WorldWideScience

Sample records for genome allotetraploid rice

  1. Genome evolution in the allotetraploid frog Xenopus laevis

    Science.gov (United States)

    Session, Adam M.; Uno, Yoshinobu; Kwon, Taejoon; Chapman, Jarrod A.; Toyoda, Atsushi; Takahashi, Shuji; Fukui, Akimasa; Hikosaka, Akira; Suzuki, Atsushi; Kondo, Mariko; van Heeringen, Simon J.; Quigley, Ian; Heinz, Sven; Ogino, Hajime; Ochi, Haruki; Hellsten, Uffe; Lyons, Jessica B; Simakov, Oleg; Putnam, Nicholas; Stites, Jonathan; Kuroki, Yoko; Tanaka, Toshiaki; Michiue, Tatsuo; Watanabe, Minoru; Bogdanovic, Ozren; Lister, Ryan; Georgiou, Georgios; Paranjpe, Sarita S.; van Kruijsbergen, Ila; Shu, Shengquiang; Carlson, Joseph; Kinoshita, Tsutomu; Ohta, Yuko; Mawaribuchi, Shuuji; Jenkins, Jerry; Grimwood, Jane; Schmutz, Jeremy; Mitros, Therese; Mozaffari, Sahar; Suzuki, Yutaka; Haramoto, Yoshikazu; Yamamoto, Takamasa S.; Takagi, Chiyo; Heald, Rebecca; Miller, Kelly; Haudenschild, Christian; Kitzman, Jacob; Nakayama, Takuya; Izutsu, Yumi; Robert, Jacques; Fortriede, Joshua; Burns, Kevin; Lotay, Vaneet; Karimi, Kamran; Yasuoka, Yuuri; Dichmann, Darwin S.; Flajnik, Martin F.; Houston, Douglas W; Shendure, Jay; DuPasquier, Louis; Vize, Peter D.; Zorn, Aaron M.; Ito, Michihiko; Marcotte, Ed; Wallingford, John B.; Ito, Yuzuru; Asashima, Makoto; Ueno, Naoto; Matsuda, Yoichi; Veenstra, Gert Jan C.; Fujiyama, Asao

    2017-01-01

    To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We demonstrate the allotetraploid origin of X. laevis by partitioning its genome into two homeologous subgenomes, marked by distinct families of “fossil” transposable elements. Based on the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged ~34 million years ago (Mya) and combined to form an allotetraploid ~17–18 Mya. 56% of all genes are retained in two homeologous copies. Protein function, gene expression, and the amount of flanking conserved sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression. PMID:27762356

  2. Genome evolution in the allotetraploid frog Xenopus laevis.

    Science.gov (United States)

    Session, Adam M; Uno, Yoshinobu; Kwon, Taejoon; Chapman, Jarrod A; Toyoda, Atsushi; Takahashi, Shuji; Fukui, Akimasa; Hikosaka, Akira; Suzuki, Atsushi; Kondo, Mariko; van Heeringen, Simon J; Quigley, Ian; Heinz, Sven; Ogino, Hajime; Ochi, Haruki; Hellsten, Uffe; Lyons, Jessica B; Simakov, Oleg; Putnam, Nicholas; Stites, Jonathan; Kuroki, Yoko; Tanaka, Toshiaki; Michiue, Tatsuo; Watanabe, Minoru; Bogdanovic, Ozren; Lister, Ryan; Georgiou, Georgios; Paranjpe, Sarita S; van Kruijsbergen, Ila; Shu, Shengquiang; Carlson, Joseph; Kinoshita, Tsutomu; Ohta, Yuko; Mawaribuchi, Shuuji; Jenkins, Jerry; Grimwood, Jane; Schmutz, Jeremy; Mitros, Therese; Mozaffari, Sahar V; Suzuki, Yutaka; Haramoto, Yoshikazu; Yamamoto, Takamasa S; Takagi, Chiyo; Heald, Rebecca; Miller, Kelly; Haudenschild, Christian; Kitzman, Jacob; Nakayama, Takuya; Izutsu, Yumi; Robert, Jacques; Fortriede, Joshua; Burns, Kevin; Lotay, Vaneet; Karimi, Kamran; Yasuoka, Yuuri; Dichmann, Darwin S; Flajnik, Martin F; Houston, Douglas W; Shendure, Jay; DuPasquier, Louis; Vize, Peter D; Zorn, Aaron M; Ito, Michihiko; Marcotte, Edward M; Wallingford, John B; Ito, Yuzuru; Asashima, Makoto; Ueno, Naoto; Matsuda, Yoichi; Veenstra, Gert Jan C; Fujiyama, Asao; Harland, Richard M; Taira, Masanori; Rokhsar, Daniel S

    2016-10-20

    To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.

  3. Analysis of Complete Nucleotide Sequences of 12 Gossypium Chloroplast Genomes: Origin and Evolution of Allotetraploids

    Science.gov (United States)

    Xu, Qin; Xiong, Guanjun; Li, Pengbo; He, Fei; Huang, Yi; Wang, Kunbo; Li, Zhaohu; Hua, Jinping

    2012-01-01

    Background Cotton (Gossypium spp.) is a model system for the analysis of polyploidization. Although ascertaining the donor species of allotetraploid cotton has been intensively studied, sequence comparison of Gossypium chloroplast genomes is still of interest to understand the mechanisms underlining the evolution of Gossypium allotetraploids, while it is generally accepted that the parents were A- and D-genome containing species. Here we performed a comparative analysis of 13 Gossypium chloroplast genomes, twelve of which are presented here for the first time. Methodology/Principal Findings The size of 12 chloroplast genomes under study varied from 159,959 bp to 160,433 bp. The chromosomes were highly similar having >98% sequence identity. They encoded the same set of 112 unique genes which occurred in a uniform order with only slightly different boundary junctions. Divergence due to indels as well as substitutions was examined separately for genome, coding and noncoding sequences. The genome divergence was estimated as 0.374% to 0.583% between allotetraploid species and A-genome, and 0.159% to 0.454% within allotetraploids. Forty protein-coding genes were completely identical at the protein level, and 20 intergenic sequences were completely conserved. The 9 allotetraploids shared 5 insertions and 9 deletions in whole genome, and 7-bp substitutions in protein-coding genes. The phylogenetic tree confirmed a close relationship between allotetraploids and the ancestor of A-genome, and the allotetraploids were divided into four separate groups. Progenitor allotetraploid cotton originated 0.43–0.68 million years ago (MYA). Conclusion Despite high degree of conservation between the Gossypium chloroplast genomes, sequence variations among species could still be detected. Gossypium chloroplast genomes preferred for 5-bp indels and 1–3-bp indels are mainly attributed to the SSR polymorphisms. This study supports that the common ancestor of diploid A-genome species in

  4. Evidence of Genomic Exchanges between Homeologous Chromosomes in a Cross of Peanut with Newly Synthetized Allotetraploid Hybrids

    Science.gov (United States)

    Nguepjop, Joel R.; Tossim, Hodo-Abalo; Bell, Joseph M.; Rami, Jean-François; Sharma, Shivali; Courtois, Brigitte; Mallikarjuna, Nalini; Sane, Djibril; Fonceka, Daniel

    2016-01-01

    Cultivated peanut and synthetics are allotetraploids (2n = 4x = 40) with two homeologous sets of chromosomes. Meiosis in allotetraploid peanut is generally thought to show diploid-like behavior. However, a recent study pointed out the occurrence of recombination between homeologous chromosomes, especially when synthetic allotetraploids are used, challenging the view of disomic inheritance in peanut. In this study, we investigated the meiotic behavior of allotetraploid peanut using 380 SSR markers and 90 F2 progeny derived from the cross between Arachis hypogaea cv Fleur 11 (AABB) and ISATGR278-18 (AAKK), a synthetic allotetraploid that harbors a K-genome that was reported to pair with the cultivated B-genome during meiosis. Segregation analysis of SSR markers showed 42 codominant SSRs with unexpected null bands among some progeny. Chi-square tests for these loci deviate from the expected 1:2:1 Mendelian ratio under disomic inheritance. A linkage map of 357 codominant loci aligned on 20 linkage groups (LGs) with a total length of 1728 cM, averaging 5.1 cM between markers, was developed. Among the 10 homeologous sets of LGs, one set consisted of markers that all segregated in a polysomic-like pattern, six in a likely disomic pattern and the three remaining in a mixed pattern with disomic and polysomic loci clustered on the same LG. Moreover, we reported a substitution of homeologous chromosomes in some progeny. Our results suggest that the homeologous recombination events occurred between the A and K genomes in the newly synthesized allotetraploid and have been highlighted in the progeny. Homeologous exchanges are rarely observed in tetraploid peanut and have not yet been reported for AAKK and AABB genomes. The implications of these results on peanut breeding are discussed. PMID:27847512

  5. Evidence of genomic exchanges between homeologous chromosomes in a cross of peanut with newly synthetized allotetraploid hybrids

    Directory of Open Access Journals (Sweden)

    Joel Romaric Nguepjop

    2016-11-01

    Full Text Available Cultivated peanut and synthetics are allotetraploids (2n=4x=40 with two homeologous sets of chromosomes. Meiosis in allotetraploid peanut is generally thought to show diploid-like behavior. However, a recent study pointed out the occurrence of recombination between homeologous chromosomes, especially when synthetic allotetraploids are used, challenging the view of disomic inheritance in peanut. In this study, we investigated the meiotic behavior of allotetraploid peanut using 380 SSR markers and 90 F2 progeny derived from the cross between Arachis hypogaea cv Fleur 11 (AABB and ISATGR278-18 (AAKK, a synthetic allotetraploid that harbors a K-genome that was reported to pair with the cultivated B-genome during meiosis. Segregation analysis of SSR markers showed 42 codominant SSRs with unexpected null bands among some progeny. Chi-square tests for these loci deviate from the expected 1:2:1 Mendelian ratio under disomic inheritance. A linkage map of 357 codominant loci aligned on 20 linkage groups (LGs with a total length of 1728 cM, averaging 5.1 cM between markers, was developed. Among the ten homeologous sets of LGs, one set consisted of markers that all segregated in a polysomic-like pattern, 6 in a likely disomic pattern and the 3 remaining in a mixed pattern with disomic and polysomic loci clustered on the same LG. Moreover, we reported a substitution of homeologous chromosomes in some progeny. Our results suggest that the homeologous recombination events occurred between the A and K genomes in the newly synthesized allotetraploid and have been highlighted in the progeny. Homeologous exchanges are rarely observed in tetraploid peanut and have not yet been reported for AAKK and AABB genomes. The implications of these results on peanut breeding are discussed.

  6. Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons

    Science.gov (United States)

    Cotton domestication was achieved by converting perennial trees into annual crops. After ploidization, two allotetraploid species, Gossypium hirsutum and G. barbadense, were domesticated and are cultivated worldwide. However, the overall genetic diversity between and within the cultivated species is...

  7. Genetic Segregation and Genomic Hybridization Patterns Support an Allotetraploid Structure and Disomic Inheritance for Salix Species

    Directory of Open Access Journals (Sweden)

    Gianni Barcaccia

    2014-09-01

    Full Text Available The Salix alba L. (white willow—Salix fragilis L. (crack willow complex includes closely related polyploid species, mainly tetraploid (2n = 4x = 76, which are dioecious and hence obligate allogamous. Because little is known about the genome constitution and chromosome behavior of these pure willow trees, genetic analysis of their naturally occurring interspecific polyploid hybrids is still very difficult. A two-way pseudo-testcross strategy was exploited using single-dose AFLP markers in order to assess the main inheritance patterns of tetraploid biotypes (disomy vs. tetrasomy in segregating populations stemmed from S. alba × S. fragilis crosses and reciprocals. In addition, a genomic in situ hybridization (GISH technology was implemented in willow to shed some light on the genome structure of S. alba and S. fragilis species, and their hybrids (allopolyploidy vs. autopolyploidy. The frequency of S. alba-specific molecular markers was almost double compared to that of S. fragilis-specific ones, suggesting the phylogenetic hypothesis of S. fragilis as derivative species from S. alba-like progenitors. Cytogenetic observations at pro-metaphase revealed about half of the chromosome complements being less contracted than the remaining ones, supporting an allopolyploid origin of both S. alba and S. fragilis. Both genetic segregation and genomic hybridization data are consistent with an allotetraploid nature of the Salix species. In particular, the vast majority of the AFLP markers were inherited according to disomic patterns in S. alba × S. fragilis populations and reciprocals. Moreover, in all S. alba against S. fragilis hybridizations and reciprocals, GISH signals were observed only on the contracted chromosomes whereas the non-contracted chromosomes were never hybridized. In conclusion, half of the chromosomes of the pure species S. alba and S. fragilis are closely related and they could share a common diploid ancestor, while the rest of

  8. Comparative genomics analysis of rice and pineapple contributes to understand the chromosome number reduction and genomic changes in grasses

    Directory of Open Access Journals (Sweden)

    Jinpeng Wang

    2016-10-01

    Full Text Available 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 5 or 7 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.

  9. Genome-Wide Gene Expressions Respond Differently to A-subgenome Origins in Brassica napus Synthetic Hybrids and Natural Allotetraploid

    Science.gov (United States)

    Zhang, Dawei; Pan, Qi; Tan, Chen; Zhu, Bin; Ge, Xianhong; Shao, Yujiao; Li, Zaiyun

    2016-01-01

    The young allotetraploid Brassica napus (2n = 38, AACC) is one of models to study genomic responses to allopolyploidization. The extraction of AA component from natural B. napus and then restitution of progenitor B. rapa should provide a unique opportunity to reveal the genome interplay for gene expressions during the evolution. Herein, B. napus hybrids (2n = 19, AC) between the extracted and extant B. rapa (2n = 20, AA) and the same B. oleracea genotype (2n = 18, CC) were studied by RNA-seq and compared with natural B. napus donor, to reveal the gene expression changes from hybridization and domestication and the effects of A genome with different origins. Upon the initial merger of two diploid genomes, additive gene expression was prevalent in these two hybrids, for non-additively expressed genes only represented a small portion of total expressed genes. A high proportion of genes exhibited expression level dominance, with no preference to either of the parental genomes. Comparison of homoeolog expressions also showed no bias toward any genomes and the parental expression patterns were often maintained in the hybrids and natural allotetraploids. Although, the overall patterns of gene expression were highly conserved between two hybrids, the extracted B. rapa responded less and appeared more compatible for hybridization than the extant B. rapa. Our results suggested that expression level dominance and homoeolog expressions bias were balanced at the initial stage of genome merger, and such balance were largely maintained during the domestication of B. napus, despite the increased extent over time. PMID:27790227

  10. Small RNA in rice genome

    Institute of Scientific and Technical Information of China (English)

    王凯; 朱小蓬; 钟兰; 陈润生

    2002-01-01

    Rice has many characteristics of a model plant. The recent completion of the draft of the rice genome represents an important advance in our knowledge of plant biology and also has an important contribution to the understanding of general genomic evolution. Besides the rice genome finishing map, the next urgent step for rice researchers is to annotate the genes and noncoding functional sequences. The recent work shows that noncoding RNAs (ncRNAs) play significant roles in biological systems. We have explored all the known small RNAs (a kind of ncRNA) within rice genome and other six species sequences, including Arabidopsis, maize, yeast, worm, mouse and pig. As a result we find 160 out of 552 small RNAs (sRNAs) in database have homologs in 108 rice scaffolds, and almost all of them (99.41%) locate in intron regions of rice by gene predication. 19 sRNAs only appear in rice. More importantly, we find two special U14 sRNAs: one is located in a set of sRNA ZMU14SNR9(s) which only appears in three plants, 86% sequences of them can be compared as the same sequence in rice, Arabidopsis and maize; the other conserved sRNA XLHS7CU14 has a segment which appears in almost all these species from plants to animals. All these results indicate that sRNA do not have evident borderline between plants and animals.

  11. Whole Genome Fine Map of Rice Completed

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ Rice is a staple crop for more than half of the world's population, and it was hoped that the availability of its genome sequence might enable scientists to develop more productive and environment friendly rice strains.Furthermore, the rice genome might provide the key to understanding the genetics of other major cereal crops,as all of them have much larger genomes.

  12. Assembly and sorting of homologous BAC contigs in allotetraploid cotton genomes

    Science.gov (United States)

    Upland cotton (G. hirsutum) is a diploidized allopolyploid species containing At and Dt sub-genomes that have partial homology. Assembly and sorting of homologous BAC contigs into their subgenomes and further to individual chromosomes are of both great interest and great challenge for genome-wide i...

  13. Structural and functional analysis of rice genome

    Indian Academy of Sciences (India)

    Akhilesh K. Tyagi; Jitendra P. Khurana; Paramjit Khurana; Saurabh Raghuvanshi; Anupama Gaur; Anita Kapur; Vikrant Gupta; Dibyendu Kumar; V. Ravi; Shubha Vij; Parul Khurana; Sulabha Sharma

    2004-04-01

    Rice is an excellent system for plant genomics as it represents a modest size genome of 430 Mb. It feeds more than half the population of the world. Draft sequences of the rice genome, derived by whole-genome shotgun approach at relatively low coverage (4–6 X), were published and the International Rice Genome Sequencing Project (IRGSP) declared high quality (>10 X), genetically anchored, phase 2 level sequence in 2002. In addition, phase 3 level finished sequence of chromosomes 1, 4 and 10 (out of 12 chromosomes of rice) has already been reported by scientists from IRGSP consortium. Various estimates of genes in rice place the number at > 50,000. Already, over 28,000 full-length cDNAs have been sequenced, most of which map to genetically anchored genome sequence. Such information is very useful in revealing novel features of macro- and micro-level synteny of rice genome with other cereals. Microarray analysis is unraveling the identity of rice genes expressing in temporal and spatial manner and should help target candidate genes useful for improving traits of agronomic importance. Simultaneously, functional analysis of rice genome has been initiated by marker-based characterization of useful genes and employing functional knock-outs created by mutation or gene tagging. Integration of this enormous information is expected to catalyze tremendous activity on basic and applied aspects of rice genomics.

  14. Rice-Map: a new-generation rice genome browser

    Directory of Open Access Journals (Sweden)

    Luo Jingchu

    2011-03-01

    Full Text Available Abstract Background The concurrent release of rice genome sequences for two subspecies (Oryza sativa L. ssp. japonica and Oryza sativa L. ssp. indica facilitates rice studies at the whole genome level. Since the advent of high-throughput analysis, huge amounts of functional genomics data have been delivered rapidly, making an integrated online genome browser indispensable for scientists to visualize and analyze these data. Based on next-generation web technologies and high-throughput experimental data, we have developed Rice-Map, a novel genome browser for researchers to navigate, analyze and annotate rice genome interactively. Description More than one hundred annotation tracks (81 for japonica and 82 for indica have been compiled and loaded into Rice-Map. These pre-computed annotations cover gene models, transcript evidences, expression profiling, epigenetic modifications, inter-species and intra-species homologies, genetic markers and other genomic features. In addition to these pre-computed tracks, registered users can interactively add comments and research notes to Rice-Map as User-Defined Annotation entries. By smoothly scrolling, dragging and zooming, users can browse various genomic features simultaneously at multiple scales. On-the-fly analysis for selected entries could be performed through dedicated bioinformatic analysis platforms such as WebLab and Galaxy. Furthermore, a BioMart-powered data warehouse "Rice Mart" is offered for advanced users to fetch bulk datasets based on complex criteria. Conclusions Rice-Map delivers abundant up-to-date japonica and indica annotations, providing a valuable resource for both computational and bench biologists. Rice-Map is publicly accessible at http://www.ricemap.org/, with all data available for free downloading.

  15. The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology.

    Science.gov (United States)

    Wang, Dapeng; Xia, Yan; Li, Xinna; Hou, Lixia; Yu, Jun

    2013-01-01

    Over the past 10 years, genomes of cultivated rice cultivars and their wild counterparts have been sequenced although most efforts are focused on genome assembly and annotation of two major cultivated rice (Oryza sativa L.) subspecies, 93-11 (indica) and Nipponbare (japonica). To integrate information from genome assemblies and annotations for better analysis and application, we now introduce a comparative rice genome database, the Rice Genome Knowledgebase (RGKbase, http://rgkbase.big.ac.cn/RGKbase/). RGKbase is built to have three major components: (i) integrated data curation for rice genomics and molecular biology, which includes genome sequence assemblies, transcriptomic and epigenomic data, genetic variations, quantitative trait loci (QTLs) and the relevant literature; (ii) User-friendly viewers, such as Gbrowse, GeneBrowse and Circos, for genome annotations and evolutionary dynamics and (iii) Bioinformatic tools for compositional and synteny analyses, gene family classifications, gene ontology terms and pathways and gene co-expression networks. RGKbase current includes data from five rice cultivars and species: Nipponbare (japonica), 93-11 (indica), PA64s (indica), the African rice (Oryza glaberrima) and a wild rice species (Oryza brachyantha). We are also constantly introducing new datasets from variety of public efforts, such as two recent releases-sequence data from ∼1000 rice varieties, which are mapped into the reference genome, yielding ample high-quality single-nucleotide polymorphisms and insertions-deletions.

  16. Functional genomics strategies with transposons in rice

    NARCIS (Netherlands)

    Greco, R.

    2003-01-01

    Rice is a major staple food crop and a recognizedmonocotylenedousmodel plant from which gene function discovery is projected to contribute to improvements in a variety of cereals like wheat and maize. The recent release of rough drafts of the rice genome sequence for public

  17. A comparison of rice chloroplast genomes

    DEFF Research Database (Denmark)

    Tang, Jiabin; Xia, Hong'ai; Cao, Mengliang

    2004-01-01

    Using high quality sequence reads extracted from our whole genome shotgun repository, we assembled two chloroplast genome sequences from two rice (Oryza sativa) varieties, one from 93-11 (a typical indica variety) and the other from PA64S (an indica-like variety with maternal origin of japonica),...

  18. The 3,000 rice genomes project: new opportunities and challenges for future rice research

    OpenAIRE

    Li, Jia-Yang; Wang, Jun; Zeigler, Robert S.

    2014-01-01

    Rice is the world’s most important staple grown by millions of small-holder farmers. Sustaining rice production relies on the intelligent use of rice diversity. The 3,000 Rice Genomes Project is a giga-dataset of publically available genome sequences (averaging 14× depth of coverage) derived from 3,000 accessions of rice with global representation of genetic and functional diversity. The seed of these accessions is available from the International Rice Genebank Collection. Together, they are ...

  19. Perspective Rice 2020:A Call For An I nternational Coordinated Effort In Rice Fu nctional Genomics

    Institute of Scientific and Technical Information of China (English)

    Qifa Zhang; Jiayang Li; Yongbiao Xue; Bin Han; Xing Wang Deng

    2008-01-01

    We describe a call for an international coordinated effort in rice functional genomics in the form of a project named RICE2020.The mission of the project will be:to determine the function of every gene in the rice genome by the year 2020,to identify functional diversity of alleles for agriculturally useful genes from the primary gene pool of rice,and to apply the findings of functional genomics research to rice genetic improvement.

  20. Gene conversion in the rice genome

    DEFF Research Database (Denmark)

    Xu, Shuqing; Clark, Terry; Zheng, Hongkun;

    2008-01-01

    BACKGROUND: Gene conversion causes a non-reciprocal transfer of genetic information between similar sequences. Gene conversion can both homogenize genes and recruit point mutations thereby shaping the evolution of multigene families. In the rice genome, the large number of duplicated genes...... is not tightly linked to natural selection in the rice genome. To assess the contribution of segmental duplication on gene conversion statistics, we determined locations of conversion partners with respect to inter-chromosomal segment duplication. The number of conversions associated with segmentation is less...

  1. Introgression into the allotetraploid coffee ( Coffea arabica L.): segregation and recombination of the C. canephora genome in the tetraploid interspecific hybrid ( C. arabicax C. canephora).

    Science.gov (United States)

    Herrera, J. C.; Combes, M. C.; Anthony, F.; Charrier, A.; Lashermes, P.

    2002-03-01

    Transfer of desired characters from the diploid relative species such as Coffea canephora into the cultivated allotetraploid coffee species ( Coffea arabica L.) is essential to the continued improvement of varieties. Behaviour of the C. canephora genome and its interaction with the C. arabica genome were investigated in tetraploid interspecific hybrids ( C. arabicax C. canephora 4 x) resulting from a cross between an accession of C. arabica and a tetraploid plant of C. canephora obtained following colchicine treatment. Segregation and co-segregation of restriction fragment length polymorphism (RFLP) and microsatellite loci-markers were studied in two BC(1) populations. These two populations of 28 and 45 individuals, respectively, resulted from the backcross of two tetraploid F(1)plants to C. arabica. The presence in BC(1) plants of specific C. canephora markers was scored for 24 loci (11 RFLP and 13 microsatellites) distributed on at least 7 of the 11 linkage groups identified in C. canephora. At almost all loci analysed, the segregation of C. canephora alleles transmitted by the ( C. arabicax C. canephora 4 x) hybrids conformed to the expected ratio assuming random chromosome segregation and the absence of selection. The recombination fractions of C. canephorachromosome segments were estimated for seven marker intervals, and compared with the recombination fractions previously observed in C. canephora for the equivalent marker intervals. The recombination frequencies estimated in both plant materials were rather similar, suggesting that recombination in the ( C. arabicax C. canephora 4 x) hybrid is not significantly restricted by the genetic differentiation between chromosomes belonging to the different genomes. The hybrid ( C. arabicax C. canephora 4 x) therefore appeared particularly favourable to intergenomic recombination events and gene introgressions.

  2. Comparative genome research between maize and rice using genomic in situ hybridization

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Using the genomic DNAs of maize and rice as probes respectively,the homology of maize and rice genomes was assessed by genomic in situ hybridization. When rice genomic DNAs were hybridized to maize, all chromosomes displayed many multiple discrete regions, while each rice chromosome delineated a single consecutive chromosomal region after they were hybridized with maize genomic DNAs. The results indicate that the genomes of maize and rice share high homology, and confirm the proposal that maize and rice are diverged from a common ancestor.

  3. Genetic resources offer efficient tools for rice functional genomics research.

    Science.gov (United States)

    Lo, Shuen-Fang; Fan, Ming-Jen; Hsing, Yue-Ie; Chen, Liang-Jwu; Chen, Shu; Wen, Ien-Chie; Liu, Yi-Lun; Chen, Ku-Ting; Jiang, Mirng-Jier; Lin, Ming-Kuang; Rao, Meng-Yen; Yu, Lin-Chih; Ho, Tuan-Hua David; Yu, Su-May

    2016-05-01

    Rice is an important crop and major model plant for monocot functional genomics studies. With the establishment of various genetic resources for rice genomics, the next challenge is to systematically assign functions to predicted genes in the rice genome. Compared with the robustness of genome sequencing and bioinformatics techniques, progress in understanding the function of rice genes has lagged, hampering the utilization of rice genes for cereal crop improvement. The use of transfer DNA (T-DNA) insertional mutagenesis offers the advantage of uniform distribution throughout the rice genome, but preferentially in gene-rich regions, resulting in direct gene knockout or activation of genes within 20-30 kb up- and downstream of the T-DNA insertion site and high gene tagging efficiency. Here, we summarize the recent progress in functional genomics using the T-DNA-tagged rice mutant population. We also discuss important features of T-DNA activation- and knockout-tagging and promoter-trapping of the rice genome in relation to mutant and candidate gene characterizations and how to more efficiently utilize rice mutant populations and datasets for high-throughput functional genomics and phenomics studies by forward and reverse genetics approaches. These studies may facilitate the translation of rice functional genomics research to improvements of rice and other cereal crops.

  4. Identification and Analyses of miRNA Genes in Allotetraploid Gossypium hirsutum Fiber Cells Based on the Sequenced Diploid G.raimondii Genome

    Institute of Scientific and Technical Information of China (English)

    Qin Li; Xiang Jin; Yu-Xian Zhu

    2012-01-01

    The plant genome possesses a large number of microRNAs (miRNAs) mainly 21-24 nucleotides in length.They play a vital role in regulation of target gene expression at various stages throughout the whole plant life cycle.Here we sequenced and analyzed ~ 10 million non-coding RNAs (ncRNAs) derived from fiber tissue of the allotetraploid cotton (Gossypium hirsutum) 7 days post-anthesis using ncRNA-seq technology.In terms of distinct reads,24 nt ncRNA is by far the dominant species,followed by 21 nt and 23 nt ncRNAs.Using ab initio prediction,we identified and characterized a total of 562 candidate miRNA gene loci on the recently assembled D5 genome of the diploid cotton G.raimondii.Of all the 562 predicted miRNAs,22 were previously discovered in cotton species and 187 had sequence conservation and homology to homologous miRNAs of other plant species.Nucleotide bias analysis showed that the 9th and 1st positions were significantly conserved among different types of miRNA genes.Among the 463 putative miRNA target genes,most significant up/down-regulation occurred in 10-20 days post-anthesis,indicating that miRNAs played an important role during the elongation and secondary cell wall synthesis stages of cotton fiber developmem.The discovery of new miRNA genes will help understand the mechanisms of miRNA generation and regulation in cotton.

