigate macrosyntenic relationships between the U and M genomes of Aegilops, wheat and the model species. Five syntenic regions of Brachypodium identified genome rearrangements differentiating the U genome from the M genome and from the D genome of wheat. All of them seem to have evolved at the diploid level and to have been modified differentially in the polyploid species Ae. biuncialis and Ae. geniculata. A certain level of wheat-Aegilops homology was detected for group 1, 2, 3 and 5 chromosomes, while a clearly rearranged structure was showed for the group 4, 6 and 7 Aegilops chromosomes relative to wheat. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species, wheat and model species will facilitate the targeted development of new markers specific for U and M genomic regions and will contribute to the understanding of molecular processes related to allopolyploidization.

  5. Syntenic Relationships between the U and M Genomes of Aegilops, Wheat and the Model Species Brachypodium and Rice as Revealed by COS Markers

    PubMed Central

    Molnár, István; Šimková, Hana; Leverington-Waite, Michelle; Goram, Richard; Cseh, András; Vrána, Jan; Farkas, András; Doležel, Jaroslav; Molnár-Láng, Márta; Griffiths, Simon

    2013-01-01

    Diploid Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata are important wild gene sources for wheat. With the aim of assisting in alien gene transfer, this study provides gene-based conserved orthologous set (COS) markers for the U and M genome chromosomes. Out of the 140 markers tested on a series of wheat-Aegilops chromosome introgression lines and flow-sorted subgenomic chromosome fractions, 100 were assigned to Aegilops chromosomes and six and seven duplications were identified in the U and M genomes, respectively. The marker-specific EST sequences were BLAST-ed to Brachypodium and rice genomic sequences to investigate macrosyntenic relationships between the U and M genomes of Aegilops, wheat and the model species. Five syntenic regions of Brachypodium identified genome rearrangements differentiating the U genome from the M genome and from the D genome of wheat. All of them seem to have evolved at the diploid level and to have been modified differentially in the polyploid species Ae. biuncialis and Ae. geniculata. A certain level of wheat–Aegilops homology was detected for group 1, 2, 3 and 5 chromosomes, while a clearly rearranged structure was showed for the group 4, 6 and 7 Aegilops chromosomes relative to wheat. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species, wheat and model species will facilitate the targeted development of new markers specific for U and M genomic regions and will contribute to the understanding of molecular processes related to allopolyploidization. PMID:23940651

  6. Combining Image Analysis, Genome Wide Association Studies and Different Field Trials to Reveal Stable Genetic Regions Related to Panicle Architecture and the Number of Spikelets per Panicle in Rice

    PubMed Central

    Rebolledo, Maria C.; Peña, Alexandra L.; Duitama, Jorge; Cruz, Daniel F.; Dingkuhn, Michael; Grenier, Cecile; Tohme, Joe

    2016-01-01

    Number of spikelets per panicle (NSP) is a key trait to increase yield potential in rice (O. sativa). The architecture of the rice inflorescence which is mainly determined by the length and number of primary (PBL and PBN) and secondary (SBL and SBN) branches can influence NSP. Although several genes controlling panicle architecture and NSP in rice have been identified, there is little evidence of (i) the genetic control of panicle architecture and NSP in different environments and (ii) the presence of stable genetic associations with panicle architecture across environments. This study combines image phenotyping of 225 accessions belonging to a genetic diversity array of indica rice grown under irrigated field condition in two different environments and Genome Wide Association Studies (GWAS) based on the genotyping of the diversity panel, providing 83,374 SNPs. Accessions sown under direct seeding in one environement had reduced Panicle Length (PL), NSP, PBN, PBL, SBN, and SBL compared to those established under transplanting in the second environment. Across environments, NSP was significantly and positively correlated with PBN, SBN and PBL. However, the length of branches (PBL and SBL) was not significantly correlated with variables related to number of branches (PBN and SBN), suggesting independent genetic control. Twenty- three GWAS sites were detected with P ≤ 1.0E-04 and 27 GWAS sites with p ≤ 5.9E−04. We found 17 GWAS sites related to NSP, 10 for PBN and 11 for SBN, 7 for PBL and 11 for SBL. This study revealed new regions related to NSP, but only three associations were related to both branching number (PBN and SBN) and NSP. Two GWAS sites associated with SBL and SBN were stable across contrasting environments and were not related to genes previously reported. The new regions reported in this study can help improving NSP in rice for both direct seeded and transplanted conditions. The integrated approach of high-throughput phenotyping, multi

  7. Integrative pathway genomics of lung function and airflow obstruction.

    PubMed

    Gharib, Sina A; Loth, Daan W; Soler Artigas, María; Birkland, Timothy P; Wilk, Jemma B; Wain, Louise V; Brody, Jennifer A; Obeidat, Ma'en; Hancock, Dana B; Tang, Wenbo; Rawal, Rajesh; Boezen, H Marike; Imboden, Medea; Huffman, Jennifer E; Lahousse, Lies; Alves, Alexessander C; Manichaikul, Ani; Hui, Jennie; Morrison, Alanna C; Ramasamy, Adaikalavan; Smith, Albert Vernon; Gudnason, Vilmundur; Surakka, Ida; Vitart, Veronique; Evans, David M; Strachan, David P; Deary, Ian J; Hofman, Albert; Gläser, Sven; Wilson, James F; North, Kari E; Zhao, Jing Hua; Heckbert, Susan R; Jarvis, Deborah L; Probst-Hensch, Nicole; Schulz, Holger; Barr, R Graham; Jarvelin, Marjo-Riitta; O'Connor, George T; Kähönen, Mika; Cassano, Patricia A; Hysi, Pirro G; Dupuis, Josée; Hayward, Caroline; Psaty, Bruce M; Hall, Ian P; Parks, William C; Tobin, Martin D; London, Stephanie J

    2015-12-01

    Chronic respiratory disorders are important contributors to the global burden of disease. Genome-wide association studies (GWASs) of lung function measures have identified several trait-associated loci, but explain only a modest portion of the phenotypic variability. We postulated that integrating pathway-based methods with GWASs of pulmonary function and airflow obstruction would identify a broader repertoire of genes and processes influencing these traits. We performed two independent GWASs of lung function and applied gene set enrichment analysis to one of the studies and validated the results using the second GWAS. We identified 131 significantly enriched gene sets associated with lung function and clustered them into larger biological modules involved in diverse processes including development, immunity, cell signaling, proliferation and arachidonic acid. We found that enrichment of gene sets was not driven by GWAS-significant variants or loci, but instead by those with less stringent association P-values. Next, we applied pathway enrichment analysis to a meta-analyzed GWAS of airflow obstruction. We identified several biologic modules that functionally overlapped with those associated with pulmonary function. However, differences were also noted, including enrichment of extracellular matrix (ECM) processes specifically in the airflow obstruction study. Network analysis of the ECM module implicated a candidate gene, matrix metalloproteinase 10 (MMP10), as a putative disease target. We used a knockout mouse model to functionally validate MMP10's role in influencing lung's susceptibility to cigarette smoke-induced emphysema. By integrating pathway analysis with population-based genomics, we unraveled biologic processes underlying pulmonary function traits and identified a candidate gene for obstructive lung disease. PMID:26395457

  8. Integrative pathway genomics of lung function and airflow obstruction.

    PubMed

    Gharib, Sina A; Loth, Daan W; Soler Artigas, María; Birkland, Timothy P; Wilk, Jemma B; Wain, Louise V; Brody, Jennifer A; Obeidat, Ma'en; Hancock, Dana B; Tang, Wenbo; Rawal, Rajesh; Boezen, H Marike; Imboden, Medea; Huffman, Jennifer E; Lahousse, Lies; Alves, Alexessander C; Manichaikul, Ani; Hui, Jennie; Morrison, Alanna C; Ramasamy, Adaikalavan; Smith, Albert Vernon; Gudnason, Vilmundur; Surakka, Ida; Vitart, Veronique; Evans, David M; Strachan, David P; Deary, Ian J; Hofman, Albert; Gläser, Sven; Wilson, James F; North, Kari E; Zhao, Jing Hua; Heckbert, Susan R; Jarvis, Deborah L; Probst-Hensch, Nicole; Schulz, Holger; Barr, R Graham; Jarvelin, Marjo-Riitta; O'Connor, George T; Kähönen, Mika; Cassano, Patricia A; Hysi, Pirro G; Dupuis, Josée; Hayward, Caroline; Psaty, Bruce M; Hall, Ian P; Parks, William C; Tobin, Martin D; London, Stephanie J

    2015-12-01

    Chronic respiratory disorders are important contributors to the global burden of disease. Genome-wide association studies (GWASs) of lung function measures have identified several trait-associated loci, but explain only a modest portion of the phenotypic variability. We postulated that integrating pathway-based methods with GWASs of pulmonary function and airflow obstruction would identify a broader repertoire of genes and processes influencing these traits. We performed two independent GWASs of lung function and applied gene set enrichment analysis to one of the studies and validated the results using the second GWAS. We identified 131 significantly enriched gene sets associated with lung function and clustered them into larger biological modules involved in diverse processes including development, immunity, cell signaling, proliferation and arachidonic acid. We found that enrichment of gene sets was not driven by GWAS-significant variants or loci, but instead by those with less stringent association P-values. Next, we applied pathway enrichment analysis to a meta-analyzed GWAS of airflow obstruction. We identified several biologic modules that functionally overlapped with those associated with pulmonary function. However, differences were also noted, including enrichment of extracellular matrix (ECM) processes specifically in the airflow obstruction study. Network analysis of the ECM module implicated a candidate gene, matrix metalloproteinase 10 (MMP10), as a putative disease target. We used a knockout mouse model to functionally validate MMP10's role in influencing lung's susceptibility to cigarette smoke-induced emphysema. By integrating pathway analysis with population-based genomics, we unraveled biologic processes underlying pulmonary function traits and identified a candidate gene for obstructive lung disease.

  9. Research into the functional components and antioxidant activities of North China rice wine (Ji Mo Lao Jiu)

    PubMed Central

    He, Shuai; Mao, Xiangzhao; Liu, Pei; Lin, Hong; Du, Zuyuan; Lv, Ning; Han, Jichen; Qiu, Cuifang

    2013-01-01

    Over the last decade, considerable experimental evidence has supported the view that grape wine and South China rice wine are rich in diverse nutrients and have powerful antioxidant activity. However, little research has been carried out for North China rice wine, of which Ji Mo Lao Jiu (JMLJ) is the outstanding representative. In this study, the functional components and antioxidant activity of JMLJ were investigated. Twenty-eight free amino acids were found in JMLJ, much more than that previously reported in other Chinese rice wines (16–21). Functional oligosaccharides (5290.222 mg/L), total phenols (722.431 ± 10.970 mg/L), and mineral elements (9) were rich in JMLJ. When compared with synthetic antioxidants, such as butylated hydroxyanisole (BHA) and butylated hydroxytoluene (BHT), JMLJ showed effective 1,1-diphenyl-2-picryl-hydrazyl (DPPH) radical scavenging and reducing capacity. The results of this study lay the foundation for promoting the utilization of JMLJ and the development of North China rice wine in the food industry. PMID:24804035

  10. Updated rice kinase database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Protein kinases catalyze the transfer of a phosphate moiety from a phosphate donor to the substrate molecule, thus, playing critical roles in cell signaling and metabolism. Although plant genomes contain more than 1,000 genes that encode kinases, knowledge is limited about the precise roles for the...