  5. TALEN utilization in rice genome modifications.

    Science.gov (United States)

    Li, Ting; Liu, Bo; Chen, Chih Ying; Yang, Bing

    2014-08-15

    Transcription activator-like effector nucleases (TALENs), the newly developed and powerful genetic tools for precise genome editing, are fusion proteins of TAL effectors as DNA binding domains and the cleavage domain of FokI endonuclease. As a pair, the central repeat regions of TALENs determine the DNA binding specificity for the two sub-target sites; and the dimeric non-specific FokI cleavage domains cause a DNA double strand break (DSB) between the bound sequences. In vivo, cells repair the DSBs through either non-homologous end joining (NHEJ) pathway or homologous recombination (HR) pathway. Various methods have been developed for easy and fast assembly of TALEN genes for their utilization in a variety of eukaryotic cells or organisms. Here we present a TALEN-based rice genome modification protocol including constructing modularly assembled TALENs, rice transformation, and mutant screening.

  6. Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome.

    Directory of Open Access Journals (Sweden)

    Gopala Krishnan S

    Full Text Available BACKGROUND: Rice is a major source of human food with a predominantly Asian production base. Domestication involved selection of traits that are desirable for agriculture and to human consumers. Wild relatives of crop plants are a source of useful variation which is of immense value for crop improvement. Australian wild rices have been isolated from the impacts of domestication in Asia and represents a source of novel diversity for global rice improvement. Oryza rufipogon is a perennial wild progenitor of cultivated rice. Oryza meridionalis is a related annual species in Australia. RESULTS: We have examined the sequence of the genomes of AA genome wild rices from Australia that are close relatives of cultivated rice through whole genome re-sequencing. Assembly of the resequencing data to the O. sativa ssp. japonica cv. Nipponbare shows that Australian wild rices possess 2.5 times more single nucleotide polymorphisms than in the Asian wild rice and cultivated O. sativa ssp. indica. Analysis of the genome of domesticated rice reveals regions of low diversity that show very little variation (polymorphism deserts. Both the perennial and annual wild rice from Australia show a high degree of conservation of sequence with that found in cultivated rice in the same 4.58 Mbp region on chromosome 5, which suggests that some of the 'polymorphism deserts' in this and other parts of the rice genome may have originated prior to domestication due to natural selection. CONCLUSIONS: Analysis of genes in the 'polymorphism deserts' indicates that this selection may have been due to biotic or abiotic stress in the environment of early rice relatives. Despite having closely related sequences in these genome regions, the Australian wild populations represent an invaluable source of diversity supporting rice food security.

  7. Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication

    OpenAIRE

    Zhang, Fantao; Xu, Tao; Mao, Linyong; Yan, Shuangyong; Chen, Xiwen; Wu, Zhenfeng; Chen, Rui; Luo, Xiangdong; Xie, Jiankun; Gao, Shan

    2016-01-01

    Background It is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). Compared to other studies which concentrate on rice origin, this study is to genetically elucidate the substantially phenotypic and physiological changes from wild rice to cultivated rice at the whole genome level. Results Instead of comparing two assembled genomes, this study directly compared the Dongxiang wild rice (DXWR) Illumina sequencing reads with th...

  8. Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication.

    Science.gov (United States)

    Wang, Yu; Bai, Xuefei; Yan, Chenghai; Gui, Yiejie; Wei, Xinghua; Zhu, Qian-Hao; Guo, Longbiao; Fan, Longjiang

    2012-11-01

    The lack of a MIRNA set and genome sequence of wild rice (Oryza rufipogon) has prevented us from determining the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and a degradome of O. rufipogon were sequenced by Illumina platform and the expression levels of microRNAs (miRNAs) were investigated by miRNA chips. A de novo O. rufipogon genome was assembled using c. 55× coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on c. 5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these, O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting a loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression differences between wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated that MIRNA genes, like protein-coding genes, might have been significantly shaped during rice domestication and could be one of the driving forces that contributed to rice domestication.

  9. Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice.

    Science.gov (United States)

    Brozynska, Marta; Copetti, Dario; Furtado, Agnelo; Wing, Rod A; Crayn, Darren; Fox, Glen; Ishikawa, Ryuji; Henry, Robert J

    2016-11-27

    The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.

  10. Genome-wide patterns of nucleotide polymorphism in domesticated rice

    DEFF Research Database (Denmark)

    Caicedo, Ana L; Williamson, Scott H; Hernandez, Ryan 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...... 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...

  11. Genome-wide transcription analyses in rice using tiling microarrays

    DEFF Research Database (Denmark)

    Li, Lei; Wang, Xiangfeng; Stolc, Viktor;

    2006-01-01

    Sequencing and computational annotation revealed several features, including high gene numbers, unusual composition of the predicted genes and a large number of genes lacking homology to known genes, that distinguish the rice (Oryza sativa) genome from that of other fully sequenced model species....... We report here a full-genome transcription analysis of the indica rice subspecies using high-density oligonucleotide tiling microarrays. Our results provided expression data support for the existence of 35,970 (81.9%) annotated gene models and identified 5,464 unique transcribed intergenic regions...... activity between duplicated segments of the genome. Collectively, our results provide the first whole-genome transcription map useful for further understanding the rice genome. Udgivelsesdato: 2006-Jan...

  12. RICD: A rice indica cDNA database resource for rice functional genomics

    Directory of Open Access Journals (Sweden)

    Zhang Qifa

    2008-11-01

    Full Text Available Abstract Background The Oryza sativa L. indica subspecies is the most widely cultivated rice. During the last few years, we have collected over 20,000 putative full-length cDNAs and over 40,000 ESTs isolated from various cDNA libraries of two indica varieties Guangluai 4 and Minghui 63. A database of the rice indica cDNAs was therefore built to provide a comprehensive web data source for searching and retrieving the indica cDNA clones. Results Rice Indica cDNA Database (RICD is an online MySQL-PHP driven database with a user-friendly web interface. It allows investigators to query the cDNA clones by keyword, genome position, nucleotide or protein sequence, and putative function. It also provides a series of information, including sequences, protein domain annotations, similarity search results, SNPs and InDels information, and hyperlinks to gene annotation in both The Rice Annotation Project Database (RAP-DB and The TIGR Rice Genome Annotation Resource, expression atlas in RiceGE and variation report in Gramene of each cDNA. Conclusion The online rice indica cDNA database provides cDNA resource with comprehensive information to researchers for functional analysis of indica subspecies and for comparative genomics. The RICD database is available through our website http://www.ncgr.ac.cn/ricd.

  13. Genome-wide patterns of nucleotide polymorphism in domesticated rice.

    Directory of Open Access Journals (Sweden)

    Ana L Caicedo

    2007-09-01

    Full Text Available 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.

  14. Diverged Copies of the Seed Regulatory Opaque-2 Gene by a Segmental Duplication in the Progenitor Genome of Rice,Sorghum,and Maize

    Institute of Scientific and Technical Information of China (English)

    Jian-Hong Xu; Joachim Messing

    2008-01-01

    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(02)IOCUS,to examine the generaI features of divergences of chromosomaI segmentaI duplications in a lineagespecific manner.We took advantage of contiguous chromosomal sequence information in rice(Oryza sativa,Nipponbare).sorghum(Sorghum bicoloc 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≈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.

  15. Comparative Genetics of Floral Morphology in Diploid and Allotetraploid Gossypium

    Institute of Scientific and Technical Information of China (English)

    CHEE Peng W

    2008-01-01

    @@ The cultivated Gossypium A genome diploid species G.arboreum and G.herbaceum and the allotetraploid species G.hirsutum and G.barbadense share common morphology for various floral traits,which offers an ideal system in which to investigate genetic mechanisms that differentiate diploid and tetraploid genomes.For example,knowing how a single phenotype behaves in the diploids,and comparing the same trait with different dosage effects in the tetraploids,may provide a means to study inter- and intra-genomic interactions in the polyploid genome.

  16. Complexity of rice Hsp100 gene family: lessons from rice genome sequence data

    Indian Academy of Sciences (India)

    Gaurav Batra; Vineeta Singh Chauhan; Amanjot Singh; Neelam K Sarkar; Anil Grover

    2007-04-01

    Elucidation of genome sequence provides an excellent platform to understand detailed complexity of the various gene families. Hsp100 is an important family of chaperones in diverse living systems. There are eight putative gene loci encoding for Hsp100 proteins in Arabidopsis genome. In rice, two full-length Hsp100 cDNAs have been isolated and sequenced so far. Analysis of rice genomic sequence by in silico approach showed that two isolated rice Hsp100 cDNAs correspond to Os05g44340 and Os02g32520 genes in the rice genome database. There appears to be three additional proteins (encoded by Os03g31300, Os04g32560 and Os04g33210 gene loci) that are variably homologous to Os05g44340 and Os02g32520 throughout the entire amino acid sequence. The above five rice Hsp100 genes show significant similarities in the signature sequences known to be conserved among Hsp100 proteins. While Os05g44340 encodes cytoplasmic Hsp100 protein, those encoded by the other four genes are predicted to have chloroplast transit peptides.

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

    Directory of Open Access Journals (Sweden)

    Youko Oono

    2016-01-01

    Full Text Available 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.

  18. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

    Science.gov (United States)

    Cotton is the world’s most important natural textile fibre and a significant oilseed crop. Upland cotton (Gossypium hirsutum L.), an allotetraploid derived from A- and D-genome progenitors, accounts for >95% of world production. Here, we sequenced and assembled 88% of the 2.5-gigabase genome of the ...

  19. Draft Sequence of the Rice Genome:A Milestone Publication

    Institute of Scientific and Technical Information of China (English)

    Guo Haiyan; Zhao Baohua

    2002-01-01

    @@ Following China's announcement of its completion of the draft genome sequence of the rice indica subspecies on October 12,2001 (page 126, Bulletin of the Chinese Academy of Sciences Vol. 15 No.3), Chinese scientists published their findings in the April 5 issue of Science, the journal of the American Association for the Advancement of Science (AAAS). In the same issue, a team of scientists with the Switzerland-based Syngenta company reported a similar achievement for another major rice subspecies,japonica.

  20. Crossovers get a boost in Brassica allotriploid and allotetraploid hybrids.

    Science.gov (United States)

    Leflon, Martine; Grandont, Laurie; Eber, Frédérique; Huteau, Virginie; Coriton, Olivier; Chelysheva, Liudmila; Jenczewski, Eric; Chèvre, Anne-Marie

    2010-07-01

    Meiotic crossovers are necessary to generate balanced gametes and to increase genetic diversity. Even if crossover number is usually constrained, recent results suggest that manipulating karyotype composition could be a new way to increase crossover frequency in plants. In this study, we explored this hypothesis by analyzing the extent of crossover variation in a set of related diploid AA, allotriploid AAC, and allotetraploid AACC Brassica hybrids. We first used cytogenetic methods to describe the meiotic behavior of the different hybrids. We then combined a cytogenetic estimation of class I crossovers in the entire genome by immunolocalization of a key protein, MutL Homolog1, which forms distinct foci on meiotic chromosomes, with genetic analyses to specifically compare crossover rates between one pair of chromosomes in the different hybrids. Our results showed that the number of crossovers in the allotriploid AAC hybrid was higher than in the diploid AA hybrid. Accordingly, the allotetraploid AACC hybrid showed an intermediate behavior. We demonstrated that this increase was related to hybrid karyotype composition (diploid versus allotriploid versus allotetraploid) and that interference was maintained in the AAC hybrids. These results could provide another efficient way to manipulate recombination in traditional breeding and genetic studies.

  1. QTL map meets population genomics: an application to rice.

    Directory of Open Access Journals (Sweden)

    Jeffrey A Fawcett

    Full Text Available Genes involved in the transition from wild to cultivated crop species should be of great agronomic importance. Population genomic approaches utilizing genome resequencing data have been recently applied for this purpose, although it only reports a large list of candidate genes with no biological information. Here, by resequencing more than 30 genomes altogether of wild rice Oryza rufipogon and cultivated rice O. sativa, we identified a number of regions with clear footprints of selection during the domestication process. We then focused on identifying candidate domestication genes in these regions by utilizing the wealth of QTL information in rice. We were able to identify a number of interesting candidates such as transcription factors that should control key domestication traits such as shattering, awn length, and seed dormancy. Other candidates include those that might have been related to the improvement of grain quality and those that might have been involved in the local adaptation to dry conditions and colder environments. Our study shows that population genomic approaches and QTL mapping information can be used together to identify genes that might be of agronomic importance.

  2. Syntenic relationships between the U and M genomes of Aegilops, wheat and the model species Brachypodium and rice as revealed by COS markers.

    Science.gov (United States)

    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.

  3. Syntenic relationships between the U and M genomes of Aegilops, wheat and the model species Brachypodium and rice as revealed by COS markers.

    Directory of Open Access Journals (Sweden)

    István Molnár

    Full Text Available 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.

  4. Genomic architecture of heterosis for yield traits in rice.

    Science.gov (United States)

    Huang, Xuehui; Yang, Shihua; Gong, Junyi; Zhao, Qiang; Feng, Qi; Zhan, Qilin; Zhao, Yan; Li, Wenjun; Cheng, Benyi; Xia, Junhui; Chen, Neng; Huang, Tao; Zhang, Lei; Fan, Danlin; Chen, Jiaying; Zhou, Congcong; Lu, Yiqi; Weng, Qijun; Han, Bin

    2016-09-29

    Increasing grain yield is a long-term goal in crop breeding to meet the demand for global food security. Heterosis, when a hybrid shows higher performance for a trait than both parents, offers an important strategy for crop breeding. To examine the genetic basis of heterosis for yield in rice, here we generate, sequence and record the phenotypes of 10,074 F2 lines from 17 representative hybrid rice crosses. We classify modern hybrid rice varieties into three groups, representing different hybrid breeding systems. Although we do not find any heterosis-associated loci shared across all lines, within each group, a small number of genomic loci from female parents explain a large proportion of the yield advantage of hybrids over their male parents. For some of these loci, we find support for partial dominance of heterozygous locus for yield-related traits and better-parent heterosis for overall performance when all of the grain-yield traits are considered together. These results inform on the genomic architecture of heterosis and rice hybrid breeding.

  5. RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome.

    Science.gov (United States)

    Thongjuea, Supat; Ruanjaichon, Vinitchan; Bruskiewich, Richard; Vanavichit, Apichart

    2009-01-01

    RiceGeneThresher is a public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, expressed sequence tags (ESTs), protein domains, gene ontology, plant stress-responsive genes, metabolic pathways and prediction of protein-protein interactions. RiceGeneThresher system integrates these diverse data sources and provides powerful web-based applications, and flexible tools for delivering customized set of biological data on rice. Its system supports whole-genome gene mining for QTL by querying using DNA marker intervals or genomic loci. RiceGeneThresher provides biologically supported evidences that are essential for targeting groups or networks of genes involved in controlling traits underlying QTL. Users can use it to discover and to assign the most promising candidate genes in preparation for the further gene function validation analysis. The web-based application is freely available at http://rice.kps.ku.ac.th.

  6. Correlation exploration of metabolic and genomic diversity in rice

    Directory of Open Access Journals (Sweden)

    Shinozaki Kazuo

    2009-12-01

    Full Text Available Abstract Background It is essential to elucidate the relationship between metabolic and genomic diversity to understand the genetic regulatory networks associated with the changing metabolo-phenotype among natural variation and/or populations. Recent innovations in metabolomics technologies allow us to grasp the comprehensive features of the metabolome. Metabolite quantitative trait analysis is a key approach for the identification of genetic loci involved in metabolite variation using segregated populations. Although several attempts have been made to find correlative relationships between genetic and metabolic diversity among natural populations in various organisms, it is still unclear whether it is possible to discover such correlations between each metabolite and the polymorphisms found at each chromosomal location. To assess the correlative relationship between the metabolic and genomic diversity found in rice accessions, we compared the distance matrices for these two "omics" patterns in the rice accessions. Results We selected 18 accessions from the world rice collection based on their population structure. To determine the genomic diversity of the rice genome, we genotyped 128 restriction fragment length polymorphism (RFLP markers to calculate the genetic distance among the accessions. To identify the variations in the metabolic fingerprint, a soluble extract from the seed grain of each accession was analyzed with one dimensional 1H-nuclear magnetic resonance (NMR. We found no correlation between global metabolic diversity and the phylogenetic relationships among the rice accessions (rs = 0.14 by analyzing the distance matrices (calculated from the pattern of the metabolic fingerprint in the 4.29- to 0.71-ppm 1H chemical shift and the genetic distance on the basis of the RFLP markers. However, local correlation analysis between the distance matrices (derived from each 0.04-ppm integral region of the 1H chemical shift against genetic

  7. Ac/Ds-induced chromosomal rearrangements in rice genomes.

    Science.gov (United States)

    Xuan, Yuan Hu; Zhang, Jianbo; Peterson, Thomas; Han, Chang-Deok

    2012-03-01

    A closely-linked pair of Ac/Ds elements induces chromosomal rearrangements in Arabidopsis and maize. This report summarizes the Ac/Ds systems that generate an exceptionally high frequency of chromosomal rearrangements in rice genomes. From a line containing a single Ds element inserted at the OsRLG5 locus, plants containing a closely-linked pair of inversely-oriented Ds elements were obtained at 1% frequency among the population regenerated from tissue culture. Subsequent regeneration of the lines containing cis-paired Ds elements via tissue culture led to a high frequency (35.6%) of plants containing chromosomal rearrangements at the OsRLG5 locus. Thirty-four rearrangement events were characterized, revealing diverse chromosomal aberrations including deletions, inversions and duplications. Many rearrangements could be explained by sister chromatid transposition (SCT) and homologous recombination (HR), events previously demonstrated in Arabidopsis and maize. In addition, novel events were detected and presumably generated via a new alternative transposition mechanism. This mechanism, termed single chromatid transposition (SLCT), resulted in juxtaposed inversions and deletions on the same chromosome. This study demonstrated that the Ac/Ds system coupled with tissue culture-mediated plant regeneration could induce higher frequencies and a greater diversity of chromosomal rearrangements than previously reported. Understanding transposon-induced chromosomal rearrangements can provide new insights into the relationship between transposable elements and genome evolution, as well as a means to perform chromosomal engineering for crop improvement. Rice is a staple cereal crop worldwide. Complete genome sequencing and rich genetic resources are great advantages for the study of the genomic complexity induced by transposable elements.(1) (-) (2) The combination of tissue culture with genetic lines carrying a pair of closely located Ac/Ds elements greatly increases the

  8. Draft genome sequence of an inbred line of Chenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties.

    Science.gov (United States)

    Yasui, Yasuo; Hirakawa, Hideki; Oikawa, Tetsuo; Toyoshima, Masami; Matsuzaki, Chiaki; Ueno, Mariko; Mizuno, Nobuyuki; Nagatoshi, Yukari; Imamura, Tomohiro; Miyago, Manami; Tanaka, Kojiro; Mise, Kazuyuki; Tanaka, Tsutomu; Mizukoshi, Hiroharu; Mori, Masashi; Fujita, Yasunari

    2016-12-01

    Chenopodium quinoa Willd. (quinoa) originated from the Andean region of South America, and is a pseudocereal crop of the Amaranthaceae family. Quinoa is emerging as an important crop with the potential to contribute to food security worldwide and is considered to be an optimal food source for astronauts, due to its outstanding nutritional profile and ability to tolerate stressful environments. Furthermore, plant pathologists use quinoa as a representative diagnostic host to identify virus species. However, molecular analysis of quinoa is limited by its genetic heterogeneity due to outcrossing and its genome complexity derived from allotetraploidy. To overcome these obstacles, we established the inbred and standard quinoa accession Kd that enables rigorous molecular analysis, and presented the draft genome sequence of Kd, using an optimized combination of high-throughput next generation sequencing on the Illumina Hiseq 2500 and PacBio RS II sequencers. The de novo genome assembly contained 25 k scaffolds consisting of 1 Gbp with N50 length of 86 kbp. Based on these data, we constructed the free-access Quinoa Genome DataBase (QGDB). Thus, these findings provide insights into the mechanisms underlying agronomically important traits of quinoa and the effect of allotetraploidy on genome evolution.

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

    Science.gov (United States)

    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.

  10. Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice.

    Science.gov (United States)

    Tong, Wei; He, Qiang; Park, Yong-Jin

    2017-03-03

    Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level.

  11. Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice

    Science.gov (United States)

    Tong, Wei; He, Qiang; Park, Yong-Jin

    2017-01-01

    Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level. PMID:28256554

  12. Rice TOGO Browser: A platform to retrieve integrated information on rice functional and applied genomics.

    Science.gov (United States)

    Nagamura, Yoshiaki; Antonio, Baltazar A; Sato, Yutaka; Miyao, Akio; Namiki, Nobukazu; Yonemaru, Jun-ichi; Minami, Hiroshi; Kamatsuki, Kaori; Shimura, Kan; Shimizu, Yuji; Hirochika, Hirohiko

    2011-02-01

    The Rice TOGO Browser is an online public resource designed to facilitate integration and visualization of mapping data of bacterial artificial chromosome (BAC)/P1-derived artificial chromosome (PAC) clones, genes, restriction fragment length polymorphism (RFLP)/simple sequence repeat (SSR) markers and phenotype data represented as quantitative trait loci (QTLs) onto the genome sequence, and to provide a platform for more efficient utilization of genome information from the point of view of applied genomics as well as functional genomics. Three search options, namely keyword search, region search and trait search, generate various types of data in a user-friendly interface with three distinct viewers, a chromosome viewer, an integrated map viewer and a sequence viewer, thereby providing the opportunity to view the position of genes and/or QTLs at the chromosomal level and to retrieve any sequence information in a user-defined genome region. Furthermore, the gene list, marker list and genome sequence in a specified region delineated by RFLP/SSR markers and any sequences designed as primers can be viewed and downloaded to support forward genetics approaches. An additional feature of this database is the graphical viewer for BLAST search to reveal information not only for regions with significant sequence similarity but also for regions adjacent to those with similarity but with no hits between sequences. An easy to use and intuitive user interface can help a wide range of users in retrieving integrated mapping information including agronomically important traits on the rice genome sequence. The database can be accessed at http://agri-trait.dna.affrc.go.jp/.

  13. Evolutionary analysis of allotetraploid hybrids of red crucian carp × common carp,based on ISSR,AFLP molecular markers and cloning of cyclins genes

    Institute of Scientific and Technical Information of China (English)

    LIU LiangGuo; YAN JinPeng; LIU ShaoJun; LIU Dong; YOU CuiPing; ZHONG Huan; TAO Min; LIU Yun

    2009-01-01

    The allotetraploid hybrids of red crucian carp × common carp are the first reported artificially cultured polyploid fish with bisexual fertility and stable inheritance in vertebrate.Using ISSR and AFLP markers and the cyclins genes,the genomes and cyclin gene sequence changes were analyzed between the allotetraploid hybrids and their parents.The results indicated that the allotetraploids inherited many genetic characteristics from their parents and the genetic characteristics were stable after 15 generations.However,the allotetraploids had a closer genetic relationship with their original female parents and represented a bias toward the maternal progenitor.DNA fingerprinting analysis showed that the allotetraploids had undergone sequences deletion from their original parents and that the deleted sequences were mostly from the male parent's genome.Some non-parental bands were found in the allotetraploid hybrids.Sequences analysis of the cyclin A1 and B1 genes showed nonsynonymous substitutions of single nucleotides in codons that were different from their original parents,leading to non-parental amino acid loci.We speculate that the non-additivity in the allotetraploids,compared with their progenitors,could be an adjustment to the genomic shock from heterozygosity and polyploidy, allowing maintenance of genetic stability.

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

    Science.gov (United States)

    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.

  15. T-DNA Integration Category and Mechanism in Rice Genome

    Institute of Scientific and Technical Information of China (English)

    Jiang WANG; Lin LI; Zhen-Ying SHI; Xin-Shan WAN; Lin-Sheng AN; Jing-Liu ZHANG

    2005-01-01

    T-DNA integration is a key step in the process of plant transformation, which is proven to be important for analyzing T-DNA integration mechanism. The structures of T-DNA right borders inserted into the rice (Oryza sativa L.) genome and their flanking sequences were analyzed. It was found that the integrated ends of the T-DNA right border occurred mainly on five nucleotides "TGACA" in inverse repeat (IR)sequence of 25 bp, especially on the third base "A". However, the integrated ends would sometimes lie inward of the IR sequence, which caused the IR sequence to be lost completely. Sometimes the right integrated ends appeared on the vector sequences rightward of the T-DNA right border, which made the TDNA, carrying vector sequences, integrated into the rice genome. These results seemingly suggest that the IR sequence of the right border plays an important role in the process of T-DNA integration into the rice genome, but is not an essential element. The appearance of vector sequences neighboring the T-DNA right border suggested that before being transferred into the plant cell from Agrobacterium, the entire T-DNA possibly began from the left border in synthesis and then read through at the right border. Several nucleotides in the T-DNA right border homologous with plant DNA and filler DNAs were frequently discovered in the integrated position ofT-DNA. Some small regions in the right border could match with the plant sequence, or form better matches, accompanied by the occurrence of filler DNA, through mutual twisting, and then the TDNA was integrated into plant chromosome through a partially homologous recombination mechanism. The appearance of filler DNA would facilitate T-DNA integration. The fragments flanking the T-DNA right border in transformed rice plants could derive from different parts of the inner T-DNA region; that is, disruption and recombination could occur at arbitrary positions in the entire T-DNA, in which the homologous area was comparatively

  16. BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics

    DEFF Research Database (Denmark)

    Zhao, Wenming; Wang, Jing; He, Ximiao

    2004-01-01

    the application of the rice genomic information and to provide a foundation for functional and evolutionary studies of other important cereal crops, we implemented our Rice Information System (BGI-RIS), the most up-to-date integrated information resource as well as a workbench for comparative genomic analysis...

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

    Science.gov (United States)

    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.

  18. Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces.

    Science.gov (United States)

    Alexander, William G; Peris, David; Pfannenstiel, Brandon T; Opulente, Dana A; Kuang, Meihua; Hittinger, Chris Todd

    2016-04-01

    Saccharomyces interspecies hybrids are critical biocatalysts in the fermented beverage industry, including in the production of lager beers, Belgian ales, ciders, and cold-fermented wines. Current methods for making synthetic interspecies hybrids are cumbersome and/or require genome modifications. We have developed a simple, robust, and efficient method for generating allotetraploid strains of prototrophic Saccharomyces without sporulation or nuclear genome manipulation. S. cerevisiae×S. eubayanus, S. cerevisiae×S. kudriavzevii, and S. cerevisiae×S. uvarum designer hybrid strains were created as synthetic lager, Belgian, and cider strains, respectively. The ploidy and hybrid nature of the strains were confirmed using flow cytometry and PCR-RFLP analysis, respectively. This method provides an efficient means for producing novel synthetic hybrids for beverage and biofuel production, as well as for constructing tetraploids to be used for basic research in evolutionary genetics and genome stability. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Cross genome comparisons of serine proteases in Arabidopsis and rice

    Directory of Open Access Journals (Sweden)

    Sowdhamini R

    2006-08-01

    Full Text Available Abstract Background Serine proteases are one of the largest groups of proteolytic enzymes found across all kingdoms of life and are associated with several essential physiological pathways. The availability of Arabidopsis thaliana and rice (Oryza sativa genome sequences has permitted the identification and comparison of the repertoire of serine protease-like proteins in the two plant species. Results Despite the differences in genome sizes between Arabidopsis and rice, we identified a very similar number of serine protease-like proteins in the two plant species (206 and 222, respectively. Nearly 40% of the above sequences were identified as potential orthologues. Atypical members could be identified in the plant genomes for Deg, Clp, Lon, rhomboid proteases and species-specific members were observed for the highly populated subtilisin and serine carboxypeptidase families suggesting multiple lateral gene transfers. DegP proteases, prolyl oligopeptidases, Clp proteases and rhomboids share a significantly higher percentage orthology between the two genomes indicating substantial evolutionary divergence was set prior to speciation. Single domain architectures and paralogues for several putative subtilisins, serine carboxypeptidases and rhomboids suggest they may have been recruited for additional roles in secondary metabolism with spatial and temporal regulation. The analysis reveals some domain architectures unique to either or both of the plant species and some inactive proteases, like in rhomboids and Clp proteases, which could be involved in chaperone function. Conclusion The systematic analysis of the serine protease-like proteins in the two plant species has provided some insight into the possible functional associations of previously uncharacterised serine protease-like proteins. Further investigation of these aspects may prove beneficial in our understanding of similar processes in commercially significant crop plant species.