  11. Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy.

    PubMed

    Jung, Ki-Hong; Dardick, Christopher; Bartley, Laura E; Cao, Peijian; Phetsom, Jirapa; Canlas, Patrick; Seo, Young-Su; Shultz, Michael; Ouyang, Shu; Yuan, Qiaoping; Frank, Bryan C; Ly, Eugene; Zheng, Li; Jia, Yi; Hsia, An-Ping; An, Kyungsook; Chou, Hui-Hsien; Rocke, David; Lee, Geun Cheol; Schnable, Patrick S; An, Gynheung; Buell, C Robin; Ronald, Pamela C

    2008-10-06

    Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa). We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the biological significance of the data by analyzing sources of variation and confirming expression trends with reverse transcription polymerase chain reaction. We examined trends in the data by evaluating enrichment of gene ontology terms at multiple false discovery rate thresholds. To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org). The Oligo and EST Anatomy Viewer enables visualization of EST-based expression profiling data for all genes on the array. The Rice Multi-platform Microarray Search Tool facilitates comparison of gene expression profiles across multiple rice microarray platforms. Finally, we incorporated gene expression and biochemical pathway data to reduce the number of candidate gene products putatively participating in the eight steps of the photorespiration pathway from 52 to 10, based on expression levels of putatively functionally redundant genes. We confirmed the efficacy of this method to cope with redundancy by correctly predicting participation in photorespiration of a gene with five paralogs. Applying these methods will accelerate rice functional genomics.

  12. Structure, Function, Interaction, Co-evolution of Rice Blast Resistance Genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice blast disease caused by the fungal pathogen Magnaporthe oryzae is one of the most destructive rice diseases worldwide. Resistance (R) genes to blast encode proteins that detect pathogen signaling molecules encoded by M. oryzae avirulence (AVR) genes. R genes can be a single or a member of clu...

  13. Improvement of whole-genome annotation of cereals through comparative analyses

    PubMed Central

    Zhu, Wei; Buell, C. Robin

    2007-01-01

    Rice is an important model species for the Poaceae and other monocotyledonous plants. With the availability of a near-complete, finished, and annotated rice genome, we performed genome level comparisons between rice and all plant species in which large genomic or transcriptomic data sets are available to determine the utility of cross-species sequence for structural and functional annotation of the rice genome. Through comparative analyses with four plant genome sequence data sets and transcript assemblies from 185 plant species, we were able to confirm and improve the structural annotation of the rice genome. Support for 38,109 (89.3%) of the total 42,653 nontransposable element-related genes in the rice genome in the form of a rice expressed sequence tag, full-length cDNA, or plant homolog from our comparative analyses could be found. Although the majority of the putative homologs were obtained from Poaceae species, putative homologs were identified in dicotyledonous angiosperms, gymnosperms, and other plants such as algae, moss, and fern. A set of rice genes (7669) lacking a putative homolog was identified which may be lineage-specific genes that evolved after speciation and have a role in species diversity. Improvements to the current rice gene structural annotation could be identified from our comparative alignments and we were able to identify 487 genes which were mostly likely missed in the current rice genome annotation and another 500 genes for structural annotation review. We were able to demonstrate the utility of cross-species comparative alignments in the identification of noncoding sequences and in confirmation of gene nesting in rice. PMID:17284677

  14. Introns: The Functional Benefits of Introns in Genomes.

    PubMed

    Jo, Bong-Seok; Choi, Sun Shim

    2015-12-01

    The intron has been a big biological mystery since it was first discovered in several aspects. First, all of the completely sequenced eukaryotes harbor introns in the genomic structure, whereas no prokaryotes identified so far carry introns. Second, the amount of total introns varies in different species. Third, the length and number of introns vary in different genes, even within the same species genome. Fourth, all introns are copied into RNAs by transcription and DNAs by replication processes, but intron sequences do not participate in protein-coding sequences. The existence of introns in the genome should be a burden to some cells, because cells have to consume a great deal of energy to copy and excise them exactly at the correct positions with the help of complicated spliceosomal machineries. The existence throughout the long evolutionary history is explained, only if selective advantages of carrying introns are assumed to be given to cells to overcome the negative effect of introns. In that regard, we summarize previous research about the functional roles or benefits of introns. Additionally, several other studies strongly suggesting that introns should not be junk will be introduced. PMID:26865841

  15. Primate genome architecture influences structural variation mechanisms and functional consequences.

    PubMed

    Gokcumen, Omer; Tischler, Verena; Tica, Jelena; Zhu, Qihui; Iskow, Rebecca C; Lee, Eunjung; Fritz, Markus Hsi-Yang; Langdon, Amy; Stütz, Adrian M; Pavlidis, Pavlos; Benes, Vladimir; Mills, Ryan E; Park, Peter J; Lee, Charles; Korbel, Jan O

    2013-09-24

    Although nucleotide resolution maps of genomic structural variants (SVs) have provided insights into the origin and impact of phenotypic diversity in humans, comparable maps in nonhuman primates have thus far been lacking. Using massively parallel DNA sequencing, we constructed fine-resolution genomic structural variation maps in five chimpanzees, five orang-utans, and five rhesus macaques. The SV maps, which are comprised of thousands of deletions, duplications, and mobile element insertions, revealed a high activity of retrotransposition in macaques compared with great apes. By comparison, nonallelic homologous recombination is specifically active in the great apes, which is correlated with architectural differences between the genomes of great apes and macaque. Transcriptome analyses across nonhuman primates and humans revealed effects of species-specific whole-gene duplication on gene expression. We identified 13 gene duplications coinciding with the species-specific gain of tissue-specific gene expression in keeping with a role of gene duplication in the promotion of diversification and the acquisition of unique functions. Differences in the present day activity of SV formation mechanisms that our study revealed may contribute to ongoing diversification and adaptation of great ape and Old World monkey lineages.

  16. Primate genome architecture influences structural variation mechanisms and functional consequences

    PubMed Central

    Gokcumen, Omer; Tischler, Verena; Tica, Jelena; Zhu, Qihui; Iskow, Rebecca C.; Lee, Eunjung; Fritz, Markus Hsi-Yang; Langdon, Amy; Stütz, Adrian M.; Pavlidis, Pavlos; Benes, Vladimir; Mills, Ryan E.; Park, Peter J.; Lee, Charles; Korbel, Jan O.

    2013-01-01

    Although nucleotide resolution maps of genomic structural variants (SVs) have provided insights into the origin and impact of phenotypic diversity in humans, comparable maps in nonhuman primates have thus far been lacking. Using massively parallel DNA sequencing, we constructed fine-resolution genomic structural variation maps in five chimpanzees, five orang-utans, and five rhesus macaques. The SV maps, which are comprised of thousands of deletions, duplications, and mobile element insertions, revealed a high activity of retrotransposition in macaques compared with great apes. By comparison, nonallelic homologous recombination is specifically active in the great apes, which is correlated with architectural differences between the genomes of great apes and macaque. Transcriptome analyses across nonhuman primates and humans revealed effects of species-specific whole-gene duplication on gene expression. We identified 13 gene duplications coinciding with the species-specific gain of tissue-specific gene expression in keeping with a role of gene duplication in the promotion of diversification and the acquisition of unique functions. Differences in the present day activity of SV formation mechanisms that our study revealed may contribute to ongoing diversification and adaptation of great ape and Old World monkey lineages. PMID:24014587

  17. Multifaceted Genomic Risk for Brain Function in Schizophrenia

    PubMed Central

    Chen, Jiayu; Calhoun, Vince D.; Pearlson, Godfrey D.; Ehrlich, Stefan; Turner, Jessica A.; Ho, Beng-Choon; Wassink, Thomas H.; Michael, Andrew M; Liu, Jingyu

    2012-01-01

    Recently, deriving candidate endophenotypes from brain imaging data has become a valuable approach to study genetic influences on schizophrenia (SZ), whose pathophysiology remains unclear. In this work we utilized a multivariate approach, parallel independent component analysis, to identify genomic risk components associated with brain function abnormalities in SZ. 5157 candidate single nucleotide polymorphisms (SNPs) were derived from genome-wide array based on their possible connections with SZ and further investigated for their associations with brain activations captured with functional magnetic resonance imaging (fMRI) during a sensorimotor task. Using data from 92 SZ patients and 116 healthy controls, we detected a significant correlation (r= 0.29; p= 2.41×10−5) between one fMRI component and one SNP component, both of which significantly differentiated patients from controls. The fMRI component mainly consisted of precentral and postcentral gyri, the major activated regions in the motor task. On average, higher activation in these regions was observed in participants with higher loadings of the linked SNP component, predominantly contributed to by 253 SNPs. 138 identified SNPs were from known coding regions of 100 unique genes. 31 identified SNPs did not differ between groups, but moderately correlated with some other group-discriminating SNPs, indicating interactions among alleles contributing towards elevated SZ susceptibility. The genes associated with the identified SNPs participated in four neurotransmitter pathways: GABA receptor signaling, dopamine receptor signaling, neuregulin signaling and glutamate receptor signaling. In summary, our work provides further evidence for the complexity of genomic risk to the functional brain abnormality in SZ and suggests a pathological role of interactions between SNPs, genes and multiple neurotransmitter pathways. PMID:22440650

  18. High-resolution functional profiling of the norovirus genome.

    PubMed

    Thorne, Lucy; Bailey, Dalan; Goodfellow, Ian

    2012-11-01

    Human noroviruses (HuNoV) are a major cause of nonbacterial gastroenteritis worldwide, yet details of the life cycle and replication of HuNoV are relatively unknown due to the lack of an efficient cell culture system. Studies with murine norovirus (MNV), which can be propagated in permissive cells, have begun to probe different aspects of the norovirus life cycle; however, our understanding of the specific functions of the viral proteins lags far behind that of other RNA viruses. Genome-wide functional profiling by insertional mutagenesis can reveal protein domains essential for replication and can lead to generation of tagged viruses, which has not yet been achieved for noroviruses. Here, transposon-mediated insertional mutagenesis was used to create 5 libraries of mutagenized MNV infectious clones, each containing a 15-nucleotide sequence randomly inserted within a defined region of the genome. Infectious virus was recovered from each library and was subsequently passaged in cell culture to determine the effect of each insertion by insertion-specific fluorescent PCR profiling. Genome-wide profiling of over 2,000 insertions revealed essential protein domains and confirmed known functional motifs. As validation, several insertion sites were introduced into a wild-type clone, successfully allowing the recovery of infectious virus. Screening of a number of reporter proteins and epitope tags led to the generation of the first infectious epitope-tagged noroviruses carrying the FLAG epitope tag in either NS4 or VP2. Subsequent work confirmed that epitope-tagged fully infectious noroviruses may be of use in the dissection of the molecular interactions that occur within the viral replication complex. PMID:22915807

  19. Gene3D: comprehensive structural and functional annotation of genomes.

    PubMed

    Yeats, Corin; Lees, Jonathan; Reid, Adam; Kellam, Paul; Martin, Nigel; Liu, Xinhui; Orengo, Christine

    2008-01-01

    Gene3D provides comprehensive structural and functional annotation of most available protein sequences, including the UniProt, RefSeq and Integr8 resources. The main structural annotation is generated through scanning these sequences against the CATH structural domain database profile-HMM library. CATH is a database of manually derived PDB-based structural domains, placed within a hierarchy reflecting topology, homology and conservation and is able to infer more ancient and divergent homology relationships than sequence-based approaches. This data is supplemented with Pfam-A, other non-domain structural predictions (i.e. coiled coils) and experimental data from UniProt. In order to enhance the investigations possible with this data, we have also incorporated a variety of protein annotation resources, including protein-protein interaction data, GO functional assignments, KEGG pathways, FUNCAT functional descriptions and links to microarray expression data. All of this data can be accessed through a newly re-designed website that has a focus on flexibility and clarity, with searches that can be restricted to a single genome or across the entire sequence database. Currently Gene3D contains over 3.5 million domain assignments for nearly 5 million proteins including 527 completed genomes. This is available at: http://gene3d.biochem.ucl.ac.uk/ PMID:18032434

  20. The Xenopus ORFeome: A resource that enables functional genomics

    PubMed Central

    Grant, Ian M.; Balcha, Dawit; Hao, Tong; Shen, Yun; Trivedi, Prasad; Patrushev, Ilya; Fortriede, Joshua D.; Karpinka, John B.; Liu, Limin; Zorn, Aaron M.; Stukenberg, P. Todd; Hill, David E.; Gilchrist, Michael J.