  20. Insights into the Bamboo Genome: Syntenic Relationships to Rice and Sorghum

    Institute of Scientific and Technical Information of China (English)

    Yi-Jie Gui; Nai-Xun Ma; Tian-Zhen Zhang; Long-Jiang Fan; Yan Zhou; Yu Wang; Sheng Wang; Sheng-Yue Wang; Yan Hu; Shi-Ping Bo; Huan Chen; Chang-Ping Zhou

    2010-01-01

    Bamboo occupies an important phylogenetic node in the grass family and plays a significant role in the forest industry.We produced 1.2 Mb of tetraploid moso bamboo(Phyllostachys pubescens E.Mazel ex H.de Leh.)sequences from 13 bacterial artificial chromosome(BAC)clones,and these are the largest genomic sequences available so far from the subfamily Bambusoideae.The content of repetitive elements(36.2%)in bamboo is similar to that in rice.Both rice and sorghum exhibit high genomic synteny with bamboo,which suggests that rice and sorghum may be useful as models for decoding Bambusoideae genomes.

  1. Molecular and cytogenetic evidence for an allotetraploid origin of Chenopodium quinoa and C. berlandieri (Amaranthaceae).

    Science.gov (United States)

    Kolano, Bozena; McCann, Jamie; Orzechowska, Maja; Siwinska, Dorota; Temsch, Eva; Weiss-Schneeweiss, Hanna

    2016-07-01

    Most of the cultivated chenopods are polyploids, but their origin and evolutionary history are still poorly understood. Phylogenetic analyses of DNA sequences of four plastid regions, nrITS and nuclear 5S rDNA spacer region (NTS) of two tetraploid chenopods (2n=4x=36), Andean C. quinoa and North American C. berlandieri, and their diploid relatives allowed inferences of their origin. The phylogenetic analyses confirmed allotetraploid origin of both tetraploids involving diploids of two different genomic groups (genomes A and B) and suggested that these two might share very similar parentage. The hypotheses on the origin of the two allopolyploid species were further tested using genomic in situ hybridization (GISH). Several diploid Chenopodium species belonging to the two lineages, genome A and B, suggested by phylogenetic analyses, were tested as putative parental taxa. GISH differentiated two sets of parental chromosomes in both tetraploids and further corroborated their allotetraploid origin. Putative diploid parental taxa have been suggested by GISH for C. quinoa and C. berlandieri. Genome sizes of the analyzed allotetraploids fit nearly perfectly the expected additive values of the putative parental taxa. Directional and uniparental loss of rDNA loci of the maternal A-subgenome was revealed for both C. berlandieri and C. quinoa.

  2. Effect of ploidy increase on transgene expression: example from Citrus diploid cybrid and allotetraploid somatic hybrid expressing the EGFP gene.

    Science.gov (United States)

    Xu, Shi-Xiao; Cai, Xiao-Dong; Tan, Bin; Li, Ding-Li; Guo, Wen-Wu

    2011-07-01

    Polyploidization is an important speciation mechanism for all eukaryotes, and it has profound impacts on biodiversity dynamics and ecosystem functioning. Green fluorescent protein (GFP) has been used as an effective marker to visually screen somatic hybrids at an early stage in protoplast fusion. We have previously reported that the intensity of GFP fluorescence of regenerated embryoids was also an early indicator of ploidy level. However, little is known concerning the effects of ploidy increase on the GFP expression in citrus somatic hybrids at the plant level. Herein, allotetraploid and diploid cybrid plants with enhanced GFP (EGFP) expression were regenerated from the fusion of embryogenic callus protoplasts from 'Murcott' tangor (Citrus reticulata Blanco × Citrus sinensis (L.) Osbeck) and mesophyll protoplasts from transgenic 'Valencia' orange (C. sinensis (L.) Osbeck) expressing the EGFP gene, via electrofusion. Subsequent simple sequence repeat (SSR), chloroplast simple sequence repeat and cleaved amplified polymorphic sequence analysis revealed that the two regenerated tetraploid plants were true allotetraploid somatic hybrids possessing nuclear genomic DNA of both parents and cytoplasmic DNA from the callus parent, while the five regenerated diploid plants were cybrids containing nuclear DNA of the leaf parent and with complex segregation of cytoplasmic DNA. Furthermore, EGFP expression was compared in cells and protoplasts from mature leaves of these diploid cybrids and allotetraploid somatic hybrids. Results showed that the intensity of GFP fluorescence per cell or protoplast in diploid was generally brighter than in allotetraploid. Moreover, same hybridization signal was detected on allotetraploid and diploid plants by Southern blot analysis. By real-time RT-PCR and Western blot analysis, GFP expression level of the diploid cybrid was revealed significantly higher than that of the allotetraploid somatic hybrid. These results suggest that ploidy

  3. Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

    OpenAIRE

    Ziwen He; Weiwei Zhai; Haijun Wen; Tian Tang; Yu Wang; Xuemei Lu; Greenberg, Anthony J.; Hudson, Richard R; Chung-I Wu; Suhua Shi

    2011-01-01

    Genealogical patterns in different genomic regions may be different due to the joint influence of gene flow and selection. The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication. We chose 66 accessions from the three rice taxa (about 22 each from Oryza sativa indica, O. sativa japonica, and O. rufipogon) for whole-genome sequencing. In the search for the signature of selection, we focus on low diversity regions (LDRs) ...

  4. Genetic control of flowering time in rice: integration of Mendelian genetics and genomics.

    Science.gov (United States)

    Hori, Kiyosumi; Matsubara, Kazuki; Yano, Masahiro

    2016-12-01

    Integration of previous Mendelian genetic analyses and recent molecular genomics approaches, such as linkage mapping and QTL cloning, dramatically strengthened our current understanding of genetic control of rice flowering time. Flowering time is one of the most important agronomic traits for seed production in rice (Oryza sativa L.). It is controlled mainly by genes associated with photoperiod sensitivity, particularly in short-day plants such as rice. Since the early twentieth century, rice breeders and researchers have been interested in elucidating the genetic basis of flowering time because its modification is important for regional adaptation and yield optimization. Although flowering time is a complex trait controlled by many quantitative trait loci (QTLs), classical genetic studies have shown that many associated genes are inherited in accordance with Mendelian laws. Decoding the rice genome sequence opened a new era in understanding the genetic control of flowering time on the basis of genome-wide mapping and gene cloning. Heading date 1 (Hd1) was the first flowering time QTL to be isolated using natural variation in rice. Recent accumulation of information on rice genome has facilitated the cloning of other QTLs, including those with minor effects on flowering time. This information has allowed us to rediscover some of the flowering genes that were identified by classical Mendelian genetics. The genes characterized so far, including Hd1, have been assigned to specific photoperiod pathways. In this review, we provide an overview of the studies that led to an in-depth understanding of the genetic control of flowering time in rice, and of the current state of improving and fine-tuning this trait for rice breeding.

  5. CAS Researchers Join Hands with World Peers for Sequenced Rice Genome

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ Adetailed analysis of the high-quality sequence of the rice genome was published in the August 11 issue of the journal Nature, marking the completion of a six-year international collaborative effort to unravel the genome of the world's most important food crop that feeds over half of the global population.

  6. Two evolutionary histories in the genome of rice: the roles of domestication genes.

    Science.gov (United States)

    He, Ziwen; Zhai, Weiwei; Wen, Haijun; Tang, Tian; Wang, Yu; Lu, Xuemei; Greenberg, Anthony J; Hudson, Richard R; Wu, Chung-I; Shi, Suhua

    2011-06-01

    Genealogical patterns in different genomic regions may be different due to the joint influence of gene flow and selection. The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication. We chose 66 accessions from the three rice taxa (about 22 each from Oryza sativa indica, O. sativa japonica, and O. rufipogon) for whole-genome sequencing. In the search for the signature of selection, we focus on low diversity regions (LDRs) shared by both cultivars. We found that the genealogical histories of these overlapping LDRs are distinct from the genomic background. While indica and japonica genomes generally appear to be of independent origin, many overlapping LDRs may have originated only once, as a result of selection and subsequent introgression. Interestingly, many such LDRs contain only one candidate gene of rice domestication, and several known domestication genes have indeed been "rediscovered" by this approach. In summary, we identified 13 additional candidate genes of domestication.

  7. Genome-wide analysis of potential cross-reactive endogenous allergens in rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    Fang Chao Zhu

    2015-01-01

    Full Text Available The proteins in the food are the source of common allergic components to certain patients. Current lists of plant endogenous allergens were based on the medical/clinical reports as well as laboratory results. Plant genome sequences made it possible to predict and characterize the genome-wide of putative endogenous allergens in rice (Oryza sativa L.. In this work, we identified and characterized 122 candidate rice allergens including the 22 allergens in present databases. Conserved domain analysis also revealed 37 domains among rice allergens including one novel domain (histidine kinase-, DNA gyrase B-, and HSP90-like ATPase, PF13589 adding to the allergen protein database. Phylogenetic analysis of the allergens revealed the diversity among the Prolamin superfamily and DnaK protein family, respectively. Additionally, some allergens proteins clustered on the rice chromosome might suggest the molecular function during the evolution.

  8. Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice

    OpenAIRE

    Waters, Daniel L. E.; Nock, Catherine J; Ishikawa, Ryuji; Rice, Nicole; Henry, Robert J.

    2012-01-01

    Cultivated rice (Oryza sativa) is an AA genome Oryza species that was most likely domesticated from wild populations of O. rufipogon in Asia. O. rufipogon and O. meridionalis are the only AA genome species found within Australia and occur as widespread populations across northern Australia. The chloroplast genome sequence of O. rufipogon from Asia and Australia and O. meridionalis and O. australiensis (an Australian member of the genus very distant from O. sativa) was obtained by massively pa...

  9. A draft sequence of the rice(Oryza sativa ssp. indica) genome

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a "whole genome shotgun" approach, we have produced a draft rice genome sequence of Oryza sativa ssp. indica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from an indica variant cultivar 93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEM- BLER, a custom-designed software package used for the initial assembly, were verified rigorously by comparisons against finished BAC clone sequences from both indica and japanica strains, available from the public databases. Over all, 96.3% of full-length cDNAs, 96.4% of STS, STR, RFLP markers, 94.0% of ESTs and 94.9% unigene clusters were identified from the draft sequence. Our preliminary analysis on the data set shows that our rice draft sequence is consistent with the comman standard accepted by the genome sequencing community. The unconditional release of the draft to the public also undoubtedly provides a fundamental resource to the international scientific communities to facilitate genomic and genetic studies on rice biology.

  10. Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis

    Directory of Open Access Journals (Sweden)

    Itoh Takeshi

    2010-02-01

    Full Text Available Abstract Background Rice is one of the most important food crops in the world. With increasing world demand for food crops, there is an urgent need to develop new cultivars that have enhanced performance with regard to yield, disease resistance, and so on. Wild rice is expected to provide useful genetic resources that could improve the present cultivated species. However, the quantity and quality of these unexplored resources remain unclear. Recent accumulation of the genomic information of both cultivated and wild rice species allows for their comparison at the molecular level. Here, we compared the genome sequence of Oryza sativa ssp. japonica with sets of bacterial artificial chromosome end sequences (BESs from two wild rice species, O. rufipogon and O. nivara, and an African rice species, O. glaberrima. Results We found that about four to five percent of the BESs of the two wild rice species and about seven percent of the African rice could not be mapped to the japonica genome, suggesting that a substantial number of genes have been lost in the japonica rice lineage; however, their close relatives still possess their counterpart genes. We estimated that during evolution, O. sativa has lost at least one thousand genes that are still preserved in the genomes of the other species. In addition, our BLASTX searches against the non-redundant protein sequence database showed that disease resistance-related proteins were significantly overrepresented in the close relative-specific genomic portions. In total, 235 unmapped BESs of the three relatives matched 83 non-redundant proteins that contained a disease resistance protein domain, most of which corresponded to an NBS-LRR domain. Conclusion We found that the O. sativa lineage appears to have recently experienced massive gene losses following divergence from its wild ancestor. Our results imply that the domestication process accelerated large-scale genomic deletions in the lineage of Asian

  11. Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice.

    Science.gov (United States)

    Waters, Daniel L E; Nock, Catherine J; Ishikawa, Ryuji; Rice, Nicole; Henry, Robert J

    2012-01-01

    Cultivated rice (Oryza sativa) is an AA genome Oryza species that was most likely domesticated from wild populations of O. rufipogon in Asia. O. rufipogon and O. meridionalis are the only AA genome species found within Australia and occur as widespread populations across northern Australia. The chloroplast genome sequence of O. rufipogon from Asia and Australia and O. meridionalis and O. australiensis (an Australian member of the genus very distant from O. sativa) was obtained by massively parallel sequencing and compared with the chloroplast genome sequence of domesticated O. sativa. Oryza australiensis differed in more than 850 sites single nucleotide polymorphism or indel from each of the other samples. The other wild rice species had only around 100 differences relative to cultivated rice. The chloroplast genomes of Australian O. rufipogon and O. meridionalis were closely related with only 32 differences. The Asian O. rufipogon chloroplast genome (with only 68 differences) was closer to O. sativa than the Australian taxa (both with more than 100 differences). The chloroplast sequences emphasize the genetic distinctness of the Australian populations and their potential as a source of novel rice germplasm. The Australian O. rufipogon may be a perennial form of O. meridionalis.

  12. Genome-wide identification of R genes and exploitation of candidate RGA markers in rice

    Institute of Scientific and Technical Information of China (English)

    WANG Xusheng; WU Weiren; JIN Gulei; ZHU Jun

    2005-01-01

    By scanning the whole genomic sequence of japonica rice using 45 known plant disease resistance (R) genes, we identified 2119 resistance gene homologs or analogs (RGAs) and verified that RGAs are not randomly distributed but tend to cluster in the rice genome. The RGAs were classified into 21 families according to their functional domain based on Hidden Markov model (HMM). By comparing the RGAs of japonica rice with the whole genomic sequence of indica rice, we found 702 RGAs allelic between the two subspecies and revealed that 671 (95.6%) of them have length difference (InDels) in their genomic sequences (including coding and non-coding regions) between the two subspecies, suggesting that RGAs are highly polymorphic between the two subspecies in rice. We also exploited 402 PCR-based and co-dominant candidate RGA markers by designing primer pairs on the regions flanking the InDels and validating them via e-PCR. The length differences of the candidate RGA markers between the two subspecies are from 1 to 742 bp, with an average of 10.26 bp. All related information of the RGAs is available from our web site (http://ibi.zju.edu.cn/RGAs/index.html).

  13. Diversity and selective sweep in the OsAMT1;1 genomic region of rice

    Directory of Open Access Journals (Sweden)

    Chen Sheng

    2011-03-01

    Full Text Available Abstract Background Ammonium is one of the major forms in which nitrogen is available for plant growth. OsAMT1;1 is a high-affinity ammonium transporter in rice (Oryza sativa L., responsible for ammonium uptake at low nitrogen concentration. The expression pattern of the gene has been reported. However, variations in its nucleotides and the evolutionary pathway of its descent from wild progenitors are yet to be elucidated. In this study, nucleotide diversity of the gene OsAMT1;1 and the diversity pattern of seven gene fragments spanning a genomic region approximately 150 kb long surrounding the gene were surveyed by sequencing a panel of 216 rice accessions including both cultivated rice and wild relatives. Results Nucleotide polymorphism (Pi of OsAMT1;1 was as low as 0.00004 in cultivated rice (Oryza sativa, only 2.3% of that in the common wild rice (O. rufipogon. A single dominant haplotype was fixed at the locus in O. sativa. The test values for neutrality were significantly negative in the entire region stretching 5' upstream and 3' downstream of the gene in all accessions. The value of linkage disequilibrium remained high across a 100 kb genomic region around OsAMT1;1 in O. sativa, but fell rapidly in O. rufipogon on either side of the promoter of OsAMT1;1, demonstrating a strong natural selection within or nearby the ammonium transporter. Conclusions The severe reduction in nucleotide variation at OsAMT1;1 in rice was caused by a selective sweep around OsAMT1;1, which may reflect the nitrogen uptake system under strong selection by the paddy soil during the domestication of rice. Purifying selection also occurred before the wild rice diverged into its two subspecies, namely indica and japonica. These findings would provide useful insights into the processes of evolution and domestication of nitrogen uptake genes in rice.

  14. A genome browser database for rice (Oryza sativa) and Chinese ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-19

    Oct 19, 2009 ... Northeast Asia. ... storage, integration, analysis and visualization of a wide ... integration of any biological data that can be mapped .... Screenshot of 'map view' showing the region of rice chromosomes for selection from the ...

  15. Identification of Chromosomes from Multiple Rice Genomes Using a Universal Molecular Cytogenetic Marker System

    Institute of Scientific and Technical Information of China (English)

    Xiaomin Tang; Weidong Bao; Wenli Zhang; Zhukuan Cheng

    2007-01-01

    To develop reliable techniques for chromosome identification is critical for cytogenetic research, especially for genomes with a large number and smaller-sized chromosomes. An efficient approach using bacterial artificial chromosome (BAG) clones as molecular cytological markers has been developed for many organisms. Herein, we present a set of chromosomal arm-specific molecular cytological markers derived from the gene-enriched regions of the sequenced rice genome. All these markers are able to generate very strong signals on the pachytene chromosomes of Oryza satlva L. (AA genome) when used as fluorescence in situ hybridization (FISH) probes. We further probed those markers to the pachytene chromosomes of O. punctata (BB genome) and O. officinalis (CC genome) and also got very strong signals on the relevant pachytene chromosomes. The signal position of each marker on the related chromosomes from the three different rice genomes was pretty much stable, which enabled us to identify different chromosomes among various rice genomes. We also constructed the karyotype for both O. punctata and O. officinalis with the BB and CC genomes, respectively, by analysis of 10 pachytene cells anchored by these chromosomal arm-specific markers.

  16. EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome

    Directory of Open Access Journals (Sweden)

    Hamilton John P

    2007-10-01

    Full Text Available Abstract Background Despite the improvements of tools for automated annotation of genome sequences, manual curation at the structural and functional level can provide an increased level of refinement to genome annotation. The Institute for Genomic Research Rice Genome Annotation (hereafter named the Osa1 Genome Annotation is the product of an automated pipeline and, for this reason, will benefit from the input of biologists with expertise in rice and/or particular gene families. Leveraging knowledge from a dispersed community of scientists is a demonstrated way of improving a genome annotation. This requires tools that facilitate 1 the submission of gene annotation to an annotation project, 2 the review of the submitted models by project annotators, and 3 the incorporation of the submitted models in the ongoing annotation effort. Results We have developed the Eukaryotic Community Annotation Package (EuCAP, an annotation tool, and have applied it to the rice genome. The primary level of curation by community annotators (CA has been the annotation of gene families. Annotation can be submitted by email or through the EuCAP Web Tool. The CA models are aligned to the rice pseudomolecules and the coordinates of these alignments, along with functional annotation, are stored in the MySQL EuCAP Gene Model database. Web pages displaying the alignments of the CA models to the Osa1 Genome models are automatically generated from the EuCAP Gene Model database. The alignments are reviewed by the project annotators (PAs in the context of experimental evidence. Upon approval by the PAs, the CA models, along with the corresponding functional annotations, are integrated into the Osa1 Genome Annotation. The CA annotations, grouped by family, are displayed on the Community Annotation pages of the project website http://rice.tigr.org, as well as in the Community Annotation track of the Genome Browser. Conclusion We have applied EuCAP to rice. As of July 2007, the

  17. Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences

    Directory of Open Access Journals (Sweden)

    Ganko Eric W

    2004-03-01

    Full Text Available Abstract Background LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes thus far examined. Plant genomes, in particular, have been found to be comprised of a remarkably high number of LTR retrotransposons. There is a significant body of direct and indirect evidence that LTR retrotransposons have contributed to gene and genome evolution in plants. Results To explore the evolutionary history of long terminal repeat (LTR retrotransposons and their impact on the genome of Oryza sativa, we have extended an earlier computer-based survey to include all identifiable full-length, fragmented and solo LTR elements in the rice genome database as of April 2002. A total of 1,219 retroelement sequences were identified, including 217 full-length elements, 822 fragmented elements, and 180 solo LTRs. In order to gain insight into the chromosomal distribution of LTR-retrotransposons in the rice genome, a detailed examination of LTR-retrotransposon sequences on Chromosome 10 was carried out. An average of 22.3 LTR-retrotransposons per Mb were detected in Chromosome 10. Conclusions Gypsy-like elements were found to be >4 × more abundant than copia-like elements. Eleven of the thirty-eight investigated LTR-retrotransposon families displayed significant subfamily structure. We estimate that at least 46.5% of LTR-retrotransposons in the rice genome are older than the age of the species (

  18. Genomic Rearrangement in Endogenous Long Terminal Repeat Retrotransposons of Rice Lines Introgressed by Wild Rice (Zizania latifolia Griseb.)

    Institute of Scientific and Technical Information of China (English)

    Ye SHEN; Xiu-Yun LIN; Xiao-Hui SHAN; Chun-Jing LIN; Fang-Pu HAN; Jin-Song PANG; Bao LIU

    2005-01-01

    Stochastic introgression of alien DNA may impose a genomic stress to the recipient genome.Herein, we report that apparent de novo genomic rearrangements in 10 of 13 selected endogenous, low-copy, and potentially active long terminal repeat (LTR) retrotransposons occurred in one or more of threerice lines studied that were introgressed by wild rice (Zizania latifolia Griseb.). For nine retrotransposons inwhich both the reverse-transcriptase (RT) region and the LTR region were available, largely concordantrearrangements occurred at both regions in five elements and at the RT region only in the remaining fourelements. A marked proportion of the genomic changes was shared by two or all three introgression linesthat were derived from a single F1 plant. This indicates that most of the genomic changes occurred at earlydevelopmental stages of the F1 somatic cells, which then gave rise to germline cells, and, hence, ensuredinheritance of the changes to later generations. Possible causes and potential implications of the introgres-sion-induced genomic rearrangements in LTR retrotransposons are discussed in the context of plant ge-nome evolution and breeding.

  19. Study on Young Panicle Culture in vitro From Wild Rice of Different Genomes

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Researches have been made on young panicle culture in vitro from wild rice of different genomes.Main results are as follows: 1. The induction frequencies of young panicle cultured in vitro from wild rice varied largely a relation to its genome. The optimal induction period of callus is the stamen and pistil differentiation stage of young panicle development. 2. Plantlets were regenerated through two ways: first, culture method, the induced calli were transferred onto differentiation medium; second, regenerate plantlets directly from young panicles of wild rice that were cultured on the differentiation medium. 3. The regeneration rate of green plantlets that obtained through cryopreservated calli in O. meyeriana was 10 times higher than that of control.

  20. Characterization of Interspecific Hybrids Between Oryza sativa L. and Three Wild Rice Species of China by Genomic In Situ Hybridization

    Institute of Scientific and Technical Information of China (English)

    Guang-Xuan Tan; Zhi-Yong Xiong; Hua-Jun Jin; Gang Li; Li-Li Zhu; Li-Hui Shu; Guang-Cun He

    2006-01-01

    In the genus Oryza, interspecific hybrids are useful bridges for transferring the desired genes from wild species to cultivated rice (Oryza sativa L.). In the present study, hybrids between O. sativa (AA genome)and three Chinese wild rices, namely O. rufipogon (AA genome), O. officinalis (CC genome), and O. meyeriana (GG genome), were produced. Agricultural traits of the F1 hybrids surveyed were intermediate between their parents and appreciably resembled wild rice parents. Except for the O. sativa × O. rufipogon hybrid,the other F1 hybrids were completely sterile. Genomic in situ hybridization (GISH) was used for hybrid verification. Wild rice genomic DNAs were used as probes and cultivated rice DNA was used as a block. With the exception of O. rufipogon chromosomes, this method distinguished the other two wild rice and cultivated rice chromosomes at the stage of mitotic metaphase with different blocking ratios. The results suggest that a more distant phylogenetic relationship exists between O. meyeriana and O. sativa and that O. rufipogon and O. sativa share a high degree of sequence homology. The average mitotic chromosome length of O. officinalis and O. meyeriana was 1.25- and 1.51-fold that of O. sativa, respectively. 4',6'-Diamidino2-phenylindole staining showed that the chromosomes of O. officinalis and O. meyeriana harbored more heterochromatin, suggesting that the C and G genomes were amplified with repetitive sequences compared with the A genome. Although chromocenters formed by chromatln compaction were detected with wild rice-specific signals corresponding to the C and G genomes in discrete domains of the F1 hybrid interphase nuclei, the size and number of O. meyeriana chromocenters were bigger and greater than those of O. officinalis. The present results provide an important understanding of the genomic relationships and a tool for the transfer of useful genes from three native wild rice species in China to cultivars.

  1. Draft Genome Sequence of the Rice Kernel Smut Tilletia horrida Strain QB-1.

    Science.gov (United States)

    Wang, Na; Ai, Peng; Tang, Yangfan; Zhang, Jing; Dai, Xiaojuan; Li, Ping; Zheng, Aiping

    2015-06-25

    Tilletia horrida is the most destructive fungal pathogen of rice (Oryza sativa L.). The 20,105,270-bp draft genome sequence of T. horrida strain QB-1 is reported here. Genes encoding proteins associated with key virulence factors were predicted, and this can provide information for understanding the pathogenic mechanisms in T. horrida.

  2. Draft Genome Sequence of the Rice Kernel Smut Tilletia horrida Strain QB-1

    Science.gov (United States)

    Wang, Na; Ai, Peng; Tang, Yangfan; Zhang, Jing; Dai, Xiaojuan; Li, Ping

    2015-01-01

    Tilletia horrida is the most destructive fungal pathogen of rice (Oryza sativa L.). The 20,105,270-bp draft genome sequence of T. horrida strain QB-1 is reported here. Genes encoding proteins associated with key virulence factors were predicted, and this can provide information for understanding the pathogenic mechanisms in T. horrida. PMID:26112782

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

    Science.gov (United States)

    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...

  4. Draft Genome Sequence of Beneficial Rice Rhizosphere Isolate Pseudomonas aeruginosa PUPa3

    OpenAIRE

    Uzelac, Gordana; Bertani, Iris; Kojic, Milan; Konrad H. Paszkiewicz; Studholme, David J.; Passos da Silva, Daniel; Venturi, Vittorio

    2014-01-01

    Pseudomonas aeruginosa PUPa3 is a rhizosphere-colonizing and plant growth-promoting strain isolated from the rhizosphere of rice. This strain has, however, been shown to be pathogenic in two nonmammalian infection models. Here we report the draft genome sequence of P. aeruginosa PUPa3.

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

    Science.gov (United States)

    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.

  6. 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.

    Science.gov (United States)

    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.

  7. 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.

    Directory of Open Access Journals (Sweden)

    Jennifer Spindel

    2015-02-01

    Full Text Available 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.

  8. Non-additive gene regulation in a citrus allotetraploid somatic hybrid between C. reticulata Blanco and C. limon (L.) Burm.

    Science.gov (United States)

    Bassene, J B; Froelicher, Y; Dubois, C; Ferrer, R M; Navarro, L; Ollitrault, P; Ancillo, G

    2010-09-01

    Polyploid plants often produce new phenotypes, exceeding the range of variability existing in the diploid gene pool. Several hundred citrus allotetraploid hybrids have been created by somatic hybridization. These genotypes are interesting models to study the immediate effects of allopolyploidization on the regulation of gene expression. Here, we report genome-wide gene expression analysis in fruit pulp of a Citrus interspecific somatic allotetraploid between C. reticulata cv 'Willowleaf mandarin'+C. limon cv 'Eureka lemon', using a Citrus 20K cDNA microarray. Around 4% transcriptome divergence was observed between the two parental species, and 212 and 160 genes were more highly expressed in C. reticulata and C. limon, respectively. Differential expression of certain genes was confirmed by quantitative real-time RT-PCR. A global downregulation of the allotetraploid hybrid transcriptome was observed, as compared with a theoretical mid parent, for the genes displaying interspecific expression divergence between C. reticulata and C. limon. The genes underexpressed in mandarin, as compared with lemon, were also systematically repressed in the allotetraploid. When genes were overexpressed in C. reticulata compared with C. limon, the distribution of allotetraploid gene expression was far more balanced. Cluster analysis on the basis of gene expression clearly indicated the hybrid was much closer to C. reticulata than to C. limon. These results suggest there is a global dominance of the mandarin transcriptome, in consistence with our previous studies on aromatic compounds and proteomics. Interspecific differentiation of gene expression and non-additive gene regulation involved various biological pathways and different cellular components.

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

    Directory of Open Access Journals (Sweden)

    Partha Talukdar

    Full Text Available 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.

  10. The allotetraploid Arabidopsis thaliana-Arabidopsis lyrata subsp. petraea as an alternative model system for the study of polyploidy in plants.

    Science.gov (United States)

    Beaulieu, Julien; Jean, Martine; Belzile, François

    2009-04-01

    Polyploidy is known to be common in plants and recent work has focused on the rapid changes in genome structure and expression that occur upon polyploidization. In Arabidopsis, much of this work has been done on a synthetic allotetraploid obtained by crossing a tetraploid Arabidopsis thaliana (2n = 4x = 20) with A. arenosa (2n = 4x = 32). To explore an alternative route to polyploidy in this model species, we have developed a synthetic allopolyploid by crossing two diploid species: A. thaliana (2n = 2x = 10) and Arabidopsis lyrata subsp. petraea (2n = 2x = 16). F(1) hybrids were easy to obtain and phenotypically more similar to A. lyrata. Spontaneous chromosome doubling events occurred in about 25% of the F(1)s, thus restoring fertility. The resulting allotetraploids (2n = 26) exhibited many genomic changes typically reported upon polyploidization. Nucleolar dominance was observed as only the A. lyrata rDNA loci were expressed in the F(1) and allotetraploids. Changes in the degree of methylation were observed at almost 25% of the loci examined by MSAP analysis. Finally, structural genomic alterations did occur as a large deletion covering a significant portion of the upper arm of chromosome II was detected but no evidence of increased mobility of transposons was obtained. Such allotetraploids derived from two parents with sequenced (or soon to be sequenced) genomes offer much promise in elucidating the various changes that occur in newly synthesized polyploids.

  11. Global identification and characterization of transcriptionally active regions in the rice genome.

    Directory of Open Access Journals (Sweden)

    Lei Li

    Full Text Available Genome tiling microarray studies have consistently documented rich transcriptional activity beyond the annotated genes. However, systematic characterization and transcriptional profiling of the putative novel transcripts on the genome scale are still lacking. We report here the identification of 25,352 and 27,744 transcriptionally active regions (TARs not encoded by annotated exons in the rice (Oryza. sativa subspecies japonica and indica, respectively. The non-exonic TARs account for approximately two thirds of the total TARs detected by tiling arrays and represent transcripts likely conserved between japonica and indica. Transcription of 21,018 (83% japonica non-exonic TARs was verified through expression profiling in 10 tissue types using a re-array in which annotated genes and TARs were each represented by five independent probes. Subsequent analyses indicate that about 80% of the japonica TARs that were not assigned to annotated exons can be assigned to various putatively functional or structural elements of the rice genome, including splice variants, uncharacterized portions of incompletely annotated genes, antisense transcripts, duplicated gene fragments, and potential non-coding RNAs. These results provide a systematic characterization of non-exonic transcripts in rice and thus expand the current view of the complexity and dynamics of the rice transcriptome.

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

    Science.gov (United States)

    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.

  13. Genome-wide analysis of glutathione reductase (GR) genes from rice and Arabidopsis.

    Science.gov (United States)

    Trivedi, Dipesh Kumar; Gill, Sarvajeet Singh; Yadav, Sandep; Tuteja, Narendra

    2013-02-01

    Plant cells and tissues remain always on risk under abiotic and biotic stresses due to increased production of reactive oxygen species (ROS). Plants protect themselves against ROS induced oxidative damage by the upregulation of antioxidant machinery. Out of many components of antioxidant machinery, glutathione reductase (GR, EC 1.6.4.2) and glutathione (GSH, γ-Glu-Cys-Gly) play important role in the protection of cell against oxidative damage. In stress condition, the GR helps in maintaining the reduced glutathione pool for strengthening the antioxidative processes in plants. Present study investigates genome wide analysis of GR from rice and Arabidopsis. We were able to identify 3 rice GR genes (LOC_Os02 g56850, LOC_Os03 g06740, LOC_Os10 g28000) and 2 Arabidopsis GR genes (AT3G54660, AT3G24170) from their respective genomes on the basis of their annotation as well as the presence of pyridine nucleotide-disulphide oxidoreductases class-I active site. The evolutionary relationship of the GR genes from rice and Arabidopsis genomes was analyzed using the multiple sequence alignment and phylogenetic tree. This revealed evolutionary conserved pyridine nucleotide-disulphide oxidoreductases class-I active site among the GR protein in rice and Arabidopsis. This study should make an important contribution to our better understanding of the GR under normal and stress condition in plants.

  14. Construction and utility of 10-kb libraries for efficient clone-gap closure for rice genome sequencing.

    Science.gov (United States)

    Yang, Tae-Jin; Yu, Yeisoo; Nah, Gyoungju; Atkins, Michael; Lee, Seunghee; Frisch, David A; Wing, Rod A

    2003-08-01

    Rice is an important crop and a model system for monocot genomics, and is a target for whole genome sequencing by the International Rice Genome Sequencing Project (IRGSP). The IRGSP is using a clone by clone approach to sequence rice based on minimum tiles of BAC or PAC clones. For chromosomes 10 and 3 we are using an integrated physical map based on two fingerprinted and end-sequenced BAC libraries to identifying a minimum tiling path of clones. In this study we constructed and tested two rice genomic libraries with an average insert size of 10 kb (10-kb library) to support the gap closure and finishing phases of the rice genome sequencing project. The HaeIII library contains 166,752 clones covering approximately 4.6x rice genome equivalents with an average insert size of 10.5 kb. The Sau3AI library contains 138,960 clones covering 4.2x genome equivalents with an average insert size of 11.6 kb. Both libraries were gridded in duplicate onto 11 high-density filters in a 5 x 5 pattern to facilitate screening by hybridization. The libraries contain an unbiased coverage of the rice genome with less than 5% contamination by clones containing organelle DNA or no insert. An efficient method was developed, consisting of pooled overgo hybridization, the selection of 10-kb gap spanning clones using end sequences, transposon sequencing and utilization of in silico draft sequence, to close relatively small gaps between sequenced BAC clones. Using this method we were able to close a majority of the gaps (up to approximately 50 kb) identified during the finishing phase of chromosome-10 sequencing. This method represents a useful way to close clone gaps and thus to complete the entire rice genome.

  15. Test Data Sets and Evaluation of Gene Prediction Programs on the Rice Genome

    Institute of Scientific and Technical Information of China (English)

    Heng Li; Tao Liu; Hai-Hong Li; Yan Li; Li-Jun Fang; Hui-Min Xie; Wei-Mou Zheng; Bai-Lin Hao; Jin-Song Liu; Zhao Xu; Jiao Jin; Lin Fang; Lei Gao; Yu-Dong Li; Zi-Xing Xing; Shao-Gen Gao

    2005-01-01

    With several rice genome projects approaching completion gene prediction/finding by computer algorithms has become an urgent task. Two test sets were constructed by mapping the newly published 28,469 full-length KOME rice cDNA to the RGP BAC clone sequences of Oryza sativa ssp. japonica: a single-gene set of 550 sequences and a multi-gene set of 62 sequences with 271 genes. These data sets were used to evaluate five ab initio gene prediction programs: RiceHMM,GlimmerR, GeneMark, FGENSH and BGF. The predictions were compared on nucleotide, exon and whole gene structure levels using commonly accepted measures and several new measures. The test results show a progress in performance in chronological order. At the same time complementarity of the programs hints on the possibility of further improvement and on the feasibility of reaching better performance by combining several gene-finders.

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

    Science.gov (United States)

    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.

  17. Two evolutionary histories in the genome of rice: the roles of domestication genes.

    Directory of Open Access Journals (Sweden)

    Ziwen He

    2011-06-01

    Full Text Available Genealogical patterns in different genomic regions may be different due to the joint influence of gene flow and selection. The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication. We chose 66 accessions from the three rice taxa (about 22 each from Oryza sativa indica, O. sativa japonica, and O. rufipogon for whole-genome sequencing. In the search for the signature of selection, we focus on low diversity regions (LDRs shared by both cultivars. We found that the genealogical histories of these overlapping LDRs are distinct from the genomic background. While indica and japonica genomes generally appear to be of independent origin, many overlapping LDRs may have originated only once, as a result of selection and subsequent introgression. Interestingly, many such LDRs contain only one candidate gene of rice domestication, and several known domestication genes have indeed been "rediscovered" by this approach. In summary, we identified 13 additional candidate genes of domestication.

  18. Comparative analysis of the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae.

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    Minfeng Xue

    Full Text Available Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice worldwide. The fungal pathogen is notorious for its ability to overcome host resistance. To better understand its genetic variation in nature, we sequenced the genomes of two field isolates, Y34 and P131. In comparison with the previously sequenced laboratory strain 70-15, both field isolates had a similar genome size but slightly more genes. Sequences from the field isolates were used to improve genome assembly and gene prediction of 70-15. Although the overall genome structure is similar, a number of gene families that are likely involved in plant-fungal interactions are expanded in the field isolates. Genome-wide analysis on asynonymous to synonymous nucleotide substitution rates revealed that many infection-related genes underwent diversifying selection. The field isolates also have hundreds of isolate-specific genes and a number of isolate-specific gene duplication events. Functional characterization of randomly selected isolate-specific genes revealed that they play diverse roles, some of which affect virulence. Furthermore, each genome contains thousands of loci of transposon-like elements, but less than 30% of them are conserved among different isolates, suggesting active transposition events in M. oryzae. A total of approximately 200 genes were disrupted in these three strains by transposable elements. Interestingly, transposon-like elements tend to be associated with isolate-specific or duplicated sequences. Overall, our results indicate that gain or loss of unique genes, DNA duplication, gene family expansion, and frequent translocation of transposon-like elements are important factors in genome variation of the rice blast fungus.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Institute of Scientific and Technical Information of China (English)

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

    2015-01-01

    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 17 kb 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. Localizing introgression on the chromosome of rice by genomic in ...

    African Journals Online (AJOL)

    USER

    2010-07-26

    Jul 26, 2010 ... 1Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan. ... Genomic in situ hybridization was used to detect introgressed segment .... Gene transfer and molecular characterization of introgression.

  3. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome.

    Directory of Open Access Journals (Sweden)

    Keyan Zhao

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  5. Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis

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    Katiyar Amit

    2012-10-01

    Full Text Available Abstract Background The MYB gene family comprises one of the richest groups of transcription factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA-binding domain. MYB proteins are classified into four major groups namely, 1R-MYB, 2R-MYB, 3R-MYB and 4R-MYB based on the number and position of MYB repeats. MYB transcription factors are involved in plant development, secondary metabolism, hormone signal transduction, disease resistance and abiotic stress tolerance. A comparative analysis of MYB family genes in rice and Arabidopsis will help reveal the evolution and function of MYB genes in plants. Results A genome-wide analysis identified at least 155 and 197 MYB genes in rice and Arabidopsis, respectively. Gene structure analysis revealed that MYB family genes possess relatively more number of introns in the middle as compared with C- and N-terminal regions of the predicted genes. Intronless MYB-genes are highly conserved both in rice and Arabidopsis. MYB genes encoding R2R3 repeat MYB proteins retained conserved gene structure with three exons and two introns, whereas genes encoding R1R2R3 repeat containing proteins consist of six exons and five introns. The splicing pattern is similar among R1R2R3 MYB genes in Arabidopsis. In contrast, variation in splicing pattern was observed among R1R2R3 MYB members of rice. Consensus motif analysis of 1kb upstream region (5′ to translation initiation codon of MYB gene ORFs led to the identification of conserved and over-represented cis-motifs in both rice and Arabidopsis. Real-time quantitative RT-PCR analysis showed that several members of MYBs are up-regulated by various abiotic stresses both in rice and Arabidopsis. Conclusion A comprehensive genome-wide analysis of chromosomal distribution, tandem repeats and phylogenetic relationship of MYB family genes in rice and Arabidopsis suggested their evolution via duplication. Genome-wide comparative analysis of MYB genes and

  6. Progress on Transferring Elite Genes from Non-AA Genome Wild Rice into Oryza sativa through Interspecific Hybridization

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The progress of research on transferring elite genes from non-AA genome wild rice into Oryza sativa through interspecific hybridization are in three respects,that is,breeding monosomic alien addition lines (MAALs),constructing introgression lines (ILs) and analyzing the heredity of the characters and mapping the related genes.There are serious reproductive barriers,mainly incrossability and hybrid sterility,in the interspecific hybridization of O.sativa with non-AA genome wild rice.These are the 'bottleneck' for transferring elite genes from wild rice to O.sativa.Combining traditional crossing method with biotechnique is a reliable way to overcome the reproductive barriers and to improve the utilizing efficiency of non-AA genome wild rice.

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

    Science.gov (United States)

    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

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

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    Malali Gowda

    2015-09-01

    Full Text Available 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.

  9. Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution

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    Kishima Yuji

    2004-10-01

    Full Text Available Abstract Background Plant genomes contain various kinds of repetitive sequences such as transposable elements, microsatellites, tandem repeats and virus-like sequences. Most of them, with the exception of virus-like sequences, do not allow us to trace their origins nor to follow the process of their integration into the host genome. Recent discoveries of virus-like sequences in plant genomes led us to set the objective of elucidating the origin of the repetitive sequences. Endogenous rice tungro bacilliform virus (RTBV-like sequences (ERTBVs have been found throughout the rice genome. Here, we reconstructed putative virus structures from RTBV-like sequences in the rice genome and characterized to understand evolutionary implication, integration manner and involvements of endogenous virus segments in the corresponding disease response. Results We have collected ERTBVs from the rice genomes. They contain rearranged structures and no intact ORFs. The identified ERTBV segments were shown to be phylogenetically divided into three clusters. For each phylogenetic cluster, we were able to make a consensus alignment for a circular virus-like structure carrying two complete ORFs. Comparisons of DNA and amino acid sequences suggested the closely relationship between ERTBV and RTBV. The Oryza AA-genome species vary in the ERTBV copy number. The species carrying low-copy-number of ERTBV segments have been reported to be extremely susceptible to RTBV. The DNA methylation state of the ERTBV sequences was correlated with their copy number in the genome. Conclusions These ERTBV segments are unlikely to have functional potential as a virus. However, these sequences facilitate to establish putative virus that provided information underlying virus integration and evolutionary relationship with existing virus. Comparison of ERTBV among the Oryza AA-genome species allowed us to speculate a possible role of endogenous virus segments against its related disease.

  10. Genome wide association mapping for grain shape traits in indica rice.

    Science.gov (United States)

    Feng, Yue; Lu, Qing; Zhai, Rongrong; Zhang, Mengchen; Xu, Qun; Yang, Yaolong; Wang, Shan; Yuan, Xiaoping; Yu, Hanyong; Wang, Yiping; Wei, Xinghua

    2016-10-01

    Using genome-wide association mapping, 47 SNPs within 27 significant loci were identified for four grain shape traits, and 424 candidate genes were predicted from public database. Grain shape is a key determinant of grain yield and quality in rice (Oryza sativa L.). However, our knowledge of genes controlling rice grain shape remains limited. Genome-wide association mapping based on linkage disequilibrium (LD) has recently emerged as an effective approach for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. In this study, association mapping based on 5291 single nucleotide polymorphisms (SNPs) was conducted to identify significant loci associated with grain shape traits in a global collection of 469 diverse rice accessions. A total of 47 SNPs were located in 27 significant loci for four grain traits, and explained ~44.93-65.90 % of the phenotypic variation for each trait. In total, 424 candidate genes within a 200 kb extension region (±100 kb of each locus) of these loci were predicted. Of them, the cloned genes GS3 and qSW5 showed very strong effects on grain length and grain width in our study. Comparing with previously reported QTLs for grain shape traits, we found 11 novel loci, including 3, 3, 2 and 3 loci for grain length, grain width, grain length-width ratio and thousand grain weight, respectively. Validation of these new loci would be performed in the future studies. These results revealed that besides GS3 and qSW5, multiple novel loci and mechanisms were involved in determining rice grain shape. These findings provided valuable information for understanding of the genetic control of grain shape and molecular marker assistant selection (MAS) breeding in rice.

  11. Development of new transformation-competent artificial chromosome vectors and rice genomic libraries for efficient gene cloning.

    Science.gov (United States)

    Liu, Yao-Guang; Liu, Hongmei; Chen, Letian; Qiu, Weihua; Zhang, Qunyu; Wu, Hao; Yang, Chunyi; Su, Jing; Wang, Zhonghua; Tian, Dongsheng; Mei, Mantong

    2002-01-09

    The transformation-competent artificial chromosome vector (TAC) system has been shown to be very useful for efficient gene isolation in Arabidopsis thaliana (Proc. Natl. Acad. Sci. USA 96 (1998) 6535). To adapt the vector system for gene isolation in crops, two new TAC vectors and rice genomic libraries were developed. The new vectors pYLTAC17 and pYLTAC27 use the Bar gene and Hpt gene driven by the rice Act1 promoter as the plant selectable markers, respectively, and are suitable for transformation of rice and other grasses. Two representative genomic libraries (I and II) of an Indica rice variety Minghui63, a fertility restorer line for hybrid rice, were constructed with pYLTAC17 using different size classes of partially digested DNA fragments. Library I and library II consisted of 34,560 and 1.2 x 10(5) clones, with average insert sizes of approximately 77 and 39 kb, respectively. The genome coverage of the libraries I and II was estimated to be about 5 and 11 haploid genome equivalents, respectively. Clones of the library I were stored individually in ninety 384-well plates, and those of the library II were collected as bulked pools each containing 30-50 clones and stored in eight 384-well plates. A number of probes were used to hybridize high-density colony filters of the library I prepared by an improved replicating method and each detected 2-9 positive clones. A method for rapid screening of the library II by pooled colony hybridization was developed. A TAC clone having an 80 kb rice DNA insert was successfully transferred into rice genome via Agrobacterium-mediated transformation. The new vectors and the genomic libraries should be useful for gene cloning and genetic engineering in rice and other crops.

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

    Science.gov (United States)

    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. Genome wide association study (GWAS) for grain yield in rice cultivated under water deficit.

    Science.gov (United States)

    Pantalião, Gabriel Feresin; Narciso, Marcelo; Guimarães, Cléber; Castro, Adriano; Colombari, José Manoel; Breseghello, Flavio; Rodrigues, Luana; Vianello, Rosana Pereira; Borba, Tereza Oliveira; Brondani, Claudio

    2016-12-01

    The identification of rice drought tolerant materials is crucial for the development of best performing cultivars for the upland cultivation system. This study aimed to identify markers and candidate genes associated with drought tolerance by Genome Wide Association Study analysis, in order to develop tools for use in rice breeding programs. This analysis was made with 175 upland rice accessions (Oryza sativa), evaluated in experiments with and without water restriction, and 150,325 SNPs. Thirteen SNP markers associated with yield under drought conditions were identified. Through stepwise regression analysis, eight SNP markers were selected and validated in silico, and when tested by PCR, two out of the eight SNP markers were able to identify a group of rice genotypes with higher productivity under drought. These results are encouraging for deriving markers for the routine analysis of marker assisted selection. From the drought experiment, including the genes inherited in linkage blocks, 50 genes were identified, from which 30 were annotated, and 10 were previously related to drought and/or abiotic stress tolerance, such as the transcription factors WRKY and Apetala2, and protein kinases.

  14. Neighboring-Nucleotide Effects on the Mutation Patterns of the Rice Genome

    Institute of Scientific and Technical Information of China (English)

    Hui Zhao; Qi-Zhai Li; Chang-Qing Zeng; Huan-Ming Yang; Jun Yu

    2005-01-01

    DNA composition dynamics across genomes of diverse taxonomy is a major subject of genome analyses. DNA composition changes are characteristics of both replication and repair machineries. We investigated 3,611,007 single nucleotide polymorphisms (SNPs) generated by comparing two sequenced rice genomes from distant inbred lines (subspecies), including those from 242,811 introns and 45,462 protein-coding sequences (CDSs). Neighboring-nucleotide effects (NNEs) of these SNPs are diverse, depending on structural content-based classifications (genomewide, intronic, and CDS) and sequence context-based categories (A/C, A/G, A/T,C/G, C/T, and G/T substitutions) of the analyzed SNPs. Strong and evident NNEs and nucleotide proportion biases surrounding the analyzed SNPs were observed in 1-3 bp sequences on both sides of an SNP. Strong biases were observed around neighboring nucleotides of protein-coding SNPs, which exhibit a periodicity of three in nucleotide content, constrained by a combined effect of codon-related rules and DNA repair mechanisms. Unlike a previous finding in the human genome,we found negative correlation between GC contents of chromosomes and the magnitude of corresponding bias of nucleotide C at -1 site and G at +1 site. These results will further our understanding of the mutation mechanism in rice as well as its evolutionary implications.

  15. Alterations in DNA methylation and genome structure in two rice mutant lines induced by high pressure

    Institute of Scientific and Technical Information of China (English)

    SHEN; Sile; WANG; Zhenwei; SHAN; Xiaohui; WANG; Hua; LI; Ling; LIN; Xuyun; LONG; Likun; WENG; Kenan; LIU; Bao; ZOU; Guangtian

    2006-01-01

    By using high-pressure treatment, two mutant lines were obtained from a genetically stable japonica rice cultivar Bijing38. Genomic DNA of the mutant lines, together with the original line (Bijing38), was either undigested or digested by Hpa II/Msp I, and then subjected to molecular analysis using two markers, ISSR and RAPD. Results indicated that changes in the PCR amplification profiles of both markers are apparent in the two mutant lines compared with the original rice cultivar, suggesting that there had been both sequence changes and DNA methylation modifications in the mutant lines. Southern blot analysis using diverse sequences, including two cellular genes (S2 and S3), a set of retrotransposons (Osr7, Osr36, Tos19 and more), and a MITE transposon family (mPing and Pong), confirmed the results, and indicated that changes in DNA methylation pattern, genomic structure, and possible activation of some transposons indeed occurred in the mutant lines. Moreover, these changes are stably maintained through selfed generations and in different organs. Thus, our results indicate that it is possible to obtain stable mutants in rice by high pressure treatments, and the molecular basis of the mutants may include both genetic and epigenetic changes. Therefore, high hydrostatic pressure seems a promising approach for plant mutagenesis.

  16. Whole genome sequence of Pantoea ananatis R100, an antagonistic bacterium isolated from rice seed.

    Science.gov (United States)

    Wu, Liwen; Liu, Ruifang; Niu, Yaofang; Lin, Haiyan; Ye, Weijun; Guo, Longbiao; Hu, Xingming

    2016-05-10

    Pantoea ananatis is a group of bacteria, which was first reported as plant pathogen. Recently, several papers also described its biocontrol ability. In 2003, P. ananatis R100, which showed strong antagonism against several plant pathogens, was isolated from rice seeds. In this study, whole genome sequence of this strain was determined by SMRT Cell technology. The total genome size of R100 is 4,857,861bp with 4659 coding genes (CDS), 82 tRNAs and 22 rRNAs. The genome sequence of R100 may shed a light on the research of antagonism P. ananatis. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  17. Genome-wide transcriptional changes and defence-related chemical profiling of rice in response to infestation by the rice striped stem borer Chilo suppressalis.

    Science.gov (United States)

    Zhou, Guoxin; Wang, Xia; Yan, Feng; Wang, Xia; Li, Ran; Cheng, Jiaan; Lou, Yonggen

    2011-09-01

    How rice defends itself against pathogen infection is well documented, but little is known about how it defends itself against herbivore attack. We measured changes in the transcriptome and chemical profile of rice when the plant is infested by the striped stem borer (SSB) Chilo suppressalis. Infestation by SSBs resulted in changes in the expression levels of 4545 rice genes; this number accounts for about 8% of the genome and is made up of 18 functional groups with broad functions. The largest group comprised genes involved in metabolism, followed by cellular transport, transcription and cellular signaling. Infestation by SSBs modulated many genes responsible for the biosynthesis of plant hormones and plant signaling. Jasmonic acid (JA), salicylic acid (SA) and ethylene were the major hormones that shaped the SSB-induced defence responses of rice. Many secondary signal transduction components, such as those involved in Ca²⁺ signaling and G-protein signaling, receptor and non-receptor protein kinases, and transcription factors were involved in the SSB-induced responses of rice. Photosynthesis and ATP synthesis from photophosphorylation were restricted by SSB feeding. In addition, SSB infestation induced the accumulation of defence compounds, including trypsin proteinase inhibitors (TrypPIs) and volatile organic compounds. These results demonstrate that SSB-induced defences required rice to reconfigure a wide variety of its metabolic, physiological and biochemical processes.

  18. Cloning of genomic DNA of rice 5-enolpyruvylshikimate 3-phosphate synthase gene and chromosomal localization of the gene

    Institute of Scientific and Technical Information of China (English)

    徐军望; 冯德江; 李旭刚; 常团结; 朱祯

    2002-01-01

    The shikimate pathway enzyme 5-enolpyruvylshikimate 3-phosphate synthase (EPSPs) is the target of nonselective herbicide glyphosate. A partial rice epsps cDNA was generated by RT-PCR with primers designed according to EST sequence in GenBank and used as probe for rice genomic library screening. In a screen of approximately 8.0×104 clones from the rice genomic library, sixteen positive clones were obtained, which strongly hybridized to the probe. One clone, E11, was selected for further analysis and the full-length 3661 bp rice epsps genomic sequence was obtained. Sequence analysis and homologous comparison revealed that epsps gene is composed of 8 exons and 7 introns. Analysis by restriction fragment length polymorphism with the probe of rice epsps cDNA fragment confirmed that rice epsps is located on chromosome 6 with an indica-japonica (ZYQ8-JX17) double-haploid (DH) population. This is the first report on the EPSP synthase from monocotyledons.

  19. Self-similar characteristics of single nucleotide polymorphisms in the rice genome

    Science.gov (United States)

    Lee, Chang-Yong

    2016-11-01

    With single nucleotide polymorphism (SNP) data from the 3,000 rice genome project, we investigate the mutational characteristics of the rice genome from the perspective of statistical physics. From the frequency distributions of the space between adjacent SNPs, we present evidence that SNPs are not spaced randomly, but clustered across the genome. The clustering property is related to a long-range correlation in SNP locations, suggesting that a mutation occurring in a locus may affect other mutations far away along the sequence in a chromosome. In addition, the reliability of the existence of the long-range correlation is supported by the agreement between the results of two independent analysis methods. The highly-skewed and long-tailed distribution of SNP spaces is further characterized by a multi-fractal, showing that SNP spaces possess a rich structure of a statistical self-similarity. These results can be used for an optimal design of a microarray assay and a primer, as well as for genotyping quality control.

  20. Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication.

    Directory of Open Access Journals (Sweden)

    Tian Tang

    2006-11-01

    Full Text Available Genomic regions that are unusually divergent between closely related species or racial groups can be particularly informative about the process of speciation or the operation of natural selection. The two sequenced genomes of cultivated Asian rice, Oryza sativa, reveal that at least 6% of the genomes are unusually divergent. Sequencing of ten unlinked loci from the highly divergent regions consistently identified two highly divergent haplotypes with each locus in nearly complete linkage disequilibrium among 25 O. sativa cultivars and 35 lines from six wild species. The existence of two highly divergent haplotypes in high divergence regions in species from all geographical areas (Africa, Asia, and Oceania was in contrast to the low polymorphism and low linkage disequilibrium that were observed in other parts of the genome, represented by ten reference loci. While several natural processes are likely to contribute to this pattern of genomic variation, domestication may have greatly exaggerated the trend. In this hypothesis, divergent haplotypes that were adapted to different geographical and ecological environments migrated along with humans during the development of domesticated varieties. If true, these high divergence regions of the genome would be enriched for loci that contribute to the enormous range of phenotypic variation observed among domesticated breeds.