    2015-01-01

    Functional characterisation of proteins and large-scale, systems-level studies are enabled by extensive sets of cloned open reading frames (ORFs) in an easily-accessible format that enables many different applications. Here we report the release of the first stage of the Xenopus ORFeome, which contains 8673 ORFs from the Xenopus Gene Collection (XGC) for Xenopus laevis, cloned into a Gateway® donor vector enabling rapid in-frame transfer of the ORFs to expression vectors. This resource represents an estimated 7871 unique genes, approximately 40% of the non-redundant X. laevis gene complement, and includes 2724 genes where the human ortholog has an association with disease. Transfer into the Gateway system was validated by 5′ and 3′ end sequencing of the entire collection and protein expression of a set of test clones. In a parallel process, the underlying ORF predictions from the original XGC collection were re-analysed to verify quality and full-length status, identifying those proteins likely to exhibit truncations when translated. These data are integrated into Xenbase, the Xenopus community database, which associates genomic, expression, function and human disease model metadata to each ORF, enabling end-users to search for ORFeome clones with links to commercial distributors of the collection. When coupled with the experimental advantages of Xenopus eggs and embryos, the ORFeome collection represents a valuable resource for functional genomics and disease modelling. PMID:26391338

  1. Genetic Architecture of Flowering Time in Maize As Inferred From Quantitative Trait Loci Meta-analysis and Synteny Conservation With the Rice Genome

    PubMed Central

    Chardon, Fabien; Virlon, Bérangère; Moreau, Laurence; Falque, Matthieu; Joets, Johann; Decousset, Laurent; Murigneux, Alain; Charcosset, Alain

    2004-01-01

    Genetic architecture of flowering time in maize was addressed by synthesizing a total of 313 quantitative trait loci (QTL) available for this trait. These were analyzed first with an overview statistic that highlighted regions of key importance and then with a meta-analysis method that yielded a synthetic genetic model with 62 consensus QTL. Six of these displayed a major effect. Meta-analysis led in this case to a twofold increase in the precision in QTL position estimation, when compared to the most precise initial QTL position within the corresponding region. The 62 consensus QTL were compared first to the positions of the few flowering-time candidate genes that have been mapped in maize. We then projected rice candidate genes onto the maize genome using a synteny conservation approach based on comparative mapping between the maize genetic map and japonica rice physical map. This yielded 19 associations between maize QTL and genes involved in flowering time in rice and in Arabidopsis. Results suggest that the combination of meta-analysis within a species of interest and synteny-based projections from a related model plant can be an efficient strategy for identifying new candidate genes for trait variation. PMID:15611184

  2. Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome.

    PubMed

    Chardon, Fabien; Virlon, Bérangère; Moreau, Laurence; Falque, Matthieu; Joets, Johann; Decousset, Laurent; Murigneux, Alain; Charcosset, Alain

    2004-12-01

    Genetic architecture of flowering time in maize was addressed by synthesizing a total of 313 quantitative trait loci (QTL) available for this trait. These were analyzed first with an overview statistic that highlighted regions of key importance and then with a meta-analysis method that yielded a synthetic genetic model with 62 consensus QTL. Six of these displayed a major effect. Meta-analysis led in this case to a twofold increase in the precision in QTL position estimation, when compared to the most precise initial QTL position within the corresponding region. The 62 consensus QTL were compared first to the positions of the few flowering-time candidate genes that have been mapped in maize. We then projected rice candidate genes onto the maize genome using a synteny conservation approach based on comparative mapping between the maize genetic map and japonica rice physical map. This yielded 19 associations between maize QTL and genes involved in flowering time in rice and in Arabidopsis. Results suggest that the combination of meta-analysis within a species of interest and synteny-based projections from a related model plant can be an efficient strategy for identifying new candidate genes for trait variation.

  3. Integration of molecular functions at the ecosystemic level: breakthroughs and future goals of environmental genomics and post-genomics

    PubMed Central

    Vandenkoornhuyse, Philippe; Dufresne, Alexis; Quaiser, Achim; Gouesbet, Gwenola; Binet, Françoise; Francez, André-Jean; Mahé, Stéphane; Bormans, Myriam; Lagadeuc, Yvan; Couée, Ivan

    2010-01-01

    Environmental genomics and genome-wide expression approaches deal with large-scale sequence-based information obtained from environmental samples, at organismal, population or community levels. To date, environmental genomics, transcriptomics and proteomics are arguably the most powerful approaches to discover completely novel ecological functions and to link organismal capabilities, organism–environment interactions, functional diversity, ecosystem processes, evolution and Earth history. Thus, environmental genomics is not merely a toolbox of new technologies but also a source of novel ecological concepts and hypotheses. By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, environmental genomics enables the integration of sequence-based information into higher ecological and evolutionary levels. However, environmental genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate high-throughput molecular biology techniques into ecology. In this review, the validity of environmental genomics and post-genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations. Novel avenues for improving the use of these approaches to test theory-driven ecological hypotheses are also explored. PMID:20426792

  4. Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase

    PubMed Central

    Li, Dayong; Huang, Zhiyuan; Song, Shuhui; Xin, Yeyun; Mao, Donghai; Lv, Qiming; Zhou, Ming; Tian, Dongmei; Tang, Mingfeng; Wu, Qi; Liu, Xue; Chen, Tingting; Song, Xianwei; Fu, Xiqin; Zhao, Bingran; Liang, Chengzhi; Li, Aihong; Liu, Guozhen; Li, Shigui; Hu, Songnian; Cao, Xiaofeng; Yu, Jun; Yuan, Longping; Chen, Caiyan; Zhu, Lihuang

    2016-01-01

    Hybrid rice is the dominant form of rice planted in China, and its use has extended worldwide since the 1970s. It offers great yield advantages and has contributed greatly to the world’s food security. However, the molecular mechanisms underlying heterosis have remained a mystery. In this study we integrated genetics and omics analyses to determine the candidate genes for yield heterosis in a model two-line rice hybrid system, Liang-you-pei 9 (LYP9) and its parents. Phenomics study revealed that the better parent heterosis (BPH) of yield in hybrid is not ascribed to BPH of all the yield components but is specific to the BPH of spikelet number per panicle (SPP) and paternal parent heterosis (PPH) of effective panicle number (EPN). Genetic analyses then identified multiple quantitative trait loci (QTLs) for these two components. Moreover, a number of differentially expressed genes and alleles in the hybrid were mapped by transcriptome profiling to the QTL regions as possible candidate genes. In parallel, a major QTL for yield heterosis, rice heterosis 8 (RH8), was found to be the DTH8/Ghd8/LHD1 gene. Based on the shared allelic heterozygosity of RH8 in many hybrid rice cultivars, a common mechanism for yield heterosis in the present commercial hybrid rice is proposed. PMID:27663737

  5. Functional characterization of sugarcane mustang domesticated transposases and comparative diversity in sugarcane, rice, maize and sorghum

    PubMed Central

    Kajihara, Daniela; de Godoy, Fabiana; Hamaji, Thais Alves; Blanco, Silvia Regina; Van Sluys, Marie-Anne; Rossi, Magdalena

    2012-01-01

    Transposable elements (TEs) account for a large portion of plant genomes, particularly in grasses, in which they correspond to 50%–80% of the genomic content. TEs have recently been shown to be a source of new genes and new regulatory networks. The most striking contribution of TEs is referred as “molecular domestication”, by which the element coding sequence loses its movement capacity and acquires cellular function. Recently, domesticated transposases known as mustang and derived from the Mutator element have been described in sugarcane. In order to improve our understanding of the function of these proteins, we identified mustang genes from Sorghum bicolor and Zea mays and performed a phenetic analysis to assess the diversity and evolutionary history of this gene family. This analysis identified orthologous groups and showed that mustang genes are highly conserved in grass genomes. We also explored the transcriptional activity of sugarcane mustang genes in heterologous and homologous systems. These genes were found to be ubiquitously transcribed, with shoot apical meristem having the highest expression levels, and were downregulated by phytohormones. Together, these findings suggest the possible involvement of mustang proteins in the maintenance of hormonal homeostasis. PMID:23055803

  6. Generalizing complexity: a fruitful partnership of functional genomics and systems biology

    PubMed Central

    2012-01-01

    A report on the meeting 'Functional Genomics and Systems Biology 2011', Wellcome Trust Conference Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 29 November to 1 December, 2011. PMID:22348308

  7. POLYAMINE OXIDASE 1 from rice (Oryza sativa) is a functional ortholog of Arabidopsis POLYAMINE OXIDASE 5

    PubMed Central

    Liu, Taibo; Wook Kim, Dong; Niitsu, Masaru; Berberich, Thomas; Kusano, Tomonobu

    2014-01-01

    POLYAMINE OXIDASE 1 (OsPAO1), from rice (Oryza sativa), and POLYAMINE OXIDASE 5 (AtPAO5), from Arabidopsis (Arabidopsis thaliana), are enzymes sharing high identity at the amino acid level and with similar characteristics, such as polyamine specificity and pH preference; furthermore, both proteins localize to the cytosol. A loss-of-function Arabidopsis mutant, Atpao5–2, was hypersensitive to low doses of exogenous thermospermine but this phenotype could be rescued by introduction of the wild-type AtPAO5 gene. Introduction of OsPAO1, under the control of a constitutive promoter, into Atpao5–2 mutants also restored normal thermospermine sensitivity, allowing growth in the presence of low levels of thermospermine, along with a concomitant decrease in thermospermine content in plants. By contrast, introduction of OsPAO3, which encodes a peroxisome-localized polyamine oxidase, into Atpao5–2 plants could not rescue any of the mutant phenotypes in the presence of thermospermine. These results suggest that OsPAO1 is the functional ortholog of AtPAO5. PMID:25763711

  8. Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis.