  1. Comparisons of Copy Number, Genomic Structure, and Conserved Motifs for α-Amylase Genes from Barley, Rice, and Wheat

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    Qisen Zhang

    2017-10-01

    Full Text Available Barley is an important crop for the production of malt and beer. However, crops such as rice and wheat are rarely used for malting. α-amylase is the key enzyme that degrades starch during malting. In this study, we compared the genomic properties, gene copies, and conserved promoter motifs of α-amylase genes in barley, rice, and wheat. In all three crops, α-amylase consists of four subfamilies designated amy1, amy2, amy3, and amy4. In wheat and barley, members of amy1 and amy2 genes are localized on chromosomes 6 and 7, respectively. In rice, members of amy1 genes are found on chromosomes 1 and 2, and amy2 genes on chromosome 6. The barley genome has six amy1 members and three amy2 members. The wheat B genome contains four amy1 members and three amy2 members, while the rice genome has three amy1 members and one amy2 member. The B genome has mostly amy1 and amy2 members among the three wheat genomes. Amy1 promoters from all three crop genomes contain a GA-responsive complex consisting of a GA-responsive element (CAATAAA, pyrimidine box (CCTTTT and TATCCAT/C box. This study has shown that amy1 and amy2 from both wheat and barley have similar genomic properties, including exon/intron structures and GA-responsive elements on promoters, but these differ in rice. Like barley, wheat should have sufficient amy activity to degrade starch completely during malting. Other factors, such as high protein with haze issues and the lack of husk causing Lauting difficulty, may limit the use of wheat for brewing.

  2. A High-throughput Genomic Tool: Diversity Array Technology Complementary for Rice Genotyping

    Institute of Scientific and Technical Information of China (English)

    Yong Xie; Kenneth McNally; Cheng-Yun Li; Hei Leung; You-Yong Zhu

    2006-01-01

    Diversity array technology (DArTTM) was a genotyping tool characterized gel-independent and high throughput.The main purpose of present study is to validate DArT for rice (Oryza sativa L.)genotyping in a high throughput manner. Technically, the main objective was to generate a rice general purpose gene pool, and optimize this genomic tool in order to evaluate rice germplasm genetic diversity. To achieve this, firstly, a generalpurpose DArT array was developed. Ten representatives from 24 varieties were hybridized with the general-purpose array to determine the informativeness of the clones printed on the array. The informative 1 152 clones were re-arrayed on a slide and used to fingerprint 17 of 24 germplasms. Hybridizing targets prepared from the germplasm to be assayed to the DNA array gave DNA fingerprints of germplasms. Raw data were normalized and transformed into binary data, which were then analyzed by using NTSYSpc (Numerical taxonomy system for cluster and ordination analysis, v. 2.02j) software package. The graphically displayed dendrogram derived from the array experimental data was matched with simple Sequence repeats genotyping outline and varieties' pedigree deviation of the different varieties. Considering DArT is a sequence-independent genotyping approach, it will be applied in studies of the genetic diversity and the gene mapping of diverse of organisms, especially for those crops with less-developed molecular markers.

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

    Science.gov (United States)

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

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    Chang-Kug Kim

    Full Text Available 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.

  5. Genome-wide survey and comparative analysis of LTR retrotransposons and their captured genes in rice and sorghum.

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    Shu-Ye Jiang

    Full Text Available Long terminal repeat (LTR retrotransposons are the major class I mobile elements in plants. They play crucial roles in gene expansion, diversification and evolution. However, their captured genes are yet to be genome-widely identified and characterized in most of plants although many genomes have been completely sequenced. In this study, we have identified 7,043 and 23,915 full-length LTR retrotransposons in the rice and sorghum genomes, respectively. High percentages of rice full-length LTR retrotransposons were distributed near centromeric region in each of the chromosomes. In contrast, sorghum full-length LTR retrotransposons were not enriched in centromere regions. This dissimilarity could be due to the discrepant retrotransposition during and after divergence from their common ancestor thus might be contributing to species divergence. A total of 672 and 1,343 genes have been captured by these elements in rice and sorghum, respectively. Gene Ontology (GO and gene set enrichment analysis (GSEA showed that no over-represented GO term was identified in LTR captured rice genes. For LTR captured sorghum genes, GO terms with functions in DNA/RNA metabolism and chromatin organization were over-represented. Only 36% of LTR captured rice genes were expressed and expression divergence was estimated as 11.9%. Higher percentage of LTR captured rice genes have evolved into pseudogenes under neutral selection. On the contrary, higher percentage of LTR captured sorghum genes were under purifying selection and 72.4% of them were expressed. Thus, higher percentage of LTR captured sorghum genes was functional. Small RNA analysis suggested that some of LTR captured genes in rice and sorghum might have been involved in negative regulation. On the other hand, positive selection has been observed in both rice and sorghum LTR captured genes and some of them were still expressed and functional. The data suggest that some of these LTR captured genes might have

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

    Science.gov (United States)

    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

  7. Efficient targeted mutagenesis of rice and tobacco genomes using Cpf1 from Francisella novicida

    Science.gov (United States)

    Endo, Akira; Masafumi, Mikami; Kaya, Hidetaka; Toki, Seiichi

    2016-01-01

    CRISPR/Cas9 systems are nowadays applied extensively to effect genome editing in various organisms including plants. CRISPR from Prevotella and Francisella 1 (Cpf1) is a newly characterized RNA-guided endonuclease that has two distinct features as compared to Cas9. First, Cpf1 utilizes a thymidine-rich protospacer adjacent motif (PAM) while Cas9 prefers a guanidine-rich PAM. Cpf1 could be used as a sequence-specific nuclease to target AT-rich regions of a genome that Cas9 had difficulty accessing. Second, Cpf1 generates DNA ends with a 5′ overhang, whereas Cas9 creates blunt DNA ends after cleavage. “Sticky” DNA ends should increase the efficiency of insertion of a desired DNA fragment into the Cpf1-cleaved site using complementary DNA ends. Therefore, Cpf1 could be a potent tool for precise genome engineering. To evaluate whether Cpf1 can be applied to plant genome editing, we selected Cpf1 from Francisella novicida (FnCpf1), which recognizes a shorter PAM (TTN) within known Cpf1 proteins, and applied it to targeted mutagenesis in tobacco and rice. Our results show that targeted mutagenesis had occurred in transgenic plants expressing FnCpf1 with crRNA. Deletions of the targeted region were the most frequently observed mutations. Our results demonstrate that FnCpf1 can be applied successfully to genome engineering in plants. PMID:27905529

  8. Similar patterns of rDNA evolution in synthetic and recently formed natural populations of Tragopogon (Asteraceae allotetraploids

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    Soltis Pamela S

    2010-09-01

    Full Text Available Abstract Background Tragopogon mirus and T. miscellus are allotetraploids (2n = 24 that formed repeatedly during the past 80 years in eastern Washington and adjacent Idaho (USA following the introduction of the diploids T. dubius, T. porrifolius, and T. pratensis (2n = 12 from Europe. In most natural populations of T. mirus and T. miscellus, there are far fewer 35S rRNA genes (rDNA of T. dubius than there are of the other diploid parent (T. porrifolius or T. pratensis. We studied the inheritance of parental rDNA loci in allotetraploids resynthesized from diploid accessions. We investigate the dynamics and directionality of these rDNA losses, as well as the contribution of gene copy number variation in the parental diploids to rDNA variation in the derived tetraploids. Results Using Southern blot hybridization and fluorescent in situ hybridization (FISH, we analyzed copy numbers and distribution of these highly reiterated genes in seven lines of synthetic T. mirus (110 individuals and four lines of synthetic T. miscellus (71 individuals. Variation among diploid parents accounted for most of the observed gene imbalances detected in F1 hybrids but cannot explain frequent deviations from repeat additivity seen in the allotetraploid lines. Polyploid lineages involving the same diploid parents differed in rDNA genotype, indicating that conditions immediately following genome doubling are crucial for rDNA changes. About 19% of the resynthesized allotetraploid individuals had equal rDNA contributions from the diploid parents, 74% were skewed towards either T. porrifolius or T. pratensis-type units, and only 7% had more rDNA copies of T. dubius-origin compared to the other two parents. Similar genotype frequencies were observed among natural populations. Despite directional reduction of units, the additivity of 35S rDNA locus number is maintained in 82% of the synthetic lines and in all natural allotetraploids. Conclusions Uniparental reductions of

  9. Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis

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    Jakab Stephen

    2008-11-01

    Full Text Available Abstract Background The protein phosphatase 2Cs (PP2Cs from various organisms have been implicated to act as negative modulators of protein kinase pathways involved in diverse environmental stress responses and developmental processes. A genome-wide overview of the PP2C gene family in plants is not yet available. Results A comprehensive computational analysis identified 80 and 78 PP2C genes in Arabidopsis thaliana (AtPP2Cs and Oryza sativa (OsPP2Cs, respectively, which denotes the PP2C gene family as one of the largest families identified in plants. Phylogenic analysis divided PP2Cs in Arabidopsis and rice into 13 and 11 subfamilies, respectively, which are supported by the analyses of gene structures and protein motifs. Comparative analysis between the PP2C genes in Arabidopsis and rice identified common and lineage-specific subfamilies and potential 'gene birth-and-death' events. Gene duplication analysis reveals that whole genome and chromosomal segment duplications mainly contributed to the expansion of both OsPP2Cs and AtPP2Cs, but tandem or local duplication occurred less frequently in Arabidopsis than rice. Some protein motifs are widespread among the PP2C proteins, whereas some other motifs are specific to only one or two subfamilies. Expression pattern analysis suggests that 1 most PP2C genes play functional roles in multiple tissues in both species, 2 the induced expression of most genes in subfamily A by diverse stimuli indicates their primary role in stress tolerance, especially ABA response, and 3 the expression pattern of subfamily D members suggests that they may constitute positive regulators in ABA-mediated signaling pathways. The analyses of putative upstream regulatory elements by two approaches further support the functions of subfamily A in ABA signaling, and provide insights into the shared and different transcriptional regulation machineries in dicots and monocots. Conclusion This comparative genome-wide overview of the PP

  10. Gene tree discordance of wild and cultivated Asian rice deciphered by genome-wide sequence comparison.

    Science.gov (United States)

    Yang, Ching-chia; Sakai, Hiroaki; Numa, Hisataka; Itoh, Takeshi

    2011-05-15

    Although a large number of genes are expected to correctly solve a phylogenetic relationship, inconsistent gene tree topologies have been observed. This conflicting evidence in gene tree topologies, known as gene tree discordance, becomes increasingly important as advanced sequencing technologies produce an enormous amount of sequence information for phylogenomic studies among closely related species. Here, we aim to characterize the gene tree discordance of the Asian cultivated rice Oryza sativa and its progenitor, O. rufipogon, which will be an ideal case study of gene tree discordance. Using genome and cDNA sequences of O. sativa and O. rufipogon, we have conducted the first in-depth analyses of gene tree discordance in Asian rice. Our comparison of full-length cDNA sequences of O. rufipogon with the genome sequences of the japonica and indica cultivars of O. sativa revealed that 60% of the gene trees showed a topology consistent with the expected one, whereas the remaining genes supported significantly different topologies. Moreover, the proportions of the topologies deviated significantly from expectation, suggesting at least one hybridization event between the two subgroups of O. sativa, japonica and indica. In fact, a genome-wide alignment between japonica and indica indicated that significant portions of the indica genome are derived from japonica. In addition, literature concerning the pedigree of the indica cultivar strongly supported the hybridization hypothesis. Our molecular evolutionary analyses deciphered complicated evolutionary processes in closely related species. They also demonstrated the importance of gene tree discordance in the era of high-speed DNA sequencing.

  11. Genome editing in rice and wheat using the CRISPR/Cas system.

    Science.gov (United States)

    Shan, Qiwei; Wang, Yanpeng; Li, Jun; Gao, Caixia

    2014-10-01

    Targeted genome editing nucleases, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), are powerful tools for understanding gene function and for developing valuable new traits in plants. The clustered regularly interspersed short palindromic repeats (CRISPR)/Cas system has recently emerged as an alternative nuclease-based method for efficient and versatile genome engineering. In this system, only the 20-nt targeting sequence within the single-guide RNA (sgRNA) needs to be changed to target different genes. The simplicity of the cloning strategy and the few limitations on potential target sites make the CRISPR/Cas system very appealing. Here we describe a stepwise protocol for the selection of target sites, as well as the design, construction, verification and use of sgRNAs for sequence-specific CRISPR/Cas-mediated mutagenesis and gene targeting in rice and wheat. The CRISPR/Cas system provides a straightforward method for rapid gene targeting within 1-2 weeks in protoplasts, and mutated rice plants can be generated within 13-17 weeks.

  12. Cloning and sequence characteristics of the genomic gene of a rice metallothionein

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Northern blot analysis showed that a metallothionein gene, ricMT, is expressed strongly in the stem of rice with an expression level that could be more than 100-fold stronger than in leaf blades. The results suggest that the 5'upstream region flanking the coding sequence of the ricMT may contain a fairly strong promoter. To elucidate its regulation and promoter structure, the genomic clones of ricMT were screened out from a rice genomic library and a fragment of about 4 084 bp was sequenced. The fragment included a 5'upstream region of ca. 2 970 bp, a transcription region of ca. 690 bp and a 3'downstream region of ca. 420 bp. Computer analysis of the sequence homology showed that the 5'upstream region included a putative TATA box, a putative CAAT box, and a typical metal-responsive element TGCGCGCG. The results will promote further understanding of the mechanisms of gene regulation and metal response of plant metallothionein proteins.

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

    Science.gov (United States)

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

    2007-07-18

    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. 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*, Malpha, Mbeta and Mgamma 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 Mbeta group, which was considered absent in monocots, have also been identified. The expression profiles of all the MADS-box genes have been analyzed under 11 temporal stages of panicle and seed development, three abiotic stress conditions, along with three stages of vegetative development. Transcripts for 31 genes accumulate preferentially in the reproductive phase, of which, 12 genes are specifically expressed in seeds, and six genes show expression specific to panicle development. Differential expression of seven

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

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    Tyagi Akhilesh K

    2007-07-01

    Full Text Available Abstract 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

  15. Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites.

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    Philipp Wiemann

    Full Text Available 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

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

    Science.gov (United States)

    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

  17. Panicle blast 1 (Pb1) resistance is dependent on at least four QTLs in the rice genome.

    Science.gov (United States)

    Inoue, Haruhiko; Nakamura, Mitsuru; Mizubayashi, Tatsumi; Takahashi, Akira; Sugano, Shoji; Fukuoka, Shuuichi; Hayashi, Nagao

    2017-12-01

    Rice blast is the most serious disease afflicting rice and there is an urgent need for the use of disease resistance (R) genes in blast tolerance breeding programs. Pb1 is classified as a quantitative resistance gene and it does not have fungal specificity. Pb1-mediated resistance develops in the latter stages of growth. However, some cultivars, such as Kanto209 (K209), cultivar name Satojiman, despite possessing Pb1, do not exert resistance to rice blast during the reproductive stage. We found that the expression of WRKY45 gene downstream of Pb1 was weakly induced by rice blast inoculation at the full heading stage in K209. Genetic analysis using the SNP-based Golden Gate assay of K209 crossing with Koshihikari Aichi SBL (KASBL) found at least four regions related to the resistance in the rice genome (Chr8, Chr9, Chr7, Chr11). Mapping of QTL related to Chr7 confirmed the existence of factors that were required for the resistance of Pb1 in the 22 to 23 Mbp region of the rice genome. We clarified how the K209 cultivar is vulnerable to the blast disease despite possessing Pb1 and found the DNA marker responsible for the quantitative resistance of Pb1. We identified the QTL loci required for Pb1-mediated resistance to rice panicle blast. Pb1 was negatively dependent on at least three QTLs, 7, 9 and 11, and positively dependent on one, QTL 8, in the K209 genome. This finding paves the way for creating a line to select optimal QTLs in order to make use of Pb1-mediated resistance more effectively.

  18. Genome-wide profiling of genetic variation in Agrobacterium-transformed rice plants*#

    Science.gov (United States)

    Li, Wen-xu; Wu, San-ling; Liu, Yan-hua; Jin, Gu-lei; Zhao, Hai-jun; Fan, Long-jiang; Shu, Qing-yao

    2016-01-01

    Agrobacterium-mediated transformation has been widely used in producing transgenic plants, and was recently used to generate “transgene-clean” targeted genomic modifications coupled with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system. Although tremendous variation in morphological and agronomic traits, such as plant height, seed fertility, and grain size, was observed in transgenic plants, the underlying mechanisms are not yet well understood, and the types and frequency of genetic variation in transformed plants have not been fully disclosed. To reveal the genome-wide variation in transformed plants, we sequenced the genomes of five independent T0 rice plants using next-generation sequencing (NGS) techniques. Bioinformatics analyses followed by experimental validation revealed the following: (1) in addition to transfer-DNA (T-DNA) insertions, three transformed plants carried heritable plasmid backbone DNA of variable sizes (855–5216 bp) and in different configurations with the T-DNA insertions (linked or apart); (2) each transgenic plant contained an estimated 338–1774 independent genetic variations (single nucleotide variations (SNVs) or small insertion/deletions); and (3) 2–6 new Tos17 insertions were detected in each transformed plant, but no other transposable elements or bacterial genomic DNA. PMID:27921404

  19. Blast-Resistance Inheritance of Space-Induced Rice Lines and Their Genomic Polymorphism by Microsatellite Markers

    Institute of Scientific and Technical Information of China (English)

    XIAO Wu-ming; YANG Qi-yun; CHEN Zhi-qiang; WANG Hui; GUO Tao; LIU Yong-zhu; ZHU Xiao-yuan

    2009-01-01

    To understand the resistance inheritance basis of space-induced rice lines to blast,and to probe mutants'genomic DNA polymorphism compared with ground control by microsatellite markers,three space-induced lines were crossed with a highly susceptible variety LTH,and their F1 and F2 populations were inoculated by two representative blast isolates with broad pathogenicity to analyze their resistance inheritance basis.Meanwhile three mutant lines and the ground control were analyzed by 225 rice SSR(simple sequence repeat)primer pairs selected throughout the 12 chromosomes of whole rice genome,to scan the mutagenesis in genome of the mutant lines.The results indicated the blast-resistant genes harbored in these mutant lines were dominant.It was demonstrated that the resistance of mutant H1 to isolate GD0193 and GD3286 was controlled by a single gene,respectively;while mutants H2 and H3 were controlled by two pairs of major genes against isolate GD3286 and H2 showed complicated genetic mechanism to isolate GD0193.H3's resistance to isolate GD0193 was verified to be controlled by a single gene.According to the results of SSR analysis,three mutant lines showed different mutant rates as compared with the ground control,and the mutant rates also varied.Resistance genes can be induced from rice by space mutation,and different genomic variations were detected in blast-resistant lines.

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

    Science.gov (United States)

    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...

  1. Genome sequence of the verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems

    NARCIS (Netherlands)

    Passel, van M.W.J.; Vos, de W.M.; Smidt, H.

    2011-01-01

    Bacteria of the deeply branching phylum Verrucomicrobia are rarely cultured yet commonly detected in metagenomic libraries from aquatic, terrestrial, and intestinal environments. We have sequenced the genome of Opitutus terrae PB90-1, a fermentative anaerobe within this phylum, isolated from rice pa

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    Xianjin Qiu

    Full Text Available 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.

  4. Structural and Expressional Variations of the Mitochondrial Genome Conferring the Wild Abortive Type of Cytoplasmic Male Sterility in Rice

    Institute of Scientific and Technical Information of China (English)

    Zhen-Lan Liu; Hong Xu; Jing-Xin Guo; Yao-Guang Liu

    2007-01-01

    The so-called "wild abortive" (WA) type of cytoplasmic male sterility (CMS) derived from a wild rice species Oryza rufipogon has been extensively used for hybrid rice breeding. However, extensive analysis of the structure of the related mitochondrial genome has not been reported, and the CMS-associated gene(s) remain unknown. In this study, we exploited a mitochondrial genome-wide strategy to examine the structural and expressional variations in the mitochondrial genome conferring the CMS. The entire mitochondrial genomes of a CMS-WA line and two normal fertile rice lines were amplified by Long-polymerase chain reaction into tilling fragments of up to 15.2 kb. Restriction and DNA blotting analyses of these fragments revealed that structural variations occurred in several regions in the WA mitochondrial genome, as compared to those of the fertile lines. All of the amplified fragments covering the entire mitochondrial genome were used as RNA blot probes to examine the mitochondrial expression profile among the CMS-WA and fertile lines. As a result, only two mRNAs were found to be differentially expressed between the CMS-WA and the fertile lines, which were detected by a probe containing the nadS and orf153 genes and the other having the ribosomal protein gene rp15, respectively. These mRNAs are proposed to be the candidates for further identification and functional studies of the CMS gene.

  5. Genome-Wide Analysis of WOX Gene Family in Rice,Sorghum,Maize,Arabidopsis and Poplar

    Institute of Scientific and Technical Information of China (English)

    Xin Zhang; Jie Zong; Jianhua Liu; Jinyuan Yin; Dabing Zhang

    2010-01-01

    WUSCHEL-related homeobox(WOX)genes form a large gene family specifically expressed in plants.They are known to play important roles in regulating the development of plant tissues and organs by determining cell fate.Recent available whole genome sequences allow us to do more comprehensive phylogenetic analysis of the WOX genes in plants.In the present study,we identified 11 and 21 WOXs from sorghum(Sorghum bicolor)and maize(Zea mays),respectively.The 72 WOX genes from rice(Oryza sativa),sorghum,maize,Arabidopsis(Arabidopsis thaliana)and poplar(Populus trichocarpa)were grouped into three well supported clades with nine subgroups according to the amino acid sequences of their homodomains.Their phylogenetic relationship was also supported by the observation of the motifs outside the homodomain.We observed the variation of duplication events among the nine sub-groups between monocots and eudicots,for instance,more gene duplication events of WOXs within subgroup A for monocots,while,less for dicots in this subgroup.Furthermore,we observed the conserved intron/exon structural patterns of WOX genes in rice,sorghum and Arabidopsis.In addition,WUS(Wuschel)-box and EAR(the ERF-associated amphiphilic repression)-like motif were observed to be conserved among several WOX subgroups in these five plants.Comparative analysis of expression patterns of WOX genes in rice and Arabidopsis suggest that the WOX genes play conserved and various roles in plants.This work provides insights into the evolution of the WOX gene family and is useful for future research.

  6. Gene Identification and Expression Analysis of 86,136 Expressed Sequence Tags (EST) from the Rice Genome

    Institute of Scientific and Technical Information of China (English)

    Yan Zhou; Lin Ye; Li Lin; Jun Li; Xuegang Wang; Hao Xu; Yibin Pan; Wei Lin; Wei Tian; Jing Liu; Liping Wei; Jiabin Tang; Siqi Liu; Huanming Yang; Jun Yu; Jian Wang; Michael G. Walker; Xiuqing Zhang; Jun Wang; Songnian Hu; Huayong Xu; Yajun Deng; Jianhai Dong

    2003-01-01

    Expressed Sequence Tag (EST) analysis has pioneered genome-wide gene discovery and expression profiling. In order to establish a gene expression index in the rice cultivar indica, we sequenced and analyzed 86,136 ESTs from nine rice cDNA libraries from the super hybrid cultivar LYP9 and its parental cultivars. We assembled these ESTs into 13,232 contigs and leave 8,976 singletons. Overall, 7,497 sequences were found similar to the existing sequences in GenBank and 14,711 are novel. These sequences are classified by molecular function, biological process and pathways according to the Gene Ontology. We compared our sequenced ESTs with the publicly available 95,000 ESTs from japonica, and found little sequence variation, despite the large difference between genome sequences. We then assembled the combined 173,000 rice ESTs for further analysis. Using the pooled ESTs, we compared gene expression in metabolism pathway between rice and Avabidopsis according to KEGG. We further profiled gene expression patterns in different tis sues, developmental stages, and in a conditional sterile mutant, after checking the libraries are comparable by means of sequence coverage. We also identified some possible library specific genes and a number of enzymes and transcription factors that contribute to rice development.

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

    Science.gov (United States)

    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. PMID:25902056

  8. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

    Directory of Open Access Journals (Sweden)

    Szurek Boris

    2008-05-01

    Full Text Available Abstract Background Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L., a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome sequence of strain PXO99A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another. Results The PXO99A genome is a single circular chromosome of 5,240,075 bp, considerably longer than the genomes of the other strains (4,941,439 bp and 4,940,217 bp, respectively, and it contains 5083 protein-coding genes, including 87 not found in KACC10331 or MAFF311018. PXO99A contains a greater number of virulence-associated transcription activator-like effector genes and has at least ten major chromosomal rearrangements relative to KACC10331 and MAFF311018. PXO99A contains numerous copies of diverse insertion sequence elements, members of which are associated with 7 out of 10 of the major rearrangements. A rapidly-evolving CRISPR (clustered regularly interspersed short palindromic repeats region contains evidence of dozens of phage infections unique to the PXO99A lineage. PXO99A also contains a unique, near-perfect tandem repeat of 212 kilobases close to the replication terminus. Conclusion Our results provide striking evidence of genome plasticity and rapid evolution within Xanthomonas oryzae pv. oryzae. The comparisons point to sources of genomic variation and candidates for strain-specific adaptations of this pathogen that help to explain the extraordinary diversity of Xanthomonas oryzae pv. oryzae genotypes and races that have been isolated from around the world.

  9. Genetic relationships between diploid and allotetraploid cherry species (Prunus avium, Prunus x gondouinii and Prunus cerasus).

    Science.gov (United States)

    Tavaud, M; Zanetto, A; David, J L; Laigret, F; Dirlewanger, E

    2004-12-01

    Prunus avium L. (diploid, AA, 2n=2x=16), Prunus cerasus L. (allotetraploid, AAFF, 2n=4x=32) species, and their hybrid Prunus x gondouinii Rehd., constitute the most widely cultivated cherry tree species. P. cerasus is supposed to be an hybrid species produced by the union of unreduced P. avium gametes and normal P. fruticosa gametes. A continuum of morphological traits between these three species makes their assignation difficult. The aim of this paper is to study the genetic relationships between tetraploid and diploid cherry species. In all, 114 genotypes belonging to these species were analyzed using 75 AFLP markers. The coordinates of these genotypes on the first axis of a correspondence analysis allowed us to clearly distinguish each species, to identify misclassifications and to assign unknown genotypes to one species. We showed that there are specific alleles in P. cerasus, which are not present in the A genome of P. avium and which probably come from the F genome of P. cerasus. The frequencies of each marker in the A and the F genomes were estimated in order to identify A and F specific markers. We discuss the utility of these specific markers for finding the origin of the A and F genomes in the allopolyploid species.

  10. Identification of the chromosome complement and the spontaneous 1R/1V translocations in allotetraploid Secale cereale × Dasypyrum villosum hybrids through cytogenetic approaches.

    Science.gov (United States)

    Książczyk, Tomasz; Apolinarska, Barbara; Kulak-Książczyk, Sylwia; Wiśniewska, Halina; Stojałowski, Stefan; Łapiński, Mirosław

    2011-08-01

    Genome modifications that occur at the initial interspecific hybridization event are dynamic and can be consolidated during the process of stabilization in successive generations of allopolyploids. This study identifies the number and chromosomal location of ribosomal DNA (rDNA) sites between Secale cereale, Dasypyrum villosum, and their allotetraploid S. cereale × D. villosum hybrids. For the first time, we show the advantages of FISH to reveal chromosome rearrangements in the tetraploid Secale × Dasypyrum hybrids. Based on the specific hybridization patterns of ribosomal 5S, 35S DNA and rye species-specific pSc200 DNA probes, a set of genotypes with numerous Secale/Dasypyrum translocations of 1R/1V chromosomes were identified in successive generations of allotetraploid S. cereale × D. villosum hybrids. In addition we analyse rye chromosome pairs using FISH with chromosome-specific DNA sequences on S. cereale × D. villosum hybrids.

  11. An Introduction to China Rice Functional Genomics Program%中国水稻功能基因组学研究计划介绍

    Institute of Scientific and Technical Information of China (English)

    Yongbiao XUE; Zhihong XU; Jingliu ZHANG; Da LUO; Jiayang LI; Yaoguang LIU; Hongwei XUE; Kang CHONG; Hai HUANG; Guohua LIANG

    2002-01-01

    @@ To discover genes essential for agronomic performances of crops we initiated a program on rice functional genomics of important agronomic traits in rice in 1999. The program was funded by the Ministry of Science and Technology of China through the National Basic Research Initiative and is expected to last for five years.