    PubMed

    Sessitsch, A; Hardoim, P; Döring, J; Weilharter, A; Krause, A; Woyke, T; Mitter, B; Hauberg-Lotte, L; Friedrich, F; Rahalkar, M; Hurek, T; Sarkar, A; Bodrossy, L; van Overbeek, L; Brar, D; van Elsas, J D; Reinhold-Hurek, B

    2012-01-01

    Roots are the primary site of interaction between plants and microorganisms. To meet food demands in changing climates, improved yields and stress resistance are increasingly important, stimulating efforts to identify factors that affect plant productivity. The role of bacterial endophytes that reside inside plants remains largely unexplored, because analysis of their specific functions is impeded by difficulties in cultivating most prokaryotes. Here, we present the first metagenomic approach to analyze an endophytic bacterial community resident inside roots of rice, one of the most important staple foods. Metagenome sequences were obtained from endophyte cells extracted from roots of field-grown plants. Putative functions were deduced from protein domains or similarity analyses of protein-encoding gene fragments, and allowed insights into the capacities of endophyte cells. This allowed us to predict traits and metabolic processes important for the endophytic lifestyle, suggesting that the endorhizosphere is an exclusive microhabitat requiring numerous adaptations. Prominent features included flagella, plant-polymer-degrading enzymes, protein secretion systems, iron acquisition and storage, quorum sensing, and detoxification of reactive oxygen species. Surprisingly, endophytes might be involved in the entire nitrogen cycle, as protein domains involved in N(2)-fixation, denitrification, and nitrification were detected and selected genes expressed. Our data suggest a high potential of the endophyte community for plant-growth promotion, improvement of plant stress resistance, biocontrol against pathogens, and bioremediation, regardless of their culturability.

  9. Wheat EST resources for functional genomics of abiotic stress

    PubMed Central

    Houde, Mario; Belcaid, Mahdi; Ouellet, François; Danyluk, Jean; Monroy, Antonio F; Dryanova, Ani; Gulick, Patrick; Bergeron, Anne; Laroche, André; Links, Matthew G; MacCarthy, Luke; Crosby, William L; Sarhan, Fathey

    2006-01-01

    Background Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS) project. Results We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets). Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology. Conclusion We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in wheat and other cereals. PMID

  10. Functional Genome Screening to Elucidate the Colistin Resistance Mechanism

    PubMed Central

    Kumar, Mohit; Gupta, Ashutosh; Sahoo, Rajesh Kumar; Jena, Jayanti; Debata, Nagen Kumar; Subudhi, Enketeswara

    2016-01-01

    Antibiogram profile of 1590 clinical bacterial isolates based on thirteen different antimicrobial compounds showed that 1.6% of the bacterial isolates are multidrug resistant. Distribution pattern based on 16S rRNA sequence analysis showed that Pseudomonas aeruginosa constituted the largest group (83.6%) followed by Burkholderia pseudomallei sp. A191 (5.17%), Staphylococcus sp. A261 (3.45%). Among the various antibiotics used, colistin appeared to be the most effective against the Gram negative bacteria. Burkholderia pseudomallei sp. A191 and Pseudomonas aeruginosa sp. A111 showed resistance to 1500 μg/ml and 750 μg/ml of colistin respectively which constitutes 7.7% of the bacterial population. A functional genomics strategy was employed to discover the molecular support for colistin resistance in Burkholderia pseudomallei sp. A191. A pUC plasmid-based genomic expression library was constructed with an estimated library size of 2.1 × 107bp. Five colistin resistant clones were obtained after functional screening of the library. Analysis of DNA sequence of five colistin resistant clones showed homology to two component regularity systems (TCRS) encoding for a histidine kinase (mrgS) and its regulatory component (mrgR). Cross complementation assay showed that mutations in mrgS were sufficient enough to confer colistin resistant phenotype in a sensitive strain. PMID:26988670

  11. Functional Genome Screening to Elucidate the Colistin Resistance Mechanism.

    PubMed

    Kumar, Mohit; Gupta, Ashutosh; Sahoo, Rajesh Kumar; Jena, Jayanti; Debata, Nagen Kumar; Subudhi, Enketeswara

    2016-01-01

    Antibiogram profile of 1590 clinical bacterial isolates based on thirteen different antimicrobial compounds showed that 1.6% of the bacterial isolates are multidrug resistant. Distribution pattern based on 16S rRNA sequence analysis showed that Pseudomonas aeruginosa constituted the largest group (83.6%) followed by Burkholderia pseudomallei sp. A191 (5.17%), Staphylococcus sp. A261 (3.45%). Among the various antibiotics used, colistin appeared to be the most effective against the Gram negative bacteria. Burkholderia pseudomallei sp. A191 and Pseudomonas aeruginosa sp. A111 showed resistance to 1500 μg/ml and 750 μg/ml of colistin respectively which constitutes 7.7% of the bacterial population. A functional genomics strategy was employed to discover the molecular support for colistin resistance in Burkholderia pseudomallei sp. A191. A pUC plasmid-based genomic expression library was constructed with an estimated library size of 2.1 × 10(7)bp. Five colistin resistant clones were obtained after functional screening of the library. Analysis of DNA sequence of five colistin resistant clones showed homology to two component regularity systems (TCRS) encoding for a histidine kinase (mrgS) and its regulatory component (mrgR). Cross complementation assay showed that mutations in mrgS were sufficient enough to confer colistin resistant phenotype in a sensitive strain. PMID:26988670

  12. Cubozoan genome illuminates functional diversification of opsins and photoreceptor evolution.

    PubMed

    Liegertová, Michaela; Pergner, Jiří; Kozmiková, Iryna; Fabian, Peter; Pombinho, Antonio R; Strnad, Hynek; Pačes, Jan; Vlček, Čestmír; Bartůněk, Petr; Kozmik, Zbyněk

    2015-07-08

    Animals sense light primarily by an opsin-based photopigment present in a photoreceptor cell. Cnidaria are arguably the most basal phylum containing a well-developed visual system. The evolutionary history of opsins in the animal kingdom has not yet been resolved. Here, we study the evolution of animal opsins by genome-wide analysis of the cubozoan jellyfish Tripedalia cystophora, a cnidarian possessing complex lens-containing eyes and minor photoreceptors. A large number of opsin genes with distinct tissue- and stage-specific expression were identified. Our phylogenetic analysis unequivocally classifies cubozoan opsins as a sister group to c-opsins and documents lineage-specific expansion of the opsin gene repertoire in the cubozoan genome. Functional analyses provided evidence for the use of the Gs-cAMP signaling pathway in a small set of cubozoan opsins, indicating the possibility that the majority of other cubozoan opsins signal via distinct pathways. Additionally, these tests uncovered subtle differences among individual opsins, suggesting possible fine-tuning for specific photoreceptor tasks. Based on phylogenetic, expression and biochemical analysis we propose that rapid lineage- and species-specific duplications of the intron-less opsin genes and their subsequent functional diversification promoted evolution of a large repertoire of both visual and extraocular photoreceptors in cubozoans.

  13. Functional analysis of the rice rubisco activase promoter in transgenic Arabidopsis

    SciTech Connect

    Yang, Zhipan; Lu, Qingtao; Wen, Xiaogang; Chen, Fan; Lu, Congming

    2012-02-17

    Highlights: Black-Right-Pointing-Pointer Rice rubisco activase promoter was analyzed in transgenic Arabidopsis system. Black-Right-Pointing-Pointer Region conferring tissue specific and light inducible expression of Rca was identified. Black-Right-Pointing-Pointer -58 to +43 bp region mediates tissue-specific expression of rice Rca. Black-Right-Pointing-Pointer Light inducible expression of rice Rca is mediated by -297 to -58 bp region. Black-Right-Pointing-Pointer Rice nuclear proteins bind specifically with the light inducible region. -- Abstract: To gain a better understanding of the regulatory mechanism of the rice rubisco activase (Rca) gene, variants of the Rca gene promoter (one full-length and four deletion mutants) fused to the coding region of the bacterial reporter gene {beta}-glucuronidase (GUS) were introduced into Arabidopsis via Agrobacterium-mediated transformation. Our results show that a 340 bp fragment spanning from -297 to +43 bp relative to the transcription initiation site is enough to promote tissue-specific and light-inducible expression of the rice Rca gene as done by the full-length promoter (-1428 to +43 bp). Further deletion analysis indicated that the region conferring tissue-specificity of Rca expression is localized within a 105 bp fragment from -58 to +43 bp, while light-inducible expression of Rca is mediated by the region from -297 to -58 bp. Gel shift assays and competition experiments demonstrated that rice nuclear proteins bind specifically with the fragment conferring light responsiveness at more than one binding site. This implies that multiple cis-elements may be involved in light-induced expression of the rice Rca gene. These works provide a useful reference for understanding transcriptional regulation mechanism of the rice Rca gene, and lay a strong foundation for further detection of related cis-elements and trans-factors.

  14. Evolutionary insights into the origins of weediness in U.S. red rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Weedy red rice is a widespread, economically challenging problem in Southern U.S. rice fields. The two major U.S. red rice types, strawhull and blackhull, are thought to have arisen independently from Asian rice populations in the distant past. Red rice is a weedy relative of rice, a genomic model...

  15. Functional genomics of PCOS: from GWAS to molecular mechanisms.

    PubMed

    McAllister, Jan M; Legro, Richard S; Modi, Bhavi P; Strauss, Jerome F

    2015-03-01

    Polycystic ovary syndrome (PCOS) is a common endocrinopathy characterized by increased ovarian androgen biosynthesis, anovulation, and infertility. PCOS has a strong heritable component based on familial clustering and twin studies. Genome-wide association studies (GWAS) identified several PCOS candidate loci including LHCGR, FSHR, ZNF217, YAP1, INSR, RAB5B, and C9orf3. We review the functional roles of strong PCOS candidate loci focusing on FSHR, LHCGR, INSR, and DENND1A. We propose that these candidates comprise a hierarchical signaling network by which DENND1A, LHCGR, INSR, RAB5B, adapter proteins, and associated downstream signaling cascades converge to regulate theca cell androgen biosynthesis. Future elucidation of the functional gene networks predicted by the PCOS GWAS will result in new diagnostic and therapeutic approaches for women with PCOS.

  16. Cadmium accumulation retard activity of functional components of photo assimilation and growth of rice cultivars amended with vermicompost.

    PubMed

    Sebastian, Abin; Prasad, M N V

    2013-01-01

    Cadmium (Cd) uptake mediated alterations in functional components of photo assimilation during conversion of cow dung and poultry cast to vermicompost were studied in two Indian rice cultivars; MO 16 and MTU 7029. It was found that higher amount of Cd accumulate in plants grown in soil amended with vermicompost which in turn damaged functional components in photo assimilation. Enhancement of root growth was recognized as reason for Cd accumulation. Metabolic alterations noticed among plants were not taken place during application of raw materials used for vermicomposting such as cow dung and poultry cast amendment. Rice varieties accumulated Cd differentially where MTU 7029 accumulated more Cd compare to MO 16. It was also noticed that existence of negative correlation between zinc status of the plant and Cd accumulation.

  17. Comparative population genomics: power and principles for the inference of functionality.

    PubMed

    Lawrie, David S; Petrov, Dmitri A

    2014-04-01

    The availability of sequenced genomes from multiple related organisms allows the detection and localization of functional genomic elements based on the idea that such elements evolve more slowly than neutral sequences. Although such comparative genomics methods have proven useful in discovering functional elements and ascertaining levels of functional constraint in the genome as a whole, here we outline limitations intrinsic to this approach that cannot be overcome by sequencing more species. We argue that it is essential to supplement comparative genomics with ultra-deep sampling of populations from closely related species to enable substantially more powerful genomic scans for functional elements. The convergence of sequencing technology and population genetics theory has made such projects feasible and has exciting implications for functional genomics.

  18. Genome-Wide Analysis of MicroRNAs and Their Target Genes Related to Leaf Senescence of Rice

    PubMed Central

    Liu, Chaoping; Chen, Eryong; Chen, Qifeng; Zhuang, Jieyun; Shen, Bo

    2014-01-01

    Grain production of rice (Oryza sativa L.) is a top priority in ensuring food security for human beings. One of the approaches to increase yield is to delay leaf senescence and to extend the available time for photosynthesis. MicroRNAs (miRNAs) are key regulators of aging and cellular senescence in eukaryotes. Here, to help understand their biological role in rice leaf senescence, we report identification of miRNAs and their putative target genes by deep sequencing of six small RNA libraries, six RNA-seq libraries and two degradome libraries from the leaves of two super hybrid rice, Nei-2-You 6 (N2Y6, age-resistant rice) and Liang-You-Pei 9 (LYP9, age-sensitive rice). In total 372 known miRNAs, 162 miRNA candidates and 1145 targets were identified. Compared with the expression of miRNAs in the leaves of LYP9, the numbers of miRNAs up-regulated and down-regulated in the leaves of N2Y6 were 47 and 30 at early stage of grain-filling, 21 and 17 at the middle stage, and 11 and 37 at the late stage, respectively. Six miRNA families, osa-miR159, osa-miR160 osa-miR164, osa-miR167, osa-miR172 and osa-miR1848, targeting the genes encoding APETALA2 (AP2), zinc finger proteins, salicylic acid-induced protein 19 (SIP19), auxin response factors (ARF) and NAC transcription factors, respectively, were found to be involved in leaf senescence through phytohormone signaling pathways. These results provided valuable information for understanding the miRNA-mediated leaf senescence of rice, and offered an important foundation for rice breeding. PMID:25479006

  19. Functional conservation of Rel binding sites in drosophilid genomes.

    PubMed

    Copley, Richard R; Totrov, Maxim; Linnell, Jane; Field, Simon; Ragoussis, Jiannis; Udalova, Irina A

    2007-09-01

    Evolutionary constraints on gene regulatory elements are poorly understood: Little is known about how the strength of transcription factor binding correlates with DNA sequence conservation, and whether transcription factor binding sites can evolve rapidly while retaining their function. Here we use the model of the NFKB/Rel-dependent gene regulation in divergent Drosophila species to examine the hypothesis that the functional properties of authentic transcription factor binding sites are under stronger evolutionary constraints than the genomic background. Using molecular modeling we compare tertiary structures of the Drosophila Rel family proteins Dorsal, Dif, and Relish and demonstrate that their DNA-binding and protein dimerization domains undergo distinct rates of evolution. The accumulated amino acid changes, however, are unlikely to affect DNA sequence recognition and affinity. We employ our recently developed microarray-based experimental platform and principal coordinates statistical analysis to quantitatively and systematically profile DNA binding affinities of three Drosophila Rel proteins to 10,368 variants of the NFKB recognition sequences. We then correlate the evolutionary divergence of gene regulatory regions with differences in DNA binding affinities. Genome-wide analyses reveal a significant increase in the number of conserved Rel binding sites in promoters of developmental and immune genes. Significantly, the affinity of Rel proteins to these sites was higher than to less conserved sites and was maintained by the conservation of the DNA binding site sequence (static conservation) or in some cases despite significantly diverged sequences (dynamic conservation). We discuss how two types of conservation may contribute to the stabilization and optimization of a functional gene regulatory code in evolution.

  20. Functional conservation of Rel binding sites in drosophilid genomes

    PubMed Central

    Copley, Richard R.; Totrov, Maxim; Linnell, Jane; Field, Simon; Ragoussis, Jiannis; Udalova, Irina A.

    2007-01-01

    Evolutionary constraints on gene regulatory elements are poorly understood: Little is known about how the strength of transcription factor binding correlates with DNA sequence conservation, and whether transcription factor binding sites can evolve rapidly while retaining their function. Here we use the model of the NFKB/Rel-dependent gene regulation in divergent Drosophila species to examine the hypothesis that the functional properties of authentic transcription factor binding sites are under stronger evolutionary constraints than the genomic background. Using molecular modeling we compare tertiary structures of the Drosophila Rel family proteins Dorsal, Dif, and Relish and demonstrate that their DNA-binding and protein dimerization domains undergo distinct rates of evolution. The accumulated amino acid changes, however, are unlikely to affect DNA sequence recognition and affinity. We employ our recently developed microarray-based experimental platform and principal coordinates statistical analysis to quantitatively and systematically profile DNA binding affinities of three Drosophila Rel proteins to 10,368 variants of the NFKB recognition sequences. We then correlate the evolutionary divergence of gene regulatory regions with differences in DNA binding affinities. Genome-wide analyses reveal a significant increase in the number of conserved Rel binding sites in promoters of developmental and immune genes. Significantly, the affinity of Rel proteins to these sites was higher than to less conserved sites and was maintained by the conservation of the DNA binding site sequence (static conservation) or in some cases despite significantly diverged sequences (dynamic conservation). We discuss how two types of conservation may contribute to the stabilization and optimization of a functional gene regulatory code in evolution. PMID:17785540

  1. Genome-Wide Association Mapping for Yield and Other Agronomic Traits in an Elite Breeding Population of Tropical Rice (Oryza sativa)

    PubMed Central

    Lalusin, Antonio; Borromeo, Teresita; Gregorio, Glenn; Hernandez, Jose; Virk, Parminder; Collard, Bertrand; McCouch, Susan R.

    2015-01-01

    Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models. PMID:25785447

  2. Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa).

    PubMed

    Begum, Hasina; Spindel, Jennifer E; Lalusin, Antonio; Borromeo, Teresita; Gregorio, Glenn; Hernandez, Jose; Virk, Parminder; Collard, Bertrand; McCouch, Susan R

    2015-01-01

    Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.

  3. Biocatalysis for the production of industrial products and functional foods from rice and other agricultural produce.

    PubMed

    Akoh, Casimir C; Chang, Shu-Wei; Lee, Guan-Chiun; Shaw, Jei-Fu

    2008-11-26

    Many industrial products and functional foods can be obtained from cheap and renewable raw agricultural materials. For example, starch can be converted to bioethanol as biofuel to reduce the current demand for petroleum or fossil fuel energy. On the other hand, starch can also be converted to useful functional ingredients, such as high fructose and high maltose syrups, wine, glucose, and trehalose. The conversion process involves fermentation by microorganisms and use of biocatalysts such as hydrolases of the amylase superfamily. Amylases catalyze the process of liquefaction and saccharification of starch. It is possible to perform complete hydrolysis of starch by using the fusion product of both linear and debranching thermostable enzymes. This will result in saving energy otherwise needed for cooling before the next enzyme can act on the substrate, if a sequential process is utilized. Recombinant enzyme technology, protein engineering, and enzyme immobilization are powerful tools available to enhance the activity of enzymes, lower the cost of enzyme through large scale production in a heterologous host, increase their thermostability, improve pH stability, enhance their productivity, and hence making it competitive with the chemical processes involved in starch hydrolysis and conversions. This review emphasizes the potential of using biocatalysis for the production of useful industrial products and functional foods from cheap agricultural produce and transgenic plants. Rice was selected as a typical example to illustrate many applications of biocatalysis in converting low-value agricultural produce to high-value commercial food and industrial products. The greatest advantages of using enzymes for food processing and for industrial production of biobased products are their environmental friendliness and consumer acceptance as being a natural process. PMID:18942836

  4. Biocatalysis for the production of industrial products and functional foods from rice and other agricultural produce.

    PubMed

    Akoh, Casimir C; Chang, Shu-Wei; Lee, Guan-Chiun; Shaw, Jei-Fu

    2008-11-26

    Many industrial products and functional foods can be obtained from cheap and renewable raw agricultural materials. For example, starch can be converted to bioethanol as biofuel to reduce the current demand for petroleum or fossil fuel energy. On the other hand, starch can also be converted to useful functional ingredients, such as high fructose and high maltose syrups, wine, glucose, and trehalose. The conversion process involves fermentation by microorganisms and use of biocatalysts such as hydrolases of the amylase superfamily. Amylases catalyze the process of liquefaction and saccharification of starch. It is possible to perform complete hydrolysis of starch by using the fusion product of both linear and debranching thermostable enzymes. This will result in saving energy otherwise needed for cooling before the next enzyme can act on the substrate, if a sequential process is utilized. Recombinant enzyme technology, protein engineering, and enzyme immobilization are powerful tools available to enhance the activity of enzymes, lower the cost of enzyme through large scale production in a heterologous host, increase their thermostability, improve pH stability, enhance their productivity, and hence making it competitive with the chemical processes involved in starch hydrolysis and conversions. This review emphasizes the potential of using biocatalysis for the production of useful industrial products and functional foods from cheap agricultural produce and transgenic plants. Rice was selected as a typical example to illustrate many applications of biocatalysis in converting low-value agricultural produce to high-value commercial food and industrial products. The greatest advantages of using enzymes for food processing and for industrial production of biobased products are their environmental friendliness and consumer acceptance as being a natural process.

  5. A novel Azotobacter vinellandii (SRIAz 3) functions in salinity stress tolerance in rice.

    PubMed

    Sahoo, Ranjan Kumar; Ansari, Mohammad Wahid; Pradhan, Madhusmita; Dangar, Tushar K; Mohanty, Santanu; Tuteja, Narendra

    2014-05-29

    The plant growth promoting rhizobacteria (PGPRs) as a biofertilizer provide agricultural benefits to advance various crops productivity. Recently, we discovered a novel Azotobacter vinellandii (SRIAz 3) from rice rhizosphere, which is well competent to improve rice productivity. In this study, we investigated a role of A. vinellandii to confer salinity tolerance in rice (var. IR64). A. vinellandii inoculated rice plants showed higher proline and malondialdehyde content under 200 mM NaCl stress as compared with uninoculated one. The endogenous level of plant hormones viz., indole-3 acetic acid (IAA), gibberellins (GA 3), zeatint (Zt) was higher in A. vinellandii inoculated plants under high salinity. The fresh biomass of root and shoot were relatively elevated in A. vinellandii inoculated rice. Further, the macronutrient profile was superior in A. vinellandii inoculated plants under salinity as compared with non-inoculated plants. The present findings further suggest that A. vinellandii, a potent biofertilzer, potentially confer salinity stress tolerance in rice via sustaining growth and improving compatible solutes and nutrients profile and thereby crop improvement.

  6. Epigenetic regulation of rice flowering and reproduction

    PubMed Central

    Shi, Jinlei; Dong, Aiwu; Shen, Wen-Hui

    2015-01-01

    Current understanding of the epigenetic regulator roles in plant growth and development has largely derived from studies in the dicotyledonous model plant Arabidopsis thaliana. Rice (Oryza sativa) is one of the most important food crops in the world and has more recently becoming a monocotyledonous model plant in functional genomics research. During the past few years, an increasing number of studies have reported the impact of DNA methylation, non-coding RNAs and histone modifications on transcription regulation, flowering time control, and reproduction in rice. Here, we review these studies to provide an updated complete view about chromatin modifiers characterized in rice and in particular on their roles in epigenetic regulation of flowering time, reproduction, and seed development. PMID:25674094

  7. Understanding salinity responses and adopting 'omics-based' approaches to generate salinity tolerant cultivars of rice.