  12. High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences.

    Science.gov (United States)

    Zhang, Chengjun; Wang, Jun; Marowsky, Nicholas C; Long, Manyuan; Wing, Rod A; Fan, Chuanzhu

    2013-01-01

    In an effort to identify newly evolved genes in rice, we searched the genomes of Asian-cultivated rice Oryza sativa ssp. japonica and its wild progenitors, looking for lineage-specific genes. Using genome pairwise comparison of approximately 20-Mb DNA sequences from the chromosome 3 short arm (Chr3s) in six rice species, O. sativa, O. nivara, O. rufipogon, O. glaberrima, O. barthii, and O. punctata, combined with synonymous substitution rate tests and other evidence, we were able to identify potential recently duplicated genes, which evolved within the last 1 Myr. We identified 28 functional O. sativa genes, which likely originated after O. sativa diverged from O. glaberrima. These genes account for around 1% (28/3,176) of all annotated genes on O. sativa's Chr3s. Among the 28 new genes, two recently duplicated segments contained eight genes. Fourteen of the 28 new genes consist of chimeric gene structure derived from one or multiple parental genes and flanking targeting sequences. Although the majority of these 28 new genes were formed by single or segmental DNA-based gene duplication and recombination, we found two genes that were likely originated partially through exon shuffling. Sequence divergence tests between new genes and their putative progenitors indicated that new genes were most likely evolving under natural selection. We showed all 28 new genes appeared to be functional, as suggested by Ka/Ks analysis and the presence of RNA-seq, cDNA, expressed sequence tag, massively parallel signature sequencing, and/or small RNA data. The high rate of new gene origination and of chimeric gene formation in rice may demonstrate rice's broad diversification, domestication, its environmental adaptation, and the role of new genes in rice speciation.

  13. Rapid genome evolution in Pms1 region of rice revealed by comparative sequence analysis

    Institute of Scientific and Technical Information of China (English)

    YU JinSheng; FAN YouRong; LIU Nan; SHAN Yan; LI XiangHua; ZHANG QiFa

    2007-01-01

    Pms1, a locus for photoperiod sensitive genic male sterility in rice, was identified and mapped to chromosome 7 in previous studies. Here we report an effort to identify the candidate genes for Pms1 by comparative sequencing of BAC clones from two cultivars Minghui 63 and Nongken 58, the parents for the initial mapping population. Annotation and comparison of the sequences of the two clones resulted in a total of five potential candidates which should be functionally tested. We also conducted comparative analysis of sequences of these two cultivars with two other cultivars, Nipponbare and 93-11,for which sequence data were available in public databases. The analysis revealed large differences in sequence composition among the four genotypes in the Pms1 region primarily due to retroelement activity leading to rapid recent growth and divergence of the genomes. High levels of polymorphism in the forms of indels and SNPs were found both in intra- and inter-subspecific comparisons. Dating analysis using LTRs of the retroelements in this region showed that the substitution rate of LTRs was much higher than reported in the literature. The results provided strong evidence for rapid genomic evolution of this region as a consequence of natural and artificial selection.

  14. Rapid Genome-wide Single Nucleotide Polymorphism Discovery in Soybean and Rice via Deep Resequencing of Reduced Representation Libraries with the Illumina Genome Analyzer

    Directory of Open Access Journals (Sweden)

    Stéphane Deschamps

    2010-07-01

    Full Text Available Massively parallel sequencing platforms have allowed for the rapid discovery of single nucleotide polymorphisms (SNPs among related genotypes within a species. We describe the creation of reduced representation libraries (RRLs using an initial digestion of nuclear genomic DNA with a methylation-sensitive restriction endonuclease followed by a secondary digestion with the 4bp-restriction endonuclease This strategy allows for the enrichment of hypomethylated genomic DNA, which has been shown to be rich in genic sequences, and the digestion with serves to increase the number of common loci resequenced between individuals. Deep resequencing of these RRLs performed with the Illumina Genome Analyzer led to the identification of 2618 SNPs in rice and 1682 SNPs in soybean for two representative genotypes in each of the species. A subset of these SNPs was validated via Sanger sequencing, exhibiting validation rates of 96.4 and 97.0%, in rice ( and soybean (, respectively. Comparative analysis of the read distribution relative to annotated genes in the reference genome assemblies indicated that the RRL strategy was primarily sampling within genic regions for both species. The massively parallel sequencing of methylation-sensitive RRLs for genome-wide SNP discovery can be applied across a wide range of plant species having sufficient reference genomic sequence.

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

    Directory of Open Access Journals (Sweden)

    Filippo Biscarini

    Full Text Available 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.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.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.

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

    Science.gov (United States)

    Biscarini, Filippo; 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

    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. 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). 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.

  17. Comprehensive genomic analysis and expression profiling of phospholipase C gene family during abiotic stresses and development in rice.

    Science.gov (United States)

    Singh, Amarjeet; Kanwar, Poonam; Pandey, Amita; Tyagi, Akhilesh K; Sopory, Sudhir K; Kapoor, Sanjay; Pandey, Girdhar K

    2013-01-01

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

  18. Comprehensive genomic analysis and expression profiling of phospholipase C gene family during abiotic stresses and development in rice.

    Directory of Open Access Journals (Sweden)

    Amarjeet Singh

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

  19. Genome-wide association mapping of root traits in a japonica rice panel.

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    Brigitte Courtois

    Full Text Available 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 (r(2>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.

  20. Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice.

    Science.gov (United States)

    Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

    2014-10-08

    Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gene, SD1. Based on a performance evaluation of the HRPF and GWAS results, we demonstrate that high-throughput phenotyping has the potential to replace traditional phenotyping techniques and can provide valuable gene identification information. The combination of the multifunctional phenotyping tools HRPF and GWAS provides deep insights into the genetic architecture of important traits.

  1. Cytomolecular analysis of ribosomal DNA evolution in a natural allotetraploid Brachypodium hybridum and its putative ancestors – dissecting complex repetitive structure of intergenic spacers

    Directory of Open Access Journals (Sweden)

    Natalia Borowska-Zuchowska

    2016-10-01

    Full Text Available Nucleolar dominance is an epigenetic phenomenon associated with nuclear 35S rRNA genes and consists in selective suppression of gene loci inherited from one of the progenitors in the allopolyploid. Our understanding of the exact mechanisms that determine this process is still fragmentary, especially in case of the grass species. This study aimed to shed some light on the molecular basis of this genome-specific inactivation of 35S rDNA loci in an allotetraploid Brachypodium hybridum (2n=30, which arose from the interspecific hybridization between two diploid ancestors that were very similar to modern B. distachyon (2n=10 and B. stacei (2n=20. Using fluorescence in situ hybridization with 25S rDNA and chromosome-specific BAC clones as probes we revealed that the nucleolar dominance is present not only in meristematic root-tip cells but also in differentiated cell fraction of B. hybridum. Additionally, the intergenic spacers (IGSs from both of the putative ancestors and the allotetraploid were sequenced and analyzed. The presumptive transcription initiation sites, spacer promoters and repeated elements were identified within the IGSs. Two different length variants, 2.3 kb and 3.5 kb, of IGSs were identified in B. distachyon and B. stacei, respectively, however only the IGS that had originated from B. distachyon-like ancestor was present in the allotetraploid. The amplification pattern of B. hybridum IGSs suggests that some genetic changes occurred in inactive B. stacei-like rDNA loci during the evolution of the allotetraploid. We hypothesize that their preferential silencing is an effect of structural changes in the sequence rather than just the result of the sole inactivation at the epigenetic level.

  2. A population genetic model to infer allotetraploid speciation and long-term evolution applied to two yarrow species.

    Science.gov (United States)

    Guo, Yan-Ping; Tong, Xiao-Yuan; Wang, Lan-Wei; Vogl, Claus

    2013-07-01

    Allotetraploid speciation, that is, the generation of a hybrid tetraploid species from two diploid species, and the long-term evolution of tetraploid populations and species are important in plants. We developed a population genetic model to infer population genetic parameters of tetraploid populations from data of the progenitor and descendant species. Two yarrow species, Achillea alpina-4x and A. wilsoniana-4x, arose by allotetraploidization from the diploid progenitors, A. acuminata-2x and A. asiatica-2x. Yet, the population genetic process has not been studied in detail. We applied the model to sequences of three nuclear genes in populations of the four yarrow species and compared their pattern of variability with that in four plastid regions. The plastid data indicated that the two tetraploid species probably originated from multiple independent allopolyploidization events and have accumulated many mutations since. With the nuclear data, we found a low rate of homeologous recombination or gene conversion and a reduction in diversity relative to the level of both diploid species combined. The present analysis with a novel probabilistic model suggests a genetic bottleneck during tetraploid speciation, that the two tetraploid species have a long evolutionary history, and that they have a small amount of genetic exchange between the homeologous genomes.

  3. Complete Genomic Structure of the Cultivated Rice Endophyte Azospirillum sp. B510

    Science.gov (United States)

    Kaneko, Takakazu; Minamisawa, Kiwamu; Isawa, Tsuyoshi; Nakatsukasa, Hiroki; Mitsui, Hisayuki; Kawaharada, Yasuyuki; Nakamura, Yasukazu; Watanabe, Akiko; Kawashima, Kumiko; Ono, Akiko; Shimizu, Yoshimi; Takahashi, Chika; Minami, Chiharu; Fujishiro, Tsunakazu; Kohara, Mitsuyo; Katoh, Midori; Nakazaki, Naomi; Nakayama, Shinobu; Yamada, Manabu; Tabata, Satoshi; Sato, Shusei

    2010-01-01

    We determined the nucleotide sequence of the entire genome of a diazotrophic endophyte, Azospirillum sp. B510. Strain B510 is an endophytic bacterium isolated from stems of rice plants (Oryza sativa cv. Nipponbare). The genome of B510 consisted of a single chromosome (3 311 395 bp) and six plasmids, designated as pAB510a (1 455 109 bp), pAB510b (723 779 bp), pAB510c (681 723 bp), pAB510d (628 837 bp), pAB510e (537 299 bp), and pAB510f (261 596 bp). The chromosome bears 2893 potential protein-encoding genes, two sets of rRNA gene clusters (rrns), and 45 tRNA genes representing 37 tRNA species. The genomes of the six plasmids contained a total of 3416 protein-encoding genes, seven sets of rrns, and 34 tRNAs representing 19 tRNA species. Eight genes for plasmid-specific tRNA species are located on either pAB510a or pAB510d. Two out of eight genomic islands are inserted in the plasmids, pAB510b and pAB510e, and one of the islands is inserted into trnfM-CAU in the rrn located on pAB510e. Genes other than the nif gene cluster that are involved in N2 fixation and are homologues of Bradyrhizobium japonicum USDA110 include fixABCX, fixNOQP, fixHIS, fixG, and fixLJK. Three putative plant hormone-related genes encoding tryptophan 2-monooxytenase (iaaM) and indole-3-acetaldehyde hydrolase (iaaH), which are involved in IAA biosynthesis, and ACC deaminase (acdS), which reduces ethylene levels, were identified. Multiple gene-clusters for tripartite ATP-independent periplasmic-transport systems and a diverse set of malic enzymes were identified, suggesting that B510 utilizes C4-dicarboxylate during its symbiotic relationship with the host plant. PMID:20047946

  4. Significant Comparative Characteristics between Orphan and Nonorphan Genes in the Rice (Oryza sativa L. Genome

    Directory of Open Access Journals (Sweden)

    Wen-Jiu Guo

    2007-01-01

    Full Text Available Microsatellites are short tandem repeats of one to six bases in genomic DNA. As microsatellites are highly polymorphic and play a vital role in gene function and recombination, they are an attractive subject for research in evolution and in the genetics and breeding of animals and plants. Orphan genes have no known homologs in existing databases. Using bioinformatic computation and statistical analysis, we identified 19,26 orphan genes in the rice (Oryza sativa ssp. Japanica cv. Nipponbare proteome. We found that a larger proportion of orphan genes are expressed after sexual maturation and under environmental pressure than nonorphan genes. Orphan genes generally have shorter protein lengths and intron size, and are faster evolving. Additionally, orphan genes have fewer PROSITE patterns with larger pattern sizes than those in nonorphan genes. The average microsatellite content and the percentage of trinucleotide repeats in orphan genes are also significantly higher than in nonorphan genes. Microsatellites are found less often in PROSITE patterns in orphan genes. Taken together, these orphan gene characteristics suggest that microsatellites play an important role in orphan gene evolution and expression.

  5. Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies.

    Science.gov (United States)

    Xu, Chunming; Bai, Yan; Lin, Xiuyun; Zhao, Na; Hu, Lanjuan; Gong, Zhiyun; Wendel, Jonathan F; Liu, Bao

    2014-05-01

    Hybridization and polyploidization are prominent processes in plant evolution. Hybrids and allopolyploids typically exhibit radically altered gene expression patterns relative to their parents, a phenomenon termed "transcriptomic shock." To distinguish the effects of hybridization from polyploidization on coregulation of divergent alleles, we analyzed expression of parental copies (homoeologs) of 11,608 genes using RNA-seq-based transcriptome profiling in reciprocal hybrids and tetraploids constructed from subspecies japonica and indica of Asian rice (Oryza sativa L.). The diploid hybrids and their derived allopolyploids differ dramatically in morphology, despite having the same suite of genes and genic proportions. Allelic and homoeolog-specific transcripts were unequivocally diagnosed in the hybrids and tetraploids based on parent-specific SNPs. Compared with the in silico hybrid (parental mix), the range of progenitor expression divergence was significantly reduced in both reciprocally generated F1 hybrids, presumably due to the ameliorating effects of a common trans environment on divergent cis-factors. In contrast, parental expression differences were greatly elaborated at the polyploid level, which we propose is a consequence of stoichiometric disruptions associated with the numerous chromosomal packaging and volumetric changes accompanying nascent polyploidy. We speculate that the emergent property of "whole genome doubling" has repercussions that reverberate throughout the transcriptome and downstream, ultimately generating altered phenotypes. This perspective may yield insight into the nature of adaptation and the origin of evolutionary novelty accompanying polyploidy.

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

    Indian Academy of Sciences (India)

    Rahul Shaw; Sudip Kundu

    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.

  7. Improvement of Appearance Traits of elite Rice Zhenshan 97B by Molecular Introgression of Targeted about 800 kb Interval from Indica Rice Jiafuzhan Genome

    Institute of Scientific and Technical Information of China (English)

    X.J. Fang; L.R. Jiang

    2007-01-01

    Rice appearance trait is mainly mean grain length (GL), grain width (GW), ratio of length and width (L/W), chalkiness (CH) and transparence (TR). Appearance is the first impression, and rice appearance traits effect significantly the value of commodity. Hybrid rice is relatively low quality, especially on rice appearance quality,which restricts partially its extend and badly export of hybrid seed and rice in China.Shanyou 63, the most famous hybrid rice combination of China, could not be also sustainable application because of its poor qualities. In this studies, We attempt to improve appearance quality of the elite rice maintainer of Zhenshan 97B by using molecular approach of genomic interval targeted introgression. Three F2 populations were constructed to study the classical and molecular genetic of rice appearance traits, at the same time, molecular marker-asisted toimprove the main maintainer line, Zhenshan 97B were performed. There some following results:Three F2 populations were constructed based on crosses of Guangluai 4×Jiafuzhan (GJ popu.), Minghui 86×Jiafuzhan (MJ popu.) and Zhenshan 97B×Jiafuzhan (ZJ popu.). ZJ popu and GJ popu were produced to reconstruct the linkage maps related with rice appearance traits based on BSA, and detect QTL of target traits based on IM.In ZJ popu, 9 QTLs of target traits were detected. The interval, RM169~RM516 on Chromosome 5, was genetic locus of GW, L/W, CH and BW, and the explained variances were 10.9%, 14.9%, 12.0% and 14.2%, respectively.RM214 on chromosome 7, RM339 on chromosome 8 were genetic loci if CH and BW, and the explained variances were 9.4%, 10.0%, 11.0% and 12.1%. besides there is a genetic locus, RM347, of G/W on chromosome 3, and the explained varance was 10.3%. In GJ popu, 5 QTLs of rice appearance traits were detected. The interval, RM169-RM516 on Chromosome 5, were also the genetic loci of GW, CH and BW, and the explained variances were 9.0%, 12.5%, and 13.6%, respectively. RM264~RM80 on

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

    Science.gov (United States)

    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...

  9. Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map

    Institute of Scientific and Technical Information of China (English)

    WANG Xu-sheng; ZHU Jun; MANSUETO Locedie; BRUSKIEWICH Richard

    2005-01-01

    Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related traits under stressed and well-water conditions were assayed in mapping populations derived from crosses of Azucena×IR64 and Azucena×Bala. To find the candidate rice genes underlying Quantitative Trait Loci (QTL) in these populations, we conducted in silico analysis of a candidate region flanked by the genetic markers RM212 and RM319on chromosome 1, proximal to the semi-dwarf (sd1) locus. A total of 175annotated genes were identified from this region. These included 48 genes annotated by functional homology to known genes, 23pseudogenes, 24 ab initio predicted genes supported by an alignment match to an EST (Expressed sequence tag) of unknown function, and 80 hypothetical genes predicted solely by ab initio means. Among these, 16 candidate genes could potentially be involved in drought stress response.

  10. Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding.

    Science.gov (United States)

    Zhou, Degui; Chen, Wei; Lin, Zechuan; Chen, Haodong; Wang, Chongrong; Li, Hong; Yu, Renbo; Zhang, Fengyun; Zhen, Gang; Yi, Junliang; Li, Kanghuo; Liu, Yaoguang; Terzaghi, William; Tang, Xiaoyan; He, Hang; Zhou, Shaochuan; Deng, Xing Wang

    2016-02-01

    Analyses of genome variations with high-throughput assays have improved our understanding of genetic basis of crop domestication and identified the selected genome regions, but little is known about that of modern breeding, which has limited the usefulness of massive elite cultivars in further breeding. Here we deploy pedigree-based analysis of an elite rice, Huanghuazhan, to exploit key genome regions during its breeding. The cultivars in the pedigree were resequenced with 7.6× depth on average, and 2.1 million high-quality single nucleotide polymorphisms (SNPs) were obtained. Tracing the derivation of genome blocks with pedigree and information on SNPs revealed the chromosomal recombination during breeding, which showed that 26.22% of Huanghuazhan genome are strictly conserved key regions. These major effect regions were further supported by a QTL mapping of 260 recombinant inbred lines derived from the cross of Huanghuazhan and a very dissimilar cultivar, Shuanggui 36, and by the genome profile of eight cultivars and 36 elite lines derived from Huanghuazhan. Hitting these regions with the cloned genes revealed they include numbers of key genes, which were then applied to demonstrate how Huanghuazhan were bred after 30 years of effort and to dissect the deficiency of artificial selection. We concluded the regions are helpful to the further breeding based on this pedigree and performing breeding by design. Our study provides genetic dissection of modern rice breeding and sheds new light on how to perform genomewide breeding by design. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  11. RAPD-based genetic analysis of offsprings from the sexual cross using allotetraploid citrus somatic hybrid as pollen parent

    Institute of Scientific and Technical Information of China (English)

    YI HuaLin; DENG XiuXin

    2007-01-01

    Huazhong Agricultural University, Wuhan 430070, ChinaThirty-one polymorphic decamer primers were selected to genotype 92 progenies from the cross between Yiben No,4, a monoembryonic diploid F1 hybrid of Citrus reticulata Blanco cv Huanongbendizao tangerine and C. ichangensis Swingle, and [Hamlin sweet orange + Rough lemon], an allotetraploid somatic hybrid of Citrus sinensis Osbeck cv. Hamlin and C. jambhiri Lush cv. Rough Lemon. x2(Chi-square) analysis of RAPD markers in the progenies indicated they were randomly transmitted from the four donor parents, without significant difference between the diploids and triploids. However,these progenies were clustered into three major groups using dendrogram constructed by UPGMA,skewed to three parents in certain degrees, 15 (13 triploids and 2 diploids) to Hamlin, 16 (9 and 7) to Yiben No. 4, and 61 (57 and 4) to [Hamlin sweet orange + Rough Lemon] from which genomic contribution was predominant in progenies, respectively.

  12. RAPD-based genetic analysis of offsprings from the sexual cross using allotetraploid citrus somatic hybrid as pollen parent

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Thirty-one polymorphic decamer primers were selected to genotype 92 progenies from the cross be- tween Yiben No.4, a monoembryonic diploid F1 hybrid of Citrus reticulata Blanco cv Huanongbendizao tangerine and C. ichangensis Swingle, and [Hamlin sweet orange + Rough lemon], an allotetraploid somatic hybrid of Citrus sinensis Osbeck cv. Hamlin and C. jambhiri Lush cv. Rough Lemon. χ2 (Chi-square) analysis of RAPD markers in the progenies indicated they were randomly transmitted from the four donor parents, without significant difference between the diploids and triploids. However, these progenies were clustered into three major groups using dendrogram constructed by UPGMA, skewed to three parents in certain degrees, 15 (13 triploids and 2 diploids) to Hamlin, 16 (9 and 7) to Yiben No. 4, and 61 (57 and 4) to [Hamlin sweet orange + Rough Lemon] from which genomic contribu- tion was predominant in progenies, respectively.

  13. Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms

    Directory of Open Access Journals (Sweden)

    Shibaya Taeko

    2010-04-01

    Full Text Available Abstract Background To create useful gene combinations in crop breeding, it is necessary to clarify the dynamics of the genome composition created by breeding practices. A large quantity of single-nucleotide polymorphism (SNP data is required to permit discrimination of chromosome segments among modern cultivars, which are genetically related. Here, we used a high-throughput sequencer to conduct whole-genome sequencing of an elite Japanese rice cultivar, Koshihikari, which is closely related to Nipponbare, whose genome sequencing has been completed. Then we designed a high-throughput typing array based on the SNP information by comparison of the two sequences. Finally, we applied this array to analyze historical representative rice cultivars to understand the dynamics of their genome composition. Results The total 5.89-Gb sequence for Koshihikari, equivalent to 15.7× the entire rice genome, was mapped using the Pseudomolecules 4.0 database for Nipponbare. The resultant Koshihikari genome sequence corresponded to 80.1% of the Nipponbare sequence and led to the identification of 67 051 SNPs. A high-throughput typing array consisting of 1917 SNP sites distributed throughout the genome was designed to genotype 151 representative Japanese cultivars that have been grown during the past 150 years. We could identify the ancestral origin of the pedigree haplotypes in 60.9% of the Koshihikari genome and 18 consensus haplotype blocks which are inherited from traditional landraces to current improved varieties. Moreover, it was predicted that modern breeding practices have generally decreased genetic diversity Conclusions Detection of genome-wide SNPs by both high-throughput sequencer and typing array made it possible to evaluate genomic composition of genetically related rice varieties. With the aid of their pedigree information, we clarified the dynamics of chromosome recombination during the historical rice breeding process. We also found several

  14. Characteristic and inheritance analysis of targeted mutagenesis mediated by genome editing in rice.

    Science.gov (United States)

    Li, Tang; Yaokui, Li; Dan, Zhang; Bigang, Mao; Qiming, Lv; Yuanyi, Hu; Ye, Shao; Yan, Peng; Binran, Zhao; Shitou, Xia

    2016-08-01

    The transcription activator-like effector nucleases (TALEN) and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) systems are two current genome editing technologies. Here, we compare and analyze the characteristics of the targeted mutations mediated by these two systems, such as efficiency, type, position, time, and genetic patterns. Both the TALEN and CRISPR/Cas9 systems can induce site-specific mutations in T0 rice plants effectively, but CRISPR/Cas9 is more effective. The major mutation type in both systems is the short insertion/deletion(InDel) mutation within 10 base pairs: deletions ranging from 1 to 10 bps are more often in TALEN, and 1bp insertions are more often in CRISPR/Cas9. Moreover, double-strand breaks (DSBs) generated by CRISPR/Cas9 are more precise than TALEN. In addition, DSBs could be repaired by the homologous recombination at a low frequency, causing DNA fragment duplication mutations. In some cases, the DNA fragments between the two close targets are deleted or inverted, and the mutation efficiency does not positively correlatewith the mutation efficiency of each target. Mutagenesis mediated by the TALEN or CRISPR/Cas9 system can occur as early as in transformed callus cells, and less frequently in somatic cells. Consequently, four different mutation types are formed, including homozygous, heterozygous, bi-allelic and chimeric mutations, with bi-allelic mutations having the highest rate and chimeric mutations having the lowest rate. All, except chimeric mutations, can descend stably into the next generation.

  15. Differentiation of Indica-Japonica rice revealed by insertion/deletion (InDel) fragments obtained from the comparative genomic study of DNA sequences between 93-11 (Indica) and Nipponbare (Japonica)

    Institute of Scientific and Technical Information of China (English)

    CAI Xingxing; LIU Jing; QIU Yinqiu; ZHAO Wei; SONG Zhiping; LU Baorong

    2007-01-01

    DNA polymorphisms from nucleotide insertion/deletions (InDels) in genomic sequences are the basis for developing InDel molecular markers.To validate the InDel primer pairs on the basis of the comparative genomic study on DNA sequences between an Indica rice 93-11 and a Japonica rice Nipponbare for identifying Indica and Japonica rice varieties and studying wild Oryza species,we studied 49 Indica,43 Japonica,and 24 wild rice accessions collected from ten Asian countries using 45 InDel primer pairs.Results indicated that of the 45 InDel primer pairs,41 can accurately identify Indica and Japonica rice varieties with a reliability of over 80%.The scatter plotting data of the principal component analysis (PCA) indicated that:(i) the InDel primer pairs can easily distinguish Indica from Japonica rice varieties,in addition to revealing their genetic differentiation;(ii) the AA-genome wild rice species showed a relatively close genetic relationship with the Indica rice varieties;and (iii)the non-AA genome wild rice species did not show evident differentiation into the Indica and Japonica types.It is concluded from the study that most of the InDel primer pairs obtained from DNA sequences of 93-11 and Nipponbare can be used for identifying lndica and Japonica rice varieties,and for studying genetic relationships of wild rice species,particularly in terms of the Indica-Japonica differentiation.

  16. Genome-wide Differences in DNA Methylation Changes in Two Contrasting Rice Genotypes in Response to Drought Conditions

    Directory of Open Access Journals (Sweden)

    Wensheng Wang

    2016-11-01

    Full Text Available Differences in drought stress tolerance within diverse rice genotypes have been attributed to genetic diversity and epigenetic alterations. DNA methylation is an important epigenetic modification that influences diverse biological processes, but its effects on rice drought stress tolerance are poorly understood. In this study, methylated DNA immunoprecipitation sequencing and an Affymetrix GeneChip rice genome array were used to profile the DNA methylation patterns and transcriptomes of the drought-tolerant introgression line DK151 and its drought-sensitive recurrent parent IR64 under drought and control conditions. The introgression of donor genomic DNA induced genome-wide DNA methylation changes in DK151 plants. A total of 1190 differentially methylated regions (DMRs were detected between the two genotypes under normal growth conditions, and the DMR-associated genes in DK151 plants were mainly related to stress response, programmed cell death, and nutrient reservoir activity, which are implicated to constitutive drought stress tolerance. A comparison of the DNA methylation changes in the two genotypes under drought conditions indicated that DK151 plants have a more stable methylome, with only 92 drought-induced DMRs, than IR64 plants with 506 DMRs. Gene ontology analyses of the DMR-associated genes in drought-stressed plants revealed that changes to the DNA methylation status of genotype-specific genes are associated with the epigenetic regulation of drought stress responses. Transcriptome analysis further helped to identify a set of 12 and 23 DMR-associated genes that were differentially expressed in DK151 and IR64, respectively, under drought stress compared with respective controls. Correlation analysis indicated that DNA methylation has various effects on gene expression, implying that it affects gene expression directly or indirectly through diverse regulatory pathways. Our results indicate that drought-induced alterations to DNA

  17. Metabolomic and Functional Genomic Analyses Reveal Varietal Differences in Bioactive Compounds of Cooked Rice

    Science.gov (United States)

    Heuberger, Adam L.; Lewis, Matthew R.; Chen, Ming-Hsuan; Brick, Mark A.; Leach, Jan E.; Ryan, Elizabeth P.

    2010-01-01

    Emerging evidence supports that cooked 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 traits. Metabolites from ten diverse varieties of cooked rice were detected using ultra performance liquid chromatography coupled to mass spectrometry. A total of 3,097 compounds were detected, of which 25% differed among the ten varieties. Multivariate analyses of the metabolite profiles showed that the chemical diversity among the varieties cluster according to their defined subspecies classifications: indica, japonica, and aus. Metabolite-specific genetic diversity in rice was investigated by analyzing a collection of single nucleotide polymorphisms (SNPs) in genes from biochemical pathways of nutritional importance. Two classes of bioactive compounds, phenolics and vitamin E, contained nonsynonymous SNPs and SNPs in the 5′ and 3′ untranslated regions for genes in their biosynthesis pathways. Total phenolics and tocopherol concentrations were determined to examine the effect of the genetic diversity among the ten varieties. Per gram of cooked rice, total phenolics ranged from 113.7 to 392.6 µg (gallic acid equivalents), and total tocopherols ranged between 7.2 and 20.9 µg. The variation in the cooked rice metabolome and quantities of bioactive components supports that the SNP-based genetic diversity influenced nutritional components in rice, and that this approach may guide rice improvement strategies for plant and human health. PMID:20886119

  18. Genome-wide Association Analysis Tracks Bacterial Leaf Blight Resistance Loci In Rice Diverse Germplasm

    National Research Council Canada - National Science Library

    Dilla-Ermita, Christine Jade; Tandayu, Erwin; Juanillas, Venice Margarette; Detras, Jeffrey; Lozada, Dennis Nicuh; Dwiyanti, Maria Stefanie; Vera Cruz, Casiana; Mbanjo, Edwige Gaby Nkouaya; Ardales, Edna; Diaz, Maria Genaleen; Mendioro, Merlyn; Thomson, Michael J; Kretzschmar, Tobias

    2017-01-01

    ... (BB) disease of rice, have been discovered and characterized. Several have been deployed in modern varieties, however, due to rapid evolution of Xoo, a number have already become ineffective. The continuous “arms race...

  19. ZINC-INDUCED FACILITATOR-LIKE family in plants: lineage-specific expansion in monocotyledons and conserved genomic and expression features among rice (Oryza sativa paralogs

    Directory of Open Access Journals (Sweden)

    Lopes Karina L

    2011-01-01

    Full Text Available Abstract Background Duplications are very common in the evolution of plant genomes, explaining the high number of members in plant gene families. New genes born after duplication can undergo pseudogenization, neofunctionalization or subfunctionalization. Rice is a model for functional genomics research, an important crop for human nutrition and a target for biofortification. Increased zinc and iron content in the rice grain could be achieved by manipulation of metal transporters. Here, we describe the ZINC-INDUCED FACILITATOR-LIKE (ZIFL gene family in plants, and characterize the genomic structure and expression of rice paralogs, which are highly affected by segmental duplication. Results Sequences of sixty-eight ZIFL genes, from nine plant species, were comparatively analyzed. Although related to MSF_1 proteins, ZIFL protein sequences consistently grouped separately. Specific ZIFL sequence signatures were identified. Monocots harbor a larger number of ZIFL genes in their genomes than dicots, probably a result of a lineage-specific expansion. The rice ZIFL paralogs were named OsZIFL1 to OsZIFL13 and characterized. The genomic organization of the rice ZIFL genes seems to be highly influenced by segmental and tandem duplications and concerted evolution, as rice genome contains five highly similar ZIFL gene pairs. Most rice ZIFL promoters are enriched for the core sequence of the Fe-deficiency-related box IDE1. Gene expression analyses of different plant organs, growth stages and treatments, both from our qPCR data and from microarray databases, revealed that the duplicated ZIFL gene pairs are mostly co-expressed. Transcripts of OsZIFL4, OsZIFL5, OsZIFL7, and OsZIFL12 accumulate in response to Zn-excess and Fe-deficiency in roots, two stresses with partially overlapping responses. Conclusions We suggest that ZIFL genes have different evolutionary histories in monocot and dicot lineages. In rice, concerted evolution affected ZIFL duplicated genes

  20. Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective

    Directory of Open Access Journals (Sweden)

    Bombarely Aureliano

    2012-08-01

    Full Text Available Abstract Background Polyploidization is an important mechanism in plant evolution. By analyzing the leaf transcriptomes taken from the allotetraploid Nicotiana tabacum (tobacco and parental genome donors, N. sylvesteris (S-Genome and N. tomentosiformis (T-Genome, a phylogenomic approach was taken to map the fate of homeologous gene pairs in this plant. Results A comparison between the genes present in the leaf transcriptomes of N. tabacum and modern day representatives of its progenitor species demonstrated that only 33% of assembled transcripts could be distinguished based on their sequences. A large majority of the genes (83.6% of the non parent distinguishable and 87.2% of the phylogenetic topology analyzed clusters expressed above background level (more than 5 reads showed similar overall expression levels. Homeologous sequences could be identified for 968 gene clusters, and 90% (6% of all genes of the set maintained expression of only one of the tobacco homeologs. When both homeologs were expressed, only 15% (0.5% of the total showed evidence of differential expression, providing limited evidence of subfunctionalization. Comparing the rate of synonymous nucleotide substitution (Ks and non-synonymous nucleotide substitution (Kn provided limited evidence for positive selection during the evolution of tobacco since the polyploidization event took place. Conclusions Polyploidization is a powerful mechanism for plant speciation that can occur during one generation; however millions of generations may be necessary for duplicate genes to acquire a new function. Analysis of the tobacco leaf transcriptome reveals that polyploidization, even in a young tetraploid such as tobacco, can lead to complex changes in gene expression. Gene loss and gene silencing, or subfunctionalization may explain why both homeologs are not expressed by the associated genes. With Whole Genome Duplication (WGD events, polyploid genomes usually maintain a high percentage of

  1. Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection

    Science.gov (United States)

    Trinh, Hien; Nguyen, Khoa Truong; Nguyen, Lam Van; Pham, Huy Quang; Huong, Can Thu; Xuan, Tran Dang; Anh, La Hoang; Caccamo, Mario; Ayling, Sarah; Diep, Nguyen Thuy; Trung, Khuat Huu

    2017-01-01

    Next generation sequencing technologies have provided numerous opportunities for application in the study of whole plant genomes. In this study, we present the sequencing and bioinformatic analyses of five typical rice landraces including three indica and two japonica with potential blast resistance. A total of 688.4 million 100 bp paired-end reads have yielded approximately 30-fold coverage to compare with the Nipponbare reference genome. Among them, a small number of reads were mapped to both chromosomes and organellar genomes. Over two million and eight hundred thousand single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) in indica and japonica lines have been determined, which potentially have significant impacts on multiple transcripts of genes. SNP deserts, contiguous SNP-low regions, were found on chromosomes 1, 4, and 5 of all genomes of rice examined. Based on the distribution of SNPs per 100 kilobase pairs, the phylogenetic relationships among the landraces have been constructed. This is the first step towards revealing several salient features of rice genomes in Vietnam and providing significant information resources to further marker-assisted selection (MAS) in rice breeding programs. PMID:28265566

  2. The rice B-box zinc finger gene family: genomic identification, characterization, expression profiling and diurnal analysis.

    Directory of Open Access Journals (Sweden)

    Jianyan Huang

    Full Text Available BACKGROUND: The B-box (BBX -containing proteins are a class of zinc finger proteins that contain one or two B-box domains and play important roles in plant growth and development. The Arabidopsis BBX gene family has recently been re-identified and renamed. However, there has not been a genome-wide survey of the rice BBX (OsBBX gene family until now. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we identified 30 rice BBX genes through a comprehensive bioinformatics analysis. Each gene was assigned a uniform nomenclature. We described the chromosome localizations, gene structures, protein domains, phylogenetic relationship, whole life-cycle expression profile and diurnal expression patterns of the OsBBX family members. Based on the phylogeny and domain constitution, the OsBBX gene family was classified into five subfamilies. The gene duplication analysis revealed that only chromosomal segmental duplication contributed to the expansion of the OsBBX gene family. The expression profile of the OsBBX genes was analyzed by Affymetrix GeneChip microarrays throughout the entire life-cycle of rice cultivar Zhenshan 97 (ZS97. In addition, microarray analysis was performed to obtain the expression patterns of these genes under light/dark conditions and after three phytohormone treatments. This analysis revealed that the expression patterns of the OsBBX genes could be classified into eight groups. Eight genes were regulated under the light/dark treatments, and eleven genes showed differential expression under at least one phytohormone treatment. Moreover, we verified the diurnal expression of the OsBBX genes using the data obtained from the Diurnal Project and qPCR analysis, and the results indicated that many of these genes had a diurnal expression pattern. CONCLUSIONS/SIGNIFICANCE: The combination of the genome-wide identification and the expression and diurnal analysis of the OsBBX gene family should facilitate additional functional studies of the Os

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

    Science.gov (United States)

    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.

  4. Comparative Analysis of Genomes in Oryza sativa, O.officinalis, and O. meyeriana with C0t-1 DNA and Genomic DNA of Cultivated Rice

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH) were applied to somatic chromosomes preparations of Oryza sativa, O. officinalis, and O. meyeriana with labeled probes of C0t-1 DNA and genomic DNA from the cultivated rice. The coverage percentage (%) and size (Mb) of C0t-1 DNA in O. sativa, O. officinalis, and O. meyeriana were 47.1 ±0.16, 38.61 ±0.13, 44.38±0.13, and 212.33± 1.21,269.42 ± 0.89, 532.56± 1.68 Mb, respectively. The coverage percentage and size of genomic DNA from O. sativa in O. officinalis and O. meyeriana were 91.0, 93.6% and 634, 1 123 Mb, respectively, in which 365 and 591 Mb in O. officinalis and O. meyeriana were from O. sativa genomic DNA, but not from repetitive sequences of O. sativa, and the uncoverage genome size in O. officinalis and O. meyeriana were 64 and 78 Mb, respectively. In addition, karyotype analysis was conducted based on the signal bands of C0t-1 DNA in O. sativa, O. officinalis, and O. meyeriana. The results showed that highly and moderately repetitive sequences in Oryza genus were conserved as the functional genes during evolution. The repetitive sequences reduplication may be one of the important causes of the genome enlargement of O. officinalis and O. meyeriana, and O. officinalis genome enlarged more slowly when compared with O. meyeriana. Based on the above results, it is concluded that O. officinalis and O. meyeriana were formed by reduplication, rearrangement, and gene selective loss during the evolution process.

  5. Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes.

    Science.gov (United States)

    Zhou, T; Wang, Y; Chen, J-Q; Araki, H; Jing, Z; Jiang, K; Shen, J; Tian, D

    2004-05-01

    A complete set of candidate disease resistance ( R) genes encoding nucleotide-binding sites (NBSs) was identified in the genome sequence of japonica rice ( Oryza sativaL. var. Nipponbare). These putative R genes were characterized with respect to structural diversity, phylogenetic relationships and chromosomal distribution, and compared with those in Arabidopsis thaliana. We found 535 NBS-coding sequences, including 480 non-TIR (Toll/IL-1 receptor) NBS-LRR (Leucine Rich Repeat) genes. TIR NBS-LRR genes, which are common in A. thaliana, have not been identified in the rice genome. The number of non-TIR NBS-LRR genes in rice is 8.7 times higher than that in A. thaliana, and they account for about 1% of all of predicted ORFs in the rice genome. Some 76% of the NBS genes were located in 44 gene clusters or in 57 tandem arrays, and 16 apparent gene duplications were detected in these regions. Phylogenetic analyses based both NBS and N-terminal regions classified the genes into about 200 groups, but no deep clades were detected, in contrast to the two distinct clusters found in A. thaliana. The structural and genetic diversity that exists among NBS-LRR proteins in rice is remarkable, and suggests that diversifying selection has played an important role in the evolution of R genes in this agronomically important species. (Supplemental material is available online at http://gattaca.nju.edu.cn.)

  6. Functional genomics in the rice blast fungus to unravel the fungal pathogenicity

    Institute of Scientific and Technical Information of China (English)

    Junhyun JEON; Jaehyuk CHOI; Jongsun PARK; Yong-Hwan LEE

    2008-01-01

    A rapidly growing number of successful genome sequencing projects in plant pathogenic fungi greatly increase the demands for tools and methodologies to study fungal pathogenicity at genomic scale. Magnaporthe oryzae is an economically important plant pathogenic fungus whose genome is fully sequenced. Recently we have reported the development and application of functional genomics platform technologies in M. oryzae. This model approach would have many practical ramifications in design and implementation of upcoming functional genomics studies of filamentous fungi aimed at understanding fungal pathogenicity.

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

    Science.gov (United States)

    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.

  8. Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups

    Directory of Open Access Journals (Sweden)

    Singh Nagendra

    2009-03-01

    Full Text Available Abstract Background Completely sequenced plant genomes provide scope for designing a large number of microsatellite markers, which are useful in various aspects of crop breeding and genetic analysis. With the objective of developing genic but non-coding microsatellite (GNMS markers for the rice (Oryza sativa L. genome, we characterized the frequency and relative distribution of microsatellite repeat-motifs in 18,935 predicted protein coding genes including 14,308 putative promoter sequences. Results We identified 19,555 perfect GNMS repeats with densities ranging from 306.7/Mb in chromosome 1 to 450/Mb in chromosome 12 with an average of 357.5 GNMS per Mb. The average microsatellite density was maximum in the 5' untranslated regions (UTRs followed by those in introns, promoters, 3'UTRs and minimum in the coding sequences (CDS. Primers were designed for 17,966 (92% GNMS repeats, including 4,288 (94% hypervariable class I types, which were bin-mapped on the rice genome. The GNMS markers were most polymorphic in the intronic region (73.3% followed by markers in the promoter region (53.3% and least in the CDS (26.6%. The robust polymerase chain reaction (PCR amplification efficiency and high polymorphic potential of GNMS markers over genic coding and random genomic microsatellite markers suggest their immediate use in efficient genotyping applications in rice. A set of these markers could assess genetic diversity and establish phylogenetic relationships among domesticated rice cultivar groups. We also demonstrated the usefulness of orthologous and paralogous conserved non-coding microsatellite (CNMS markers, identified in the putative rice promoter sequences, for comparative physical mapping and understanding of evolutionary and gene regulatory complexities among rice and other members of the grass family. The divergence between long-grained aromatics and subspecies japonica was estimated to be more recent (0.004 Mya compared to short

  9. Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus

    OpenAIRE

    Petit, J.; Bourgeois, E; Stenger, W.; Bes, M.; Droc, G.; Meynard, D.; Courtois, B.; Ghesquière, Alain; Sabot, François; Panaud, O.; Guiderdoni, E.

    2009-01-01

    Retrotransposons are mobile genetic elements, ubiquitous in Eukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. We investigate here the diversity of the Ty1-copia retrotransposon Tos17 in the cultivated rice of Asian origin (Oryza sativa L.) and related AA genome species of the Oryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the eleme...

  10. Whole-Genome Analysis Revealed the Positively Selected Genes during the Differentiation of indica and Temperate japonica Rice

    Science.gov (United States)

    Sun, Xinli; Jia, Qi; Guo, Yuchun; Zheng, Xiujuan; Liang, Kangjing

    2015-01-01

    To investigate the selective pressures acting on the protein-coding genes during the differentiation of indica and japonica, all of the possible orthologous genes between the Nipponbare and 93–11 genomes were identified and compared with each other. Among these genes, 8,530 pairs had identical sequences, and 27,384 pairs shared more than 90% sequence identity. Only 2,678 pairs of genes displaying a Ka/Ks ratio significantly greater than one were revealed, and most of these genes contained only nonsynonymous sites. The genes without synonymous site were further analyzed with the SNP data of 1529 O. sativa and O. rufipogon accessions, and 1068 genes were identified to be under positive selection during the differentiation of indica and temperate japonica. The positively selected genes (PSGs) are unevenly distributed on 12 chromosomes, and the proteins encoded by the PSGs are dominant with binding, transferase and hydrolase activities, and especially enriched in the plant responses to stimuli, biological regulations, and transport processes. Meanwhile, the most PSGs of the known function and/or expression were involved in the regulation of biotic/abiotic stresses. The evidence of pervasive positive selection suggested that many factors drove the differentiation of indica and japonica, which has already started in wild rice but is much lower than in cultivated rice. Lower differentiation and less PSGs revealed between the Or-It and Or-IIIt wild rice groups implied that artificial selection provides greater contribution on the differentiation than natural selection. In addition, the phylogenetic tree constructed with positively selected sites showed that the japonica varieties exhibited more diversity than indica on differentiation, and Or-III of O. rufipogon exhibited more than Or-I. PMID:25774680

  11. Two unisexual artificial polyploid clones constructed by genome addition of common carp (Cyprinus carp) and crucian carp (Carassius auratus)

    Institute of Scientific and Technical Information of China (English)

    WU; Qingjiang; (吴清江); YE; Yuzhen; (叶玉珍); DONG; Xinhong; (董新红)

    2003-01-01

    A polyploid hybrid fish with natural gynogenesis can prevent segregation and maintain their hybrid vigor in their progenies. Supposing the reproduction mode of induced polyploid fish being natural gynogenesis, allopolyploid hybrid between common carp and crucian carp into allopolyploid was performed. The purpose of this paper is to describe a lineage from sexual diploid carp transforming into allotriploid and allotetraploid unisexual clones by genome addition. The diploid hybrid between common carp and crucian carp reproduces an unreduced nucleus consisting of two parental genomes. This unreduced female pronucleus will fuse with male pronucleus and form allotriploid zygote after penetration of related species sperms. Allotriploid embryos grow normally, and part of female allotriploid can produce unreduced mature ova with three genomes. Mature ova of most allotriploid females are provided with natural gynogenetic trait and their nuclei do not fuse with any entrance sperm. All female offspring are produced by gynogenesis of allotriploid egg under activation of penetrating sperms. These offspring maintain morphological traits of their allotriploid maternal and form an allotetraploid unisexual clone by gynogenetic reproduction mode. However, female nuclei of rare allotriploid female can fuse with penetrating male pronuclei and result in the appearance of allotetraploid individuals by means of genome addition. All allotetraploid females can reproduce unreduced mature eggs containing four genomes. Therefore, mature eggs of allotetraploid maintain gynogenetic trait and allotetraploid unisexual clone is produced under activation of related species sperms.

  12. Genome-wide analysis of esterase-like genes in the striped rice stem borer, Chilo suppressalis.

    Science.gov (United States)

    Wang, Baoju; Wang, Ying; Zhang, Yang; Han, Ping; Li, Fei; Han, Zhaojun

    2015-06-01

    The striped rice stem borer, Chilo suppressalis, a destructive pest of rice, has developed high levels of resistance to certain insecticides. Esterases are reported to be involved in insecticide resistance in several insects. Therefore, this study systematically analyzed esterase-like genes in C. suppressalis. Fifty-one esterase-like genes were identified in the draft genomic sequences of the species, and 20 cDNA sequences were derived which encoded full- or nearly full-length proteins. The putative esterase proteins derived from these full-length genes are overall highly diversified. However, key residues that are functionally important including the serine residue in the active site are conserved in 18 out of the 20 proteins. Phylogenetic analysis revealed that most of these genes have homologues in other lepidoptera insects. Genes CsuEst6, CsuEst10, CsuEst11, and CsuEst51 were induced by the insecticide triazophos, and genes CsuEst9, CsuEst11, CsuEst14, and CsuEst51 were induced by the insecticide chlorantraniliprole. Our results provide a foundation for future studies of insecticide resistance in C. suppressalis and for comparative research with esterase genes from other insect species.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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. cDNA cloning and sequence analysis of genome segments S8 from rice black-streaked dwarf virus

    Institute of Scientific and Technical Information of China (English)

    张恒木; 陈剑平; 薛庆中; 雷娟利

    2002-01-01

    Genome segments S8 of two Chinese isolates of rice black-streaked dwarf virus (RBSDV), one from Zhejiang Province and another from Hebei Province, were amplified by RT-PCR and sequenced. Both segments consisted of 1936 nts in full length (EMBL accession numbers were AJ297431 and AJ297432, respectively) and contained only one big open reading frame which encoded a polypeptide with molecular weight of 68kD. The two Chinese isolates shared 94.0% and 96.5% identity at nucleotide and amino acid level, respectively. They shared 94.5-94.9% and 92.5-92.9% homology with S8 of RBSDV Japanese isolate at nucleotide and amino acid level, respectively; shared 85.1-87.6% and 91.7-91.9% homology with S7 of Italian MRDV (maize rough dwarf virus).

  17. Suppressor of RNA silencing encoded by Rice gall dwarf virus genome segment 11

    Institute of Scientific and Technical Information of China (English)

    LIU FuXiu; ZHAO Qin; RUAN XiaoLei; HE YunWei; LI HuaPing

    2008-01-01

    Rice gall dwarf virus (RGDV) is an important rice pathogen in China and Southeast Asia. However, little is known about the molecular mechanisms of RGDV interactions with plant cells. Here, we have identi-fied an RGDV protein, Pns11, which acts as a suppressor of RNA silencing in coinfiltration assays with the reporter, green fluorescent protein (GFP) in transgenic Nicotiana bentharniana line 16c carrying GFP. Pns11 suppressed local and systemic silencing induced by sense RNA. The spread of mobile FINA si-lencing signals was blocked or inactivated by Pns11. Expression of Pns11 also enhanced Potato virus X pathogenicity in N. benthamiana. This suppressor could reduce, but not eliminate, siRNA in the local and systemic RNA silencing suppression assays, suggesting that Pns11 functions by interfering with initial stages of RNA silencing.

  18. Genome-wide analysis of thioredoxin fold superfamily peroxiredoxins in Arabidopsis and rice

    OpenAIRE

    Umate, Pavan

    2010-01-01

    A broad range of peroxides generated in subcellular compartments, including chloroplasts, are detoxified with peroxidases called peroxiredoxins (Prx). The Prx are ubiquitously distributed in all organisms including bacteria, fungi, animals and also in cyanobacteria and plants. Recently, the Prx have emerged as new molecules in antioxidant defense in plants. Here, the members which belong to Prx gene family in Arabidopsis and rice are been identified. Overall, the Prx members constitute a smal...

  19. Genome-wide analysis of spatiotemporal gene expression patterns during early embryogenesis in rice.

    Science.gov (United States)

    Itoh, Jun-Ichi; Sato, Yutaka; Sato, Yutaka; Hibara, Ken-Ichiro; Shimizu-Sato, Sae; Kobayashi, Hiromi; Takehisa, Hinako; Sanguinet, Karen A; Namiki, Nobukazu; Nagamura, Yoshiaki

    2016-04-01

    Embryogenesis in rice is different from that of most dicotolydonous plants in that it shows a non-stereotypic cell division pattern, formation of dorsal-ventral polarity, and endogenous initiation of the radicle. To reveal the transcriptional features associated with developmental events during rice early embryogenesis, we used microarray analysis coupled with laser microdissection to obtain both spatial and temporal transcription profiles. Our results allowed us to determine spatial expression foci for each expressed gene in the globular embryo, which revealed the importance of phytohormone-related genes and a suite of transcription factors to early embryogenesis. Our analysis showed the polarized expression of a small number of genes along the apical-basal and dorsal-ventral axes in the globular embryo, which tended to fluctuate in later developmental stages. We also analyzed gene expression patterns in the early globular embryo and how this relates to expression in embryonic organs at later stages. We confirmed the accuracy of the expression patterns found by microarray analysis of embryo subdomains using in situ hybridization. Our study identified homologous genes from Arabidopsis thaliana with known functions in embryogenesis in addition to unique and uncharacterized genes that show polarized expression patterns during embryogenesis. The results of this study are presented in a database to provide a framework for spatiotemporal gene expression during rice embryogenesis, to serve as a resource for future functional analysis of genes, and as a basis for comparative studies of plant embryogenesis.

  20. Chromosome isolation by flow sorting in Aegilops umbellulata and Ae. comosa and their allotetraploid hybrids Ae. biuncialis and Ae. geniculata.

    Directory of Open Access Journals (Sweden)

    István Molnár

    Full Text Available This study evaluates the potential of flow cytometry for chromosome sorting in two wild diploid wheats Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata. Flow karyotypes obtained after the analysis of DAPI-stained chromosomes were characterized and content of chromosome peaks was determined. Peaks of chromosome 1U could be discriminated in flow karyotypes of Ae. umbellulata and Ae. biuncialis and the chromosome could be sorted with purities exceeding 95%. The remaining chromosomes formed composite peaks and could be sorted in groups of two to four. Twenty four wheat SSR markers were tested for their position on chromosomes of Ae. umbellulata and Ae. comosa using PCR on DNA amplified from flow-sorted chromosomes and genomic DNA of wheat-Ae. geniculata addition lines, respectively. Six SSR markers were located on particular Aegilops chromosomes using sorted chromosomes, thus confirming the usefulness of this approach for physical mapping. The SSR markers are suitable for marker assisted selection of wheat-Aegilops introgression lines. The results obtained in this work provide new opportunities for dissecting genomes of wild relatives of wheat with the aim to assist in alien gene transfer and discovery of novel genes for wheat improvement.

  1. Reticulate evolutionary history of a complex group of grasses: phylogeny of Elymus StStHH allotetraploids based on three nuclear genes.

    Directory of Open Access Journals (Sweden)

    Roberta J Mason-Gamer

    Full Text Available BACKGROUND: Elymus (Poaceae is a large genus of polyploid species in the wheat tribe Triticeae. It is polyphyletic, exhibiting many distinct allopolyploid genome combinations, and its history might be further complicated by introgression and lineage sorting. We focus on a subset of Elymus species with a tetraploid genome complement derived from Pseudoroegneria (genome St and Hordeum (H. We confirm the species' allopolyploidy, identify possible genome donors, and pinpoint instances of apparent introgression or incomplete lineage sorting. METHODOLOGY/PRINCIPAL FINDINGS: We sequenced portions of three unlinked nuclear genes-phosphoenolpyruvate carboxylase, beta-amylase, and granule-bound starch synthase I-from 27 individuals, representing 14 Eurasian and North American StStHHElymus species. Elymus sequences were combined with existing data from monogenomic representatives of the tribe, and gene trees were estimated separately for each data set using maximum likelihood. Trees were examined for evidence of allopolyploidy and additional reticulate patterns. All trees confirm the StStHH genome configuration of the Elymus species. They suggest that the StStHH group originated in North America, and do not support separate North American and European origins. Our results point to North American Pseudoroegneria and Hordeum species as potential genome donors to Elymus. Diploid P. spicata is a prospective St-genome donor, though conflict among trees involving P. spicata and the Eurasian P. strigosa suggests either introgression of GBSSI sequences from P. strigosa into North American Elymus and Pseudoroegneria, or incomplete lineage sorting of ancestral GBSSI polymorphism. Diploid H. californicum and/or allotetraploid H. jubatum are possible H-genome donors; direct involvement of an allotetraploid Hordeum species would simultaneously introduce two distinct H genomes to Elymus, consistent with some of the relationships among H-genome sequences in Hordeum and

  2. Rice black-streaked dwarf virus genome segment S5 is a bicistronic mRNA in infected plants.

    Science.gov (United States)

    Yang, Jian; Zhang, Heng-Mu; Ying, Lu; Li, Jing; Lv, Ming-Fang; Xie, Li; Li, Pei-Pei; Liu, Xiao-Ya; Liang-Ying, Dai; Chen, Jian-Ping

    2014-02-01

    Rice black-streaked dwarf virus (RBSDV) is a recognized member of the genus Fijivirus, family Reoviridae. Genome segment S5 has a putative second ORF partially overlapping the major ORF but in a different reading frame. This putative ORF is present in a published sequence and in two Chinese isolates now sequenced. Antibodies were raised against purified P5-1 and P5-2 fusion proteins expressed in a prokaryotic system. In western blots, these antibodies reacted with proteins of about 106 and 27 kDa, respectively, as predicted by sequence analysis. In immunoelectron microscopy, antibodies to P5-1 reacted with viroplasms, indicating that P5-1 is a component of viroplasms, but no labeling was observed with P5-2 antisera. Northern blot assays showed that the genome segment S5 was transcribed as a single mRNA with no subgenomic RNA. These results show that S5 is functionally bicistronic in infected plants. Possible translational mechanisms for P5-2 are discussed.

  3. Toward Elucidating the Structure of Tetraploid Cotton Genome

    Institute of Scientific and Technical Information of China (English)

    GUO Wang-zhen

    2008-01-01

    @@ Upland cotton has the highest yield,and accounts for >95% of world cotton production.Decoding upland cotton genomes will undoubtedly provide the ultimate reference and resource for structural,functional,and evolutionary studies of the species.Here,we employed GeneTrek and BAC tagging information approaches to predict the general composition and structure of the allotetraploid cotton genome.

  4. Genome-wide analysis reveals the expansion of Cytochrome P450 genes associated with xenobiotic metabolism in rice striped stem borer, Chilo suppressalis.