    PubMed

    Das, Priyanka; Nutan, Kamlesh K; Singla-Pareek, Sneh L; Pareek, Ashwani

    2015-01-01

    Soil salinity is one of the main constraints affecting production of rice worldwide, by reducing growth, pollen viability as well as yield of the plant. Therefore, detailed understanding of the response of rice towards soil salinity at the physiological and molecular level is a prerequisite for its effective management. Various approaches have been adopted by molecular biologists or breeders to understand the mechanism for salinity tolerance in plants and to develop salt tolerant rice cultivars. Genome wide analysis using 'omics-based' tools followed by identification and functional validation of individual genes is becoming one of the popular approaches to tackle this task. On the other hand, mutation breeding and insertional mutagenesis has also been exploited to obtain salinity tolerant crop plants. This review looks into various responses at cellular and whole plant level generated in rice plants toward salinity stress thus, evaluating the suitability of intervention of functional genomics to raise stress tolerant plants. We have tried to highlight the usefulness of the contemporary 'omics-based' approaches such as genomics, proteomics, transcriptomics and phenomics towards dissecting out the salinity tolerance trait in rice. In addition, we have highlighted the importance of integration of various 'omics' approaches to develop an understanding of the machinery involved in salinity response in rice and to move forward to develop salt tolerant cultivars of rice. PMID:26442026

  8. NCBI GEO: archive for high-throughput functional genomic data.

    PubMed

    Barrett, Tanya; Troup, Dennis B; Wilhite, Stephen E; Ledoux, Pierre; Rudnev, Dmitry; Evangelista, Carlos; Kim, Irene F; Soboleva, Alexandra; Tomashevsky, Maxim; Marshall, Kimberly A; Phillippy, Katherine H; Sherman, Patti M; Muertter, Rolf N; Edgar, Ron

    2009-01-01

    The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest public repository for high-throughput gene expression data. Additionally, GEO hosts other categories of high-throughput functional genomic data, including those that examine genome copy number variations, chromatin structure, methylation status and transcription factor binding. These data are generated by the research community using high-throughput technologies like microarrays and, more recently, next-generation sequencing. The database has a flexible infrastructure that can capture fully annotated raw and processed data, enabling compliance with major community-derived scientific reporting standards such as 'Minimum Information About a Microarray Experiment' (MIAME). In addition to serving as a centralized data storage hub, GEO offers many tools and features that allow users to effectively explore, analyze and download expression data from both gene-centric and experiment-centric perspectives. This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.

  9. Sugarcane Functional Genomics: Gene Discovery for Agronomic Trait Development

    PubMed Central

    Menossi, M.; Silva-Filho, M. C.; Vincentz, M.; Van-Sluys, M.-A.; Souza, G. M.

    2008-01-01

    Sugarcane is a highly productive crop used for centuries as the main source of sugar and recently to produce ethanol, a renewable bio-fuel energy source. There is increased interest in this crop due to the impending need to decrease fossil fuel usage. Sugarcane has a highly polyploid genome. Expressed sequence tag (EST) sequencing has significantly contributed to gene discovery and expression studies used to associate function with sugarcane genes. A significant amount of data exists on regulatory events controlling responses to herbivory, drought, and phosphate deficiency, which cause important constraints on yield and on endophytic bacteria, which are highly beneficial. The means to reduce drought, phosphate deficiency, and herbivory by the sugarcane borer have a negative impact on the environment. Improved tolerance for these constraints is being sought. Sugarcane's ability to accumulate sucrose up to 16% of its culm dry weight is a challenge for genetic manipulation. Genome-based technology such as cDNA microarray data indicates genes associated with sugar content that may be used to develop new varieties improved for sucrose content or for traits that restrict the expansion of the cultivated land. The genes can also be used as molecular markers of agronomic traits in traditional breeding programs. PMID:18273390

  10. Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica

    PubMed Central

    Kube, Michael; Chernikova, Tatyana N.; Al-Ramahi, Yamal; Beloqui, Ana; Lopez-Cortez, Nieves; Guazzaroni, María-Eugenia; Heipieper, Hermann J.; Klages, Sven; Kotsyurbenko, Oleg R.; Langer, Ines; Nechitaylo, Taras Y.; Lünsdorf, Heinrich; Fernández, Marisol; Juárez, Silvia; Ciordia, Sergio; Singer, Alexander; Kagan, Olga; Egorova, Olga; Alain Petit, Pierre; Stogios, Peter; Kim, Youngchang; Tchigvintsev, Anatoli; Flick, Robert; Denaro, Renata; Genovese, Maria; Albar, Juan P.; Reva, Oleg N.; Martínez-Gomariz, Montserrat; Tran, Hai; Ferrer, Manuel; Savchenko, Alexei; Yakunin, Alexander F.; Yakimov, Michail M.; Golyshina, Olga V.; Reinhardt, Richard; Golyshin, Peter N.

    2013-01-01

    Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica and show that compared with Alcanivorax borkumensis—the paradigm of mesophilic hydrocarbonoclastic bacteria—O. antarctica has a larger genome that has witnessed massive gene-transfer events. We identify an array of alkane monooxygenases, osmoprotectants, siderophores and micronutrient-scavenging pathways. We also show that at low temperatures, the main protein-folding machine Cpn60 functions as a single heptameric barrel that uses larger proteins as substrates compared with the classical double-barrel structure observed at higher temperatures. With 11 protein crystal structures, we further report the largest set of structures from one psychrotolerant organism. The most common structural feature is an increased content of surface-exposed negatively charged residues compared to their mesophilic counterparts. Our findings are relevant in the context of microbial cold-adaptation mechanisms and the development of strategies for oil-spill mitigation in cold environments. PMID:23877221

  11. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

    SciTech Connect

    Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-02

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  12. Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation.

    PubMed

    Piao, Hailan; Froula, Jeff; Du, Changbin; Kim, Tae-Wan; Hawley, Erik R; Bauer, Stefan; Wang, Zhong; Ivanova, Nathalia; Clark, Douglas S; Klenk, Hans-Peter; Hess, Matthias

    2014-08-01

    Although recent nucleotide sequencing technologies have significantly enhanced our understanding of microbial genomes, the function of ∼35% of genes identified in a genome currently remains unknown. To improve the understanding of microbial genomes and consequently of microbial processes it will be crucial to assign a function to this "genomic dark matter." Due to the urgent need for additional carbohydrate-active enzymes for improved production of transportation fuels from lignocellulosic biomass, we screened the genomes of more than 5,500 microorganisms for hypothetical proteins that are located in the proximity of already known cellulases. We identified, synthesized and expressed a total of 17 putative cellulase genes with insufficient sequence similarity to currently known cellulases to be identified as such using traditional sequence annotation techniques that rely on significant sequence similarity. The recombinant proteins of the newly identified putative cellulases were subjected to enzymatic activity assays to verify their hydrolytic activity towards cellulose and lignocellulosic biomass. Eleven (65%) of the tested enzymes had significant activity towards at least one of the substrates. This high success rate highlights that a gene context-based approach can be used to assign function to genes that are otherwise categorized as "genomic dark matter" and to identify biomass-degrading enzymes that have little sequence similarity to already known cellulases. The ability to assign function to genes that have no related sequence representatives with functional annotation will be important to enhance our understanding of microbial processes and to identify microbial proteins for a wide range of applications.

  13. Biodiversity and functional genomics in the human microbiome.

    PubMed

    Morgan, Xochitl C; Segata, Nicola; Huttenhower, Curtis

    2013-01-01

    Over the course of our lives, humans are colonized by a tremendous diversity of commensal microbes, which comprise the human microbiome. The collective genetic potential (metagenome) of the human microbiome is orders of magnitude more than the human genome, and it profoundly affects human health and disease in ways we are only beginning to understand. Advances in computing and high-throughput sequencing have enabled population-level surveys such as MetaHIT and the recently released Human Microbiome Project, detailed investigations of the microbiome in human disease, and mechanistic studies employing gnotobiotic model organisms. The resulting knowledge of human microbiome composition, function, and range of variation across multiple body sites has begun to assemble a rich picture of commensal host-microbe and microbe-microbe interactions as well as their roles in human health and disease and their potential as diagnostic and therapeutic tools.

  14. Comparative genomics of pectinacetylesterases: Insight on function and biology

    PubMed Central

    de Souza, Amancio José; Pauly, Markus

    2015-01-01

    Pectin acetylation influences the gelling ability of this important plant polysaccharide for the food industry. Plant apoplastic pectinacetylesterases (PAEs) play a key role in regulating the degree of pectin acetylation and modifying their expression thus represents one way to engineer plant polysaccharides for food applications. Identifying the major active enzymes within the PAE gene family will aid in our understanding of this biological phenomena as well as provide the tools for direct trait manipulation. Using comparative genomics we propose that there is a minimal set of 4 distinct PAEs in plants. Possible functional diversification of the PAE family in the grasses is also explored with the identification of 3 groups of PAE genes specific to grasses. PMID:26237162

  15. NCBI GEO: archive for functional genomics data sets--update.

    PubMed

    Barrett, Tanya; Wilhite, Stephen E; Ledoux, Pierre; Evangelista, Carlos; Kim, Irene F; Tomashevsky, Maxim; Marshall, Kimberly A; Phillippy, Katherine H; Sherman, Patti M; Holko, Michelle; Yefanov, Andrey; Lee, Hyeseung; Zhang, Naigong; Robertson, Cynthia L; Serova, Nadezhda; Davis, Sean; Soboleva, Alexandra

    2013-01-01

    The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community. The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable. All data are freely available for download in a variety of formats. GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data. This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data.

  16. Biodiversity and Functional Genomics in the Human Microbiome

    PubMed Central

    Morgan, Xochitl C.; Segata, Nicola; Huttenhower, Curtis

    2012-01-01

    Over the course of our lives, humans are colonized by a tremendous diversity of commensal microbes, which comprise the human microbiome. The collective genetic potential (metagenome) of the human microbiome is orders of magnitude more than the human genome, and it profoundly affects human health and disease in ways we are only beginning to understand. Advances in computing and high-throughput sequencing have enabled population-level surveys such as MetaHIT and the recently-released Human Microbiome Project, detailed investigations of the microbiome in human disease, and mechanistic studies employing gnotobiotic model organisms. The resulting knowledge of human microbiome composition, function, and range of variation across multiple body sites has begun to assemble a rich picture of commensal host-microbe and microbe- microbe interactions as well as their roles in human health and disease and their potential as diagnostic and therapeutic tools. PMID:23140990

  17. Molecular analysis of the genome segments S1, S4, S6, S7 and S12 of a Rice gall dwarf virus isolate from Thailand; completion of the genomic sequence.

    PubMed

    Moriyasu, Y; Maruyama-Funatsuki, W; Kikuchi, A; Ichimi, K; Zhong, B; Yan, J; Zhu, Y; Suga, H; Watanabe, Y; Ichiki-Uehara, T; Shimizu, T; Hagiwara, K; Kamiunten, H; Akutsu, K; Omura, T

    2007-01-01

    The complete nucleotide sequences of the double-stranded RNA segments S1, S4, S6, S7 and S12 of the genome of a Rice gall dwarf virus (RGDV) isolate from Thailand were determined. The segments consisted of 4505, 2622, 1648, 1652 and 853 nucleotides, encoding putative proteins of 1458, 725, 489, 511 and 206 amino acids with molecular masses of approximately 166, 80, 53, 59 and 24 kDa, respectively. Homology searches indicated that each of the putative proteins has a counterpart in isolates of Rice dwarf virus (RDV) and Wound tumor virus, two other species in the genus Phytoreovirus. However, no similarities were found to other registered sequences, including those of other viruses that belong to the family Reoviridae. The identities between homologous structural proteins of RGDV and RDV ranged from 34 to 51% and were thus higher than those between homologous non-structural proteins of RGDV and RDV (16-37%). Among the nonstructural proteins, the highest amino acid sequence identity (37%) was observed for RGDV Pns11 and RDV Pns10, a constituent of tubular inclusions. This observation suggests that a specific amino acid backbone might be required for maintaining not only the three-dimensional structure of virions but also that of inclusions. The entire sequence of the RGDV genome is now available.

  18. Functional genomics of tomato in a post-genome-sequencing phase

    PubMed Central

    Aoki, Koh; Ogata, Yoshiyuki; Igarashi, Kaori; Yano, Kentaro; Nagasaki, Hideki; Kaminuma, Eli; Toyoda, Atsushi

    2013-01-01

    Completion of tomato genome sequencing project has broad impacts on genetic and genomic studies of tomato and Solanaceae plants. The reference genome sequence derived from Solanum lycopersicum cv ‘Heinz 1706’ serves as the firm basis for sequencing-based approaches to tomato genomics. In this article, we first present a brief summary of the genome sequencing project and a summary of the reference genome sequence. We then focus on recent progress in transcriptome sequencing and small RNA sequencing and show how the reference genome sequence makes these analyses more comprehensive than before. We discuss the potential of in-depth analysis that is based on DNA methylome sequencing and transcription start-site detection. Finally, we describe the current status of efforts to resequence S. lycopersicum cultivars to demonstrate how resequencing can allow the use of intraspecific genomic diversity for detailed phenotyping and breeding. PMID:23641177

  19. Functional genomics of the horn fly, Haematobia irritans (Linnaeus, 1758)

    PubMed Central

    2011-01-01

    Background The horn fly, Haematobia irritans (Linnaeus, 1758) (Diptera: Muscidae) is one of the most important ectoparasites of pastured cattle. Horn flies infestations reduce cattle weight gain and milk production. Additionally, horn flies are mechanical vectors of different pathogens that cause disease in cattle. The aim of this study was to conduct a functional genomics study in female horn flies using Expressed Sequence Tags (EST) analysis and RNA interference (RNAi). Results A cDNA library was made from whole abdominal tissues collected from partially fed adult female horn flies. High quality horn fly ESTs (2,160) were sequenced and assembled into 992 unigenes (178 contigs and 814 singlets) representing molecular functions such as serine proteases, cell metabolism, mitochondrial function, transcription and translation, transport, chromatin structure, vitellogenesis, cytoskeleton, DNA replication, cell response to stress and infection, cell proliferation and cell-cell interactions, intracellular trafficking and secretion, and development. Functional analyses were conducted using RNAi for the first time in horn flies. Gene knockdown by RNAi resulted in higher horn fly mortality (protease inhibitor functional group), reduced oviposition (vitellogenin, ferritin and vATPase groups) or both (immune response and 5'-NUC groups) when compared to controls. Silencing of ubiquitination ESTs did not affect horn fly mortality and ovisposition while gene knockdown in the ferritin and vATPse functional groups reduced mortality when compared to controls. Conclusions These results advanced the molecular characterization of this important ectoparasite and suggested candidate protective antigens for the development of vaccines for the control of horn fly infestations. PMID:21310032

  20. Functional cis-regulatory genomics for systems biology

    PubMed Central

    Nam, Jongmin; Dong, Ping; Tarpine, Ryan; Istrail, Sorin; Davidson, Eric H.

    2010-01-01

    Gene expression is controlled by interactions between trans-regulatory factors and cis-regulatory DNA sequences, and these interactions constitute the essential functional linkages of gene regulatory networks (GRNs). Validation of GRN models requires experimental cis-regulatory tests of predicted linkages to authenticate their identities and proposed functions. However, cis-regulatory analysis is, at present, at a severe bottleneck in genomic system biology because of the demanding experimental methodologies currently in use for discovering cis-regulatory modules (CRMs), in the genome, and for measuring their activities. Here we demonstrate a high-throughput approach to both discovery and quantitative characterization of CRMs. The unique aspect is use of DNA sequence tags to “barcode” CRM expression constructs, which can then be mixed, injected together into sea urchin eggs, and subsequently deconvolved. This method has increased the rate of cis-regulatory analysis by >100-fold compared with conventional one-by-one reporter assays. The utility of the DNA-tag reporters was demonstrated by the rapid discovery of 81 active CRMs from 37 previously unexplored sea urchin genes. We then obtained simultaneous high-resolution temporal characterization of the regulatory activities of more than 80 CRMs. On average 2–3 CRMs were discovered per gene. Comparison of endogenous gene expression profiles with those of the CRMs recovered from each gene showed that, for most cases, at least one CRM is active in each phase of endogenous expression, suggesting that CRM recovery was comprehensive. This approach will qualitatively alter the practice of GRN construction as well as validation, and will impact many additional areas of regulatory system biology. PMID:20142491

  1. Functional Analysis of Shewanella, a cross genome comparison.

    SciTech Connect

    Serres, Margrethe H.

    2009-05-15

    The bacterial genus Shewanella includes a group of highly versatile organisms that have successfully adapted to life in many environments ranging from aquatic (fresh and marine) to sedimentary (lake and marine sediments, subsurface sediments, sea vent). A unique respiratory capability of the Shewanellas, initially observed for Shewanella oneidensis MR-1, is the ability to use metals and metalloids, including radioactive compounds, as electron acceptors. Members of the Shewanella genus have also been shown to degrade environmental pollutants i.e. halogenated compounds, making this group highly applicable for the DOE mission. S. oneidensis MR-1 has in addition been found to utilize a diverse set of nutrients and to have a large set of genes dedicated to regulation and to sensing of the environment. The sequencing of the S. oneidensis MR-1 genome facilitated experimental and bioinformatics analyses by a group of collaborating researchers, the Shewanella Federation. Through the joint effort and with support from Department of Energy S. oneidensis MR-1 has become a model organism of study. Our work has been a functional analysis of S. oneidensis MR-1, both by itself and as part of a comparative study. We have improved the annotation of gene products, assigned metabolic functions, and analyzed protein families present in S. oneidensis MR-1. The data has been applied to analysis of experimental data (i.e. gene expression, proteome) generated for S. oneidensis MR-1. Further, this work has formed the basis for a comparative study of over 20 members of the Shewanella genus. The species and strains selected for genome sequencing represented an evolutionary gradient of DNA relatedness, ranging from close to intermediate, and to distant. The organisms selected have also adapted to a variety of ecological niches. Through our work we have been able to detect and interpret genome similarities and differences between members of the genus. We have in this way contributed to the

  2. Plant Ion Channels: Gene Families, Physiology, and Functional Genomics Analyses

    PubMed Central

    Ward, John M.; Mäser, Pascal; Schroeder, Julian I.

    2016-01-01

    Distinct potassium, anion, and calcium channels in the plasma membrane and vacuolar membrane of plant cells have been identified and characterized by patch clamping. Primarily owing to advances in Arabidopsis genetics and genomics, and yeast functional complementation, many of the corresponding genes have been identified. Recent advances in our understanding of ion channel genes that mediate signal transduction and ion transport are discussed here. Some plant ion channels, for example, ALMT and SLAC anion channel subunits, are unique. The majority of plant ion channel families exhibit homology to animal genes; such families include both hyperpolarization-and depolarization-activated Shaker-type potassium channels, CLC chloride transporters/channels, cyclic nucleotide–gated channels, and ionotropic glutamate receptor homologs. These plant ion channels offer unique opportunities to analyze the structural mechanisms and functions of ion channels. Here we review gene families of selected plant ion channel classes and discuss unique structure-function aspects and their physiological roles in plant cell signaling and transport. PMID:18842100

  3. GIANT API: an application programming interface for functional genomics

    PubMed Central

    Roberts, Andrew M.; Wong, Aaron K.; Fisk, Ian; Troyanskaya, Olga G.

    2016-01-01

    GIANT API provides biomedical researchers programmatic access to tissue-specific and global networks in humans and model organisms, and associated tools, which includes functional re-prioritization of existing genome-wide association study (GWAS) data. Using tissue-specific interaction networks, researchers are able to predict relationships between genes specific to a tissue or cell lineage, identify the changing roles of genes across tissues and uncover disease-gene associations. Additionally, GIANT API enables computational tools like NetWAS, which leverages tissue-specific networks for re-prioritization of GWAS results. The web services covered by the API include 144 tissue-specific functional gene networks in human, global functional networks for human and six common model organisms and the NetWAS method. GIANT API conforms to the REST architecture, which makes it stateless, cacheable and highly scalable. It can be used by a diverse range of clients including web browsers, command terminals, programming languages and standalone apps for data analysis and visualization. The API is freely available for use at http://giant-api.princeton.edu. PMID:27098035

  4. GIANT API: an application programming interface for functional genomics.

    PubMed

    Roberts, Andrew M; Wong, Aaron K; Fisk, Ian; Troyanskaya, Olga G

    2016-07-01

    GIANT API provides biomedical researchers programmatic access to tissue-specific and global networks in humans and model organisms, and associated tools, which includes functional re-prioritization of existing genome-wide association study (GWAS) data. Using tissue-specific interaction networks, researchers are able to predict relationships between genes specific to a tissue or cell lineage, identify the changing roles of genes across tissues and uncover disease-gene associations. Additionally, GIANT API enables computational tools like NetWAS, which leverages tissue-specific networks for re-prioritization of GWAS results. The web services covered by the API include 144 tissue-specific functional gene networks in human, global functional networks for human and six common model organisms and the NetWAS method. GIANT API conforms to the REST architecture, which makes it stateless, cacheable and highly scalable. It can be used by a diverse range of clients including web browsers, command terminals, programming languages and standalone apps for data analysis and visualization. The API is freely available for use at http://giant-api.princeton.edu. PMID:27098035

  5. GIANT API: an application programming interface for functional genomics.

    PubMed

    Roberts, Andrew M; Wong, Aaron K; Fisk, Ian; Troyanskaya, Olga G

    2016-07-01

    GIANT API provides biomedical researchers programmatic access to tissue-specific and global networks in humans and model organisms, and associated tools, which includes functional re-prioritization of existing genome-wide association study (GWAS) data. Using tissue-specific interaction networks, researchers are able to predict relationships between genes specific to a tissue or cell lineage, identify the changing roles of genes across tissues and uncover disease-gene associations. Additionally, GIANT API enables computational tools like NetWAS, which leverages tissue-specific networks for re-prioritization of GWAS results. The web services covered by the API include 144 tissue-specific functional gene networks in human, global functional networks for human and six common model organisms and the NetWAS method. GIANT API conforms to the REST architecture, which makes it stateless, cacheable and highly scalable. It can be used by a diverse range of clients including web browsers, command terminals, programming languages and standalone apps for data analysis and visualization. The API is freely available for use at http://giant-api.princeton.edu.

  6. Genome-Wide Analysis of the Expansin Gene Superfamily Reveals Grapevine-Specific Structural and Functional Characteristics

    PubMed Central

    Tornielli, Giovanni Battista; Fasoli, Marianna; Venturini, Luca; Pezzotti, Mario; Zenoni, Sara

    2013-01-01

    Background Expansins are proteins that loosen plant cell walls in a pH-dependent manner, probably by increasing the relative movement among polymers thus causing irreversible expansion. The expansin superfamily (EXP) comprises four distinct families: expansin A (EXPA), expansin B (EXPB), expansin-like A (EXLA) and expansin-like B (EXLB). There is experimental evidence that EXPA and EXPB proteins are required for cell expansion and developmental processes involving cell wall modification, whereas the exact functions of EXLA and EXLB remain unclear. The complete grapevine (Vitis vinifera) genome sequence has allowed the characterization of many gene families, but an exhaustive genome-wide analysis of expansin gene expression has not been attempted thus far. Methodology/Principal Findings We identified 29 EXP superfamily genes in the grapevine genome, representing all four EXP families. Members of the same EXP family shared the same exon–intron structure, and phylogenetic analysis confirmed a closer relationship between EXP genes from woody species, i.e. grapevine and poplar (Populus trichocarpa), compared to those from Arabidopsis thaliana and rice (Oryza sativa). We also identified grapevine-specific duplication events involving the EXLB family. Global gene expression analysis confirmed a strong correlation among EXP genes expressed in mature and green/vegetative samples, respectively, as reported for other gene families in the recently-published grapevine gene expression atlas. We also observed the specific co-expression of EXLB genes in woody organs, and the involvement of certain grapevine EXP genes in berry development and post-harvest withering. Conclusion Our comprehensive analysis of the grapevine EXP superfamily confirmed and extended current knowledge about the structural and functional characteristics of this gene family, and also identified properties that are currently unique to grapevine expansin genes. Our data provide a model for the functional

  7. Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function

    PubMed Central

    Tran, Hoa T; Krushkal, Julia; Antommattei, Frances M; Lovley, Derek R; Weis, Robert M

    2008-01-01

    Background Geobacter species are δ-Proteobacteria and are often the predominant species in a variety of sedimentary environments where Fe(III) reduction is important. Their ability to remediate contaminated environments and produce electricity makes them attractive for further study. Cell motility, biofilm formation, and type IV pili all appear important for the growth of Geobacter in changing environments and for electricity production. Recent studies in other bacteria have demonstrated that signaling pathways homologous to the paradigm established for Escherichia coli chemotaxis can regulate type IV pili-dependent motility, the synthesis of flagella and type IV pili, the production of extracellular matrix material, and biofilm formation. The classification of these pathways by comparative genomics improves the ability to understand how Geobacter thrives in natural environments and better their use in microbial fuel cells. Results The genomes of G. sulfurreducens, G. metallireducens, and G. uraniireducens contain multiple (~70) homologs of chemotaxis genes arranged in several major clusters (six, seven, and seven, respectively). Unlike the single gene cluster of E. coli, the Geobacter clusters are not all located near the flagellar genes. The probable functions of some Geobacter clusters are assignable by homology to known pathways; others appear to be unique to the Geobacter sp. and contain genes of unknown function. We identified large numbers of methyl-accepting chemotaxis protein (MCP) homologs that have diverse sensing domain architectures and generate a potential for sensing a great variety of environmental signals. We discuss mechanisms for class-specific segregation of the MCPs in the cell membrane, which serve to maintain pathway specificity and diminish crosstalk. Finally, the regulation of gene expression in Geobacter differs from E. coli. The sequences of predicted promoter elements suggest that the alternative sigma factors σ28 and σ54 play a role

  8. A functional gene cluster for toxoflavin biosynthesis in the genome of the soil bacterium Pseudomonas protegens Pf-5

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Toxoflavin is a broad-spectrum toxin best known for its role in virulence of Burkholderia glumae, which causes panicle blight of rice. A gene cluster containing homologs of toxoflavin biosynthesis genes (toxA-E) of B. glumae is present in the genome of Pseudomonas protegens Pf-5, a biological contr...

  9. Effect of rice starch as a bath additive on the barrier function of healthy but SLS-damaged skin and skin of atopic patients.

    PubMed

    De Paepe, Kristien; Hachem, Jean-Pierre; Vanpee, Els; Roseeuw, Diane; Rogiers, Vera

    2002-01-01

    Rice starch added to bath water was studied for its possible beneficial effects on impaired barrier function as evaluated by transepidermal water loss measurements. The forearm skin of healthy volunteers was irritated by sodium lauryl sulphate. Exposure to rice-starch-containing bath water--twice daily for 15 min--led to a 20% improvement on the healing capacity of damaged skin. The beneficial effect was also observed for a rice-starch-containing lipid-free bath formulation, and an oil-in-water bath lotion enriched with evening primrose oil. Skin barrier function in patients with atopic dermatitis also improved after the addition of starch powder to bath water. Rice starch in powder or formulated in a bath product can therefore be recommended as a skin repair bathing additive for barrier damaged skin, particularly in the case of atopic dermatitis patients.

  10. Genome-Wide Association Studies Reveal that Diverse Heading Date Genes Respond to Short and Long Day Lengths between Indica and Japonica Rice

    PubMed Central

    Han, Zhongmin; Zhang, Bo; Zhao, Hu; Ayaad, Mohammed; Xing, Yongzhong

    2016-01-01

    Rice is a short-day plant. Short-day length promotes heading, and long-day length suppresses heading. Many studies have evaluated rice heading in field conditions in which some individuals in the population were exposed to various day lengths, including short and long days, prior to a growth phase transition. In this study, we investigated heading date under natural short-day conditions (SD) and long-day conditions (LD) for 100s of accessions and separately conducted genome-wide association studies within indica and japonica subpopulations. Under LD, three and four quantitative trait loci (QTLs) were identified in indica and japonica subpopulations, respectively, two of which were less than 80 kb from the known genes Hd17 and Ghd7. But no common QTLs were detected in both subpopulations. Under SD, six QTLs were detected in indica, three of which were less than 80 kb from the known heading date genes Ghd7, Ehd1, and RCN1. But no QTLs were detected in japonica subpopulation. qHd3 under SD and qHd4 under LD were two novel major QTLs, which deserve isolation in the future. Eleven known heading date genes were used to test the power of association mapping at the haplotype level. Hd17, Ghd7, Ehd1, and RCN1 were again detected at more significant level and three additional genes, Hd3a, OsMADS56, and Ghd7.1, were detected. However, of the detected seven genes, only one gene, Hd17, was commonly detected in both subpopulations and two genes, Ghd7 and Ghd7.1, were commonly detected in indica subpopulation under both conditions. Moreover, haplotype analysis identified favorable haplotypes of Ghd7 and OsMADS56 for breeding design. In conclusion, diverse heading date genes/QTLs between indica and japonica subpopulations responded to SD and LD, and haplotype-level association mapping was more powerful than SNP-level association in rice.

  11. Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice

    PubMed Central

    Lacombe, Séverine; Nagasaki, Hiroshi; Santi, Carole; Duval, David; Piégu, Benoît; Bangratz, Martine; Breitler, Jean-Christophe; Guiderdoni, Emmanuel; Brugidou, Christophe; Hirsch, Judith; Cao, Xiaofeng; Brice, Claire; Panaud, Olivier; Karlowski, Wojciech M; Sato, Yutaka; Echeverria, Manuel

    2008-01-01

    Background The plant miRNAs represent an important class of endogenous small RNAs that guide cleavage of an mRNA target or repress its translation to control development and adaptation to stresses. MiRNAs are nuclear-encoded genes transcribed by RNA polymerase II, producing a primary precursor that is subsequently processed by DCL1 an RNase III Dicer-like protein. In rice hundreds of miRNAs have been described or predicted, but little is known on their genes and precursors which are important criteria to distinguish them from siRNAs. Here we develop a combination of experimental approaches to detect novel miRNAs in rice, identify their precursor transcripts and genes and predict or validate their mRNA targets. Results We produced four cDNA libraries from small RNA fractions extracted from distinct rice tissues. By in silico analysis we selected 6 potential novel miRNAs, and confirmed that their expression requires OsDCL1. We predicted their targets and used 5'RACE to validate cleavage for three of them, targeting a PPR, an SPX domain protein and a GT-like transcription factor respectively. In addition, we identified precursor transcripts for the 6 miRNAs expressed in rice, showing that these precursors can be efficiently processed using a transient expression assay in transfected Nicotiana benthamiana leaves. Most interestingly, we describe two precursors producing tandem miRNAs, but in distinct arrays. We focus on one of them encoding osa-miR159a.2, a novel miRNA produced from the same stem-loop structure encoding the conserved osa-miR159a.1. We show that this dual osa-miR159a.2-osa-miR159a.1 structure is conserved in distant rice species and maize. Finally we show that the predicted mRNA target of osa-miR159a.2 encoding a GT-like transcription factor is cleaved in vivo at the expected site. Conclusion The combination of approaches developed here identified six novel miRNAs expressed in rice which can be clearly distinguished from siRNAs. Importantly, we show that

  12. Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses

    PubMed Central

    2012-01-01

    Background Carotenoids are isoprenoid pigments, essential for photosynthesis and photoprotection in plants. The enzyme phytoene synthase (PSY) plays an essential role in mediating condensation of two geranylgeranyl diphosphate molecules, the first committed step in carotenogenesis. PSY are nuclear enzymes encoded by a small gene family consisting of three paralogous genes (PSY1-3) that have been widely characterized in rice, maize and sorghum. Results In wheat, for which yellow pigment content is extremely important for flour colour, only PSY1 has been extensively studied because of its association with QTLs reported for yellow pigment whereas PSY2 has been partially characterized. Here, we report the isolation of bread wheat PSY3 genes from a Renan BAC library using Brachypodium as a model genome for the Triticeae to develop Conserved Orthologous Set markers prior to gene cloning and sequencing. Wheat PSY3 homoeologous genes were sequenced and annotated, unravelling their novel structure associated with intron-loss events and consequent exonic fusions. A wheat PSY3 promoter region was also investigated for the presence of cis-acting elements involved in the response to abscisic acid (ABA), since carotenoids also play an important role as precursors of signalling molecules devoted to plant development and biotic/abiotic stress responses. Expression of wheat PSYs in leaves and roots was investigated during ABA treatment to confirm the up-regulation of PSY3 during abiotic stress. Conclusions We investigated the structural and functional determinisms of PSY genes in wheat. More generally, among eudicots and monocots, the PSY gene family was found to be associated with differences in gene copy numbers, allowing us to propose an evolutionary model for the entire PSY gene family in Grasses. PMID:22672222

  13. Metabolomic Functional Analysis of Bacterial Genomes: Final Report

    SciTech Connect

    Arp, Daniel J; Sayavedra-Soto, Luis A

    2008-01-01

    The availability of the complete DNA sequence of the bacterial genome of Nitrosomonas europaea offered the opportunity for unprecedented and detailed investigations of function. We studied the function of genes involved in carbohydrate and Fe metabolism. N. europaea has genes for the synthesis and degradation of glycogen and sucrose but cannot grow on substrates other than ammonia and CO2. Granules of glycogen were detected in whole cells by electron microscopy and quantified in cell-free extracts by enzymatic methods. The cellular glycogen and sucrose content varied depending on the composition of the growth medium and cellular growth stage. N. europaea also depends heavily on iron for metabolism of ammonia, is particularly interesting since it lacks genes for siderophore production, and has genes with only low similarity to known iron reductases, yet grows relatively well in medium containing low Fe. By comparing the transcriptomes of cells grown in iron-replete medium versus iron-limited medium, 247 genes were identified as differentially expressed. Mutant strains deficient in genes for sucrose, glycogen and iron metabolism were created and are being used to further our understanding of ammonia oxidizing bacteria.