    Science.gov (United States)

    Wang, Baoju; Shahzad, Muhammad Faisal; Zhang, Zan; Sun, Haina; Han, Ping; Li, Fei; Han, Zhaojun

    2014-01-10

    The Cytochrome P450 (CYP) superfamily is a large group of ancient proteins with enzymatic activities involved in various physiological processes. The rice striped stem borer, Chilo suppressalis, is an important insect pest in rice production. Here, we report the identification and characterization of 77 CYP genes from rice striped stem borer (SSB) through genome and transcriptome sequence analyses. All these CYP genes were confirmed by RT-PCR and direct sequencing. Twenty-eight CYP transcripts have full open reading frame (ORF) and four additional transcripts have a nearly full length coding region. The SSB CYP genes were classified into four clans, the mitochondrial, CYP2, CYP3, and CYP4. Phylogenetic analysis indicated that there was an apparent expansion of the CYP3 clan in insects. The CYP6AB subfamily of the CYP3 clan had nine members in SSB. Evolutionary analysis showed that this subfamily was expanded only in lepidopteran insects. In this study, we identified a new P450 subfamily, CYP321F, which is unique to SSB and located in the genome as tandem repeats. Our work provided a foundation for future studies on the functions and mechanism of P450s in the destructive rice pest.

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

    Directory of Open Access Journals (Sweden)

    Gareth J Norton

    Full Text Available 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.

  6. Identification and characterization of genomic regions on chromosomes 4 and 8 that control the rate of photosynthesis in rice leaves

    Science.gov (United States)

    Adachi, Shunsuke; Tsuru, Yukiko; Nito, Naoko; Murata, Kazumasa; Yamamoto, Toshio; Ebitani, Takeshi; Ookawa, Taiichiro; Hirasawa, Tadashi

    2011-01-01

    DNA marker-assisted selection appears to be a promising strategy for improving rates of leaf photosynthesis in rice. The rate of leaf photosynthesis was significantly higher in a high-yielding indica variety, Habataki, than in the most popular Japanese variety, Koshihikari, at the full heading stage as a result of the higher level of leaf nitrogen at the same rate of application of nitrogen and the higher stomatal conductance even when the respective levels of leaf nitrogen were the same. The higher leaf nitrogen content of Habataki was caused by the greater accumulation of nitrogen by plants. The higher stomatal conductance of Habataki was caused by the higher hydraulic conductance. Using progeny populations and selected lines derived from a cross between Koshihikari and Habataki, it was possible to identify the genomic regions responsible for the rate of photosynthesis within a 2.1 Mb region between RM17459 and RM17552 and within a 1.2 Mb region between RM6999 and RM22529 on the long arm of chromosome 4 and on the short arm of chromosome 8, respectively. The designated region on chromosome 4 of Habataki was responsible for both the increase in the nitrogen content of leaves and hydraulic conductance in the plant by increasing the root surface area. The designated region on chromosome 8 of Habataki was responsible for the increase in hydraulic conductance by increasing the root hydraulic conductivity. The results suggest that it may be possible to improve photosynthesis in rice leaves by marker-assisted selection that focuses on these regions of chromosomes 4 and 8. PMID:21296764

  7. Identification and characterization of genomic regions on chromosomes 4 and 8 that control the rate of photosynthesis in rice leaves.

    Science.gov (United States)

    Adachi, Shunsuke; Tsuru, Yukiko; Nito, Naoko; Murata, Kazumasa; Yamamoto, Toshio; Ebitani, Takeshi; Ookawa, Taiichiro; Hirasawa, Tadashi

    2011-03-01

    DNA marker-assisted selection appears to be a promising strategy for improving rates of leaf photosynthesis in rice. The rate of leaf photosynthesis was significantly higher in a high-yielding indica variety, Habataki, than in the most popular Japanese variety, Koshihikari, at the full heading stage as a result of the higher level of leaf nitrogen at the same rate of application of nitrogen and the higher stomatal conductance even when the respective levels of leaf nitrogen were the same. The higher leaf nitrogen content of Habataki was caused by the greater accumulation of nitrogen by plants. The higher stomatal conductance of Habataki was caused by the higher hydraulic conductance. Using progeny populations and selected lines derived from a cross between Koshihikari and Habataki, it was possible to identify the genomic regions responsible for the rate of photosynthesis within a 2.1 Mb region between RM17459 and RM17552 and within a 1.2 Mb region between RM6999 and RM22529 on the long arm of chromosome 4 and on the short arm of chromosome 8, respectively. The designated region on chromosome 4 of Habataki was responsible for both the increase in the nitrogen content of leaves and hydraulic conductance in the plant by increasing the root surface area. The designated region on chromosome 8 of Habataki was responsible for the increase in hydraulic conductance by increasing the root hydraulic conductivity. The results suggest that it may be possible to improve photosynthesis in rice leaves by marker-assisted selection that focuses on these regions of chromosomes 4 and 8.

  8. A unified and comprehensible view of parametric and kernel methods for genomic prediction with application to rice

    Directory of Open Access Journals (Sweden)

    Laval Jacquin

    2016-08-01

    Full Text Available One objective of this study was to provide readers with a clear and unified understanding ofparametric statistical and kernel methods, used for genomic prediction, and to compare some ofthese in the context of rice breeding for quantitative traits. Furthermore, another objective wasto provide a simple and user-friendly R package, named KRMM, which allows users to performRKHS regression with several kernels. After introducing the concept of regularized empiricalrisk minimization, the connections between well-known parametric and kernel methods suchas Ridge regression (i.e. genomic best linear unbiased predictor (GBLUP and reproducingkernel Hilbert space (RKHS regression were reviewed. Ridge regression was then reformulatedso as to show and emphasize the advantage of the kernel trick concept, exploited by kernelmethods in the context of epistatic genetic architectures, over parametric frameworks used byconventional methods. Some parametric and kernel methods; least absolute shrinkage andselection operator (LASSO, GBLUP, support vector machine regression (SVR and RKHSregression were thereupon compared for their genomic predictive ability in the context of ricebreeding using three real data sets. Among the compared methods, RKHS regression and SVRwere often the most accurate methods for prediction followed by GBLUP and LASSO. An Rfunction 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 hasbeen developed. Moreover, a modified version of this function, which allows users to tune kernelsfor RKHS regression, has also been developed and parallelized for HPC Linux clusters. The corresponding KRMM package and all scripts have been made publicly available.

  9. The ultrastructure of pollen grain surface in allotetraploid petunia (Petunia hybrida hort. superbissima as revealed by scanning electron microscopy

    Directory of Open Access Journals (Sweden)

    S. Muszyński

    2015-05-01

    Full Text Available The ultrastructure of pollen grain surface in allotetraploid petunias was analyzed by scanning electron microscopy. The pollen grain wall is developed into characteristic pattern of convulations.

  10. Environmental Response and Genomic Regions Correlated with Rice Root Growth and Yield under Drought in the OryzaSNP Panel across Multiple Study Systems.

    Directory of Open Access Journals (Sweden)

    Len J Wade

    Full Text Available 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.

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

    Science.gov (United States)

    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

  12. Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice

    Science.gov (United States)

    Tanger, Paul; Klassen, Stephen; Mojica, Julius P.; Lovell, John T.; Moyers, Brook T.; Baraoidan, Marietta; Naredo, Maria Elizabeth B.; McNally, Kenneth L.; Poland, Jesse; Bush, Daniel R.; Leung, Hei; Leach, Jan E.; McKay, John K.

    2017-01-01

    To ensure food security in the face of population growth, decreasing water and land for agriculture, and increasing climate variability, crop yields must increase faster than the current rates. Increased yields will require implementing novel approaches in genetic discovery and breeding. Here we demonstrate the potential of field-based high throughput phenotyping (HTP) on a large recombinant population of rice to identify genetic variation underlying important traits. We find that detecting quantitative trait loci (QTL) with HTP phenotyping is as accurate and effective as traditional labor-intensive measures of flowering time, height, biomass, grain yield, and harvest index. Genetic mapping in this population, derived from a cross of an modern cultivar (IR64) with a landrace (Aswina), identified four alleles with negative effect on grain yield that are fixed in IR64, demonstrating the potential for HTP of large populations as a strategy for the second green revolution. PMID:28220807

  13. Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice.

    Science.gov (United States)

    Tanger, Paul; Klassen, Stephen; Mojica, Julius P; Lovell, John T; Moyers, Brook T; Baraoidan, Marietta; Naredo, Maria Elizabeth B; McNally, Kenneth L; Poland, Jesse; Bush, Daniel R; Leung, Hei; Leach, Jan E; McKay, John K

    2017-02-21

    To ensure food security in the face of population growth, decreasing water and land for agriculture, and increasing climate variability, crop yields must increase faster than the current rates. Increased yields will require implementing novel approaches in genetic discovery and breeding. Here we demonstrate the potential of field-based high throughput phenotyping (HTP) on a large recombinant population of rice to identify genetic variation underlying important traits. We find that detecting quantitative trait loci (QTL) with HTP phenotyping is as accurate and effective as traditional labor-intensive measures of flowering time, height, biomass, grain yield, and harvest index. Genetic mapping in this population, derived from a cross of an modern cultivar (IR64) with a landrace (Aswina), identified four alleles with negative effect on grain yield that are fixed in IR64, demonstrating the potential for HTP of large populations as a strategy for the second green revolution.

  14. Sequence and expression analyses of KIX domain proteins suggest their importance in seed development and determination of seed size in rice, and genome stability in Arabidopsis.

    Science.gov (United States)

    Thakur, Jitendra Kumar; Agarwal, Pinky; Parida, Swarup; Bajaj, Deepak; Pasrija, Richa

    2013-08-01

    The KIX domain, which mediates protein-protein interactions, was first discovered as a motif in the large multidomain transcriptional activator histone acetyltransferase p300/CBP. Later, the domain was also found in Mediator subunit MED15, where it interacts with many transcription factors. In both proteins, the KIX domain is a target of activation domains of diverse transcription activators. It was found to be an essential component of several specific gene-activation pathways in fungi and metazoans. Not much is known about KIX domain proteins in plants. This study aims to characterize all the KIX domain proteins encoded by the genomes of Arabidopsis and rice. All identified KIX domain proteins are presented, together with their chromosomal locations, phylogenetic analysis, expression and SNP analyses. KIX domains were found not only in p300/CBP- and MED15-like plant proteins, but also in F-box proteins in rice and DNA helicase in Arabidopsis, suggesting roles of KIX domains in ubiquitin-mediated proteasomal degradation and genome stability. Expression analysis revealed overlapping expression of OsKIX_3, OsKIX_5 and OsKIX_7 in different stages of rice seeds development. Moreover, an association analysis of 136 in silico mined SNP loci in 23 different rice genotypes with grain-length information identified three non-synonymous SNP loci in these three rice genes showing strong association with long- and short-grain differentiation. Interestingly, these SNPs were located within KIX domain encoding sequences. Overall, this study lays a foundation for functional analysis of KIX domain proteins in plants.

  15. Local coexpression domains in the genome of rice show no microsynteny with Arabidopsis domains

    NARCIS (Netherlands)

    Ren, X.Y.; Stiekema, W.J.; Nap, J.P.H.

    2007-01-01

    Chromosomal coexpression domains are found in a number of different genomes under various developmental conditions. The size of these domains and the number of genes they contain vary. Here, we define local coexpression domains as adjacent genes where all possible pair-wise correlations of

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

    NARCIS (Netherlands)

    Piffanelli, P.; Ciampi, A.Y.; Silva, F.R.; Santos, C.R.; Dhont, A.; Vilarinhos, A.; Pappas, G.; Souza, M.T.; Milller, R.N.G.

    2008-01-01

    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 la

  17. Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. oryzicola

    Directory of Open Access Journals (Sweden)

    Fu Bin-Ying

    2010-02-01

    Full Text Available Abstract Background Non-host resistance in rice to its bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc, mediated by a maize NBS-LRR type R gene, Rxo1 shows a typical hypersensitive reaction (HR phenotype, but the molecular mechanism(s underlying this type of non-host resistance remain largely unknown. Results A microarray experiment was performed to reveal the molecular mechanisms underlying HR of rice to Xoc mediated by Rxo1 using a pair of transgenic and non-transgenic rice lines. Our results indicated that Rxo1 appeared to function in the very early step of the interaction between rice and Xoc, and could specifically activate large numbers of genes involved in signaling pathways leading to HR and some basal defensive pathways such as SA and ET pathways. In the former case, Rxo1 appeared to differ from the typical host R genes in that it could lead to HR without activating NDR1. In the latter cases, Rxo1 was able to induce a unique group of WRKY TF genes and a large set of genes encoding PPR and RRM proteins that share the same G-box in their promoter regions with possible functions in post-transcriptional regulation. Conclusions In conclusion, Rxo1, like most host R genes, was able to trigger HR against Xoc in the heterologous rice plants by activating multiple defensive pathways related to HR, providing useful information on the evolution of plant resistance genes. Maize non-host resistance gene Rxo1 could trigger the pathogen-specific HR in heterologous rice, and ultimately leading to a localized programmed cell death which exhibits the characteristics consistent with those mediated by host resistance genes, but a number of genes encoding pentatricopeptide repeat and RNA recognition motif protein were found specifically up-regulated in the Rxo1 mediated disease resistance. These results add to our understanding the evolution of plant resistance genes.

  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

    Directory of Open Access Journals (Sweden)

    Soham Ray

    2016-08-01

    Full Text Available 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 the presence of Pi54 gene. Here, we report identification and cloning of a new fungal effector gene which interacts with resistance gene Pi54 gene in rice.

  19. Genome-Wide Binding Analysis of the Transcription Activator IDEAL PLANT ARCHITECTURE1 Reveals a Complex Network Regulating Rice Plant Architecture[W

    Science.gov (United States)

    Lu, Zefu; Yu, Hong; Xiong, Guosheng; Wang, Jing; Jiao, Yongqing; Liu, Guifu; Jing, Yanhui; Meng, Xiangbing; Hu, Xingming; Qian, Qian; Fu, Xiangdong; Wang, Yonghong; Li, Jiayang

    2013-01-01

    IDEAL PLANT ARCHITECTURE1 (IPA1) is critical in regulating rice (Oryza sativa) plant architecture and substantially enhances grain yield. To elucidate its molecular basis, we first confirmed IPA1 as a functional transcription activator and then identified 1067 and 2185 genes associated with IPA1 binding sites in shoot apices and young panicles, respectively, through chromatin immunoprecipitation sequencing assays. The SQUAMOSA PROMOTER BINDING PROTEIN-box direct binding core motif GTAC was highly enriched in IPA1 binding peaks; interestingly, a previously uncharacterized indirect binding motif TGGGCC/T was found to be significantly enriched through the interaction of IPA1 with proliferating cell nuclear antigen PROMOTER BINDING FACTOR1 or PROMOTER BINDING FACTOR2. Genome-wide expression profiling by RNA sequencing revealed IPA1 roles in diverse pathways. Moreover, our results demonstrated that IPA1 could directly bind to the promoter of rice TEOSINTE BRANCHED1, a negative regulator of tiller bud outgrowth, to suppress rice tillering, and directly and positively regulate DENSE AND ERECT PANICLE1, an important gene regulating panicle architecture, to influence plant height and panicle length. The elucidation of target genes of IPA1 genome-wide will contribute to understanding the molecular mechanisms underlying plant architecture and to facilitating the breeding of elite varieties with ideal plant architecture. PMID:24170127

  20. Genome-wide binding analysis of the transcription activator ideal plant architecture1 reveals a complex network regulating rice plant architecture.

    Science.gov (United States)

    Lu, Zefu; Yu, Hong; Xiong, Guosheng; Wang, Jing; Jiao, Yongqing; Liu, Guifu; Jing, Yanhui; Meng, Xiangbing; Hu, Xingming; Qian, Qian; Fu, Xiangdong; Wang, Yonghong; Li, Jiayang

    2013-10-01

    Ideal plant architecture1 (IPA1) is critical in regulating rice (Oryza sativa) plant architecture and substantially enhances grain yield. To elucidate its molecular basis, we first confirmed IPA1 as a functional transcription activator and then identified 1067 and 2185 genes associated with IPA1 binding sites in shoot apices and young panicles, respectively, through chromatin immunoprecipitation sequencing assays. The Squamosa promoter binding protein-box direct binding core motif GTAC was highly enriched in IPA1 binding peaks; interestingly, a previously uncharacterized indirect binding motif TGGGCC/T was found to be significantly enriched through the interaction of IPA1 with proliferating cell nuclear antigen promoter binding factor1 or promoter binding factor2. Genome-wide expression profiling by RNA sequencing revealed IPA1 roles in diverse pathways. Moreover, our results demonstrated that IPA1 could directly bind to the promoter of rice teosinte branched1, a negative regulator of tiller bud outgrowth, to suppress rice tillering, and directly and positively regulate dense and erect panicle1, an important gene regulating panicle architecture, to influence plant height and panicle length. The elucidation of target genes of IPA1 genome-wide will contribute to understanding the molecular mechanisms underlying plant architecture and to facilitating the breeding of elite varieties with ideal plant architecture.

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

    Science.gov (United States)

    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.

  2. Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization

    Directory of Open Access Journals (Sweden)

    Valot Benoît

    2007-02-01

    Full Text Available Abstract Background Allopolyploidy is a preeminent process in plant evolution that results from the merger of distinct genomes in a common nucleus via inter-specific hybridization. Allopolyploid formation is usually related to genome-wide structural and functional changes though the underlying mechanisms operating during this "genomic shock" still remain poorly known. The aim of the present study was to investigate the modifications occurring at the proteomic level following an allopolyploidization event and to determine whether these changes are related to functional properties of the proteins. In a previous report, we applied comparative proteomics to synthetic amphiploids of Brassica napus and to its diploid progenitors B. rapa and B. oleracea. Although several hundred polypeptides displayed additivity (i.e. mid-parent values in the amphiploids, many of them showed non-additivity. Here, we report the in silico functional characterization of the "non-additive" proteins (the ones with a non-additive pattern of regulation in synthetic B. napus. Results The complete set of non-additive proteins (335 in the stem and 205 in the root, as well as a subset of additive polypeptides (200 per organ, was identified by mass spectrometry. Several protein isoforms were found, and most of them (~55% displayed "different" or "opposite" patterns of regulation in the amphiploids, i.e. isoforms of the same protein showing both up-regulation and down-regulation in the synthetic B. napus compared to the mid-parent value. Components of protein complexes were identified of which ~50% also displayed "different" or "opposite" patterns of regulation in the allotetraploids. In silico functional categorization of the identified proteins was carried out, and showed that neither functional category nor metabolic pathway were systematically affected by non-additivity in the synthetic amphiploids. In addition, no subcellular compartment was found to be over- or under

  3. Experimental evidence for the ancestry of allotetraploid Trifolium repens and creation of synthetic forms with value for plant breeding

    Directory of Open Access Journals (Sweden)

    Williams Warren M

    2012-04-01

    Full Text Available Abstract Background White clover (Trifolium repens is a ubiquitous weed of the temperate world that through use of improved cultivars has also become the most important legume of grazed pastures world-wide. It has long been suspected to be allotetraploid, but the diploid ancestral species have remained elusive. Putative diploid ancestors were indicated by DNA sequence phylogeny to be T. pallescens and T. occidentale. Here, we use further DNA evidence as well as a combination of molecular cytogenetics (FISH and GISH and experimental hybridization to test the hypothesis that white clover originated as a hybrid between T. pallescens and T. occidentale. Results T. pallescens plants were identified with chloroplast trnL intron DNA sequences identical to those of white clover. Similarly, T. occidentale plants with nuclear ITS sequences identical to white clover were also identified. Reciprocal GISH experiments, alternately using labeled genomic DNA probes from each of the putative ancestral species on the same white clover cells, showed that half of the chromosomes hybridized with each probe. F1 hybrids were generated by embryo rescue and these showed strong interspecific chromosome pairing and produced a significant frequency of unreduced gametes, indicating the likely mode of polyploidization. The F1 hybrids are inter-fertile with white clover and function as synthetic white clovers, a valuable new resource for the re-incorporation of ancestral genomes into modern white clover for future plant breeding. Conclusions Evidence from DNA sequence analyses, molecular cytogenetics, interspecific hybridization and breeding experiments supports the hypothesis that a diploid alpine species (T. pallescens hybridized with a diploid coastal species (T. occidentale to generate tetraploid T. repens. The coming together of these two narrowly adapted species (one alpine and the other maritime, along with allotetraploidy, has led to a transgressive hybrid with a

  4. Physical Integration of Root QTLs with the japonica Genome and Prediction of Probable Candidate Genes for Drought Tolerance in Rice

    Institute of Scientific and Technical Information of China (English)

    K. Ulaganathan; P.S. Priya; A. Snehalatharani; M. Sashikanth; A.R. Krishna; S. Singh

    2007-01-01

    @@ Drought is becoming an increasingly important constraint limiting world's rice production (Bennett, 2003).About half of the world's rice is grown in rainfed environments where the rainfall is the major source of water supply, and yields may be seriously restricted by water deficit.

  5. Genetic architecture of cold tolerance in rice at the seedling stage and heading determined through genome-wide association studies

    Science.gov (United States)

    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...

  6. Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae

    Directory of Open Access Journals (Sweden)

    Manicacci Domenica

    2009-03-01

    Full Text Available Abstract Background Horizontal transfers (HTs refer to the transmission of genetic material between phylogenetically distant species. Although most of the cases of HTs described so far concern genes, there is increasing evidence that some involve transposable elements (TEs in Eukaryotes. The availability of the full genome sequence of two cereal species, (i.e. rice and Sorghum, as well as the partial genome sequence of maize, provides the opportunity to carry out genome-wide searches for TE-HTs in Poaceae. Results We have identified an LTR-retrotransposon, that we named Route66, with more than 95% sequence identity between rice and Sorghum. Using a combination of in silico and molecular approaches, we are able to present a substantial phylogenetic evidence that Route66 has been transferred horizontally between Panicoideae and several species of the genus Oryza. In addition, we show that it has remained active after these transfers. Conclusion This study constitutes a new case of HTs for an LTR-retrotransposon and we strongly believe that this mechanism could play a major role in the life cycle of transposable elements. We therefore propose to integrate classe I elements into the previous model of transposable element evolution through horizontal transfers.

  7. Transgenic Rice Plants Harboring Genomic DNA from Zizania latifolia Confer Bacterial Blight Resistance

    Institute of Scientific and Technical Information of China (English)

    SHEN Wei-wei; SONG Cheng-li; CHEN Jie; Fu Ya-ping; Wu Jian-li; JIANG Shao-mei

    2011-01-01

    Based on the sequence of a resistance gene analog FZ14 derived from Zizania latifolia (Griseb.),a pair of specific PCR primers FZ14P1/FZ14P2 was designed to isolate candidate disease resistance gene.The pooled-PCR approach was adopted using the primer pair to screen a genomic transformation-competent artificial chromosome (TAC) library derived from Z.latifolia.A positive TAC clone (ZR1) was obtained and confirmed by sequence analysis.The results indicated that ZR1 consisted of conserved motifs similar to P-loop (kinase 1a),kinase 2,kinase 3a and GLPL (Gly-Leu-Pro-Leu),suggesting that it could be a portion of NBS-LRR type of resistance gene.Using Agrobacterium-mediated transformation of Nipponbare mature embryo,a total of 48 independent transgenic T0 plants were obtained.Among them,36 plants were highly resistant to the virulent bacterial blight strain P×O71.The results indicate that ZR1 contains at least one functional bacterial blight resistance gene.

  8. Sequencing of the Cultivated Tetraploid CottonGenome-Gossypium hirsutum

    Institute of Scientific and Technical Information of China (English)

    YU Shu-xun; WANG Kun-bo; LI Fu-guang; KOHEL Russell J; PERCY Richard G; YU John Z

    2008-01-01

    @@ Cotton is an important cash crop in the world,and it plays an irreplaceable role in China's nationaleconomy.Cultivated upland cotton (Gossypium hirsutum L.) represents 95% of the world's cottonproduction,but it has a complex allotetraploid genome that contains at least 30000 genes in 2500 MbDNA.

  9. Sequencing of the Cultivated Tetraploid Cotton Genome-Gossypium hirsutum

    Institute of Scientific and Technical Information of China (English)

    KOHEL; Russell; J; PERCY; Richard; G; YU; John; Z

    2008-01-01

    Cotton is an important cash crop in the world,and it plays an irreplaceable role in China's national economy.Cultivated upland cotton(Gossypium hirsutum L.) represents 95% of the world's cotton production,but it has a complex allotetraploid genome that contains at least 30000 genes in 2500 Mb

  10. Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa).

    Science.gov (United States)

    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.

  11. Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus.

    Science.gov (United States)

    Petit, Julie; Bourgeois, Emmanuelle; Stenger, Wilfried; Bès, Martine; Droc, Gaétan; Meynard, Donaldo; Courtois, Brigitte; Ghesquière, Alain; Sabot, François; Panaud, Olivier; Guiderdoni, Emmanuel

    2009-12-01

    Retrotransposons are mobile genetic elements, ubiquitous in Eukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. We investigate here the diversity of the Ty1-copia retrotransposon Tos17 in the cultivated rice of Asian origin (Oryza sativa L.) and related AA genome species of the Oryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the element in the lineages. In that aim, we used a combination of Southern hybridization with a reverse transcriptase (RT) probe and an adapter-PCR mediated amplification, which allowed the sequencing of the genomic regions flanking Tos17 insertions. This analysis was carried out in a collection of 47 A-genome Oryza species accessions and 202 accessions of a core collection of Oryza sativa L. representative of the diversity of the species. Our Southern hybridization results show that Tos17 is present in all the accessions of the A-genome Oryza species, except for the South American species O. glumaepatula and the African species O. glaberrima and O. breviligulata. In O. sativa, the number of putative copies of Tos17 per accession ranged from 1 to 11 and multivariate analysis based on presence/absence of putative copies yielded a varietal clustering which is consistent with the isozyme classification of rice. Adapter PCR amplification and sequencing of flanking regions of Tos17 insertions in A-genome species other than O. sativa, followed by anchoring on the Nipponbare genome sequence, revealed 13 insertion sites of Tos17 in the surveyed O. rufipogon and O. longistaminata accessions, including one shared by both species. In O. sativa, the same approach revealed 25 insertions in the 6 varietal groups. Four insertion sites located on chromosomes 1, 2, 10, and 11 were found orthologous in O. rufipogon and O. sativa. The chromosome 1 insertion was also shared between O. rufipogon and O

  12. 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.

    Science.gov (United States)

    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.

  13. Genome-wide transcriptional analysis of salinity stressed japonica and indica rice genotypes during panicle initiation stage.

    Science.gov (United States)

    Walia, Harkamal; Wilson, Clyde; Zeng, Linghe; Ismail, Abdelbagi M; Condamine, Pascal; Close, Timothy J

    2007-03-01

    Rice yield is most sensitive to salinity stress imposed during the panicle initiation (PI) stage. In this study, we have focused on physiological and transcriptional responses of four rice genotypes exposed to salinity stress during PI. The genotypes selected included a pair of indicas (IR63731 and IR29) and a pair of japonica (Agami and M103) rice subspecies with contrasting salt tolerance. Physiological characterization showed that tolerant genotypes maintained a much lower shoot Na+ concentration relative to sensitive genotypes under salinity stress. Global gene expression analysis revealed a strikingly large number of genes which are induced by salinity stress in sensitive genotypes, IR29 and M103 relative to tolerant lines. We found 19 probe sets to be commonly induced in all four genotypes. We found several salinity modulated, ion homeostasis related genes from our analysis. We also studied the expression of SKC1, a cation transporter reported by others as a major source of variation in salt tolerance in rice. The transcript abundance of SKC1 did not change in response to salinity stress at PI stage in the shoot tissue of all four genotypes. However, we found the transcript abundance of SKC1 to be significantly higher in tolerant japonica Agami relative to sensitive japonica M103 under control and stressed conditions during PI stage.

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

    Science.gov (United States)

    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...

  15. Genetic Architecture of Cold Tolerance in Rice (Oryza sativa) Determined through High Resolution Genome-Wide Analysis

    Science.gov (United States)

    Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases se...

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

    Science.gov (United States)

    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.

  17. Comparative genomic analysis of the GRF genes in Chinese pear (Pyrus bretschneideri Rehd, poplar (Populous, grape (Vitis vinifera, Arabidopsis and rice (Oryza sativa

    Directory of Open Access Journals (Sweden)

    Yun Peng Cao

    2016-11-01

    Full Text Available Growth-regulating factors (GRFs are plant-specific transcription factors that have important functions in regulating plant growth and development. Previous studies on GRF family members focused either on a single or a small set of genes. Here, a comparative genomic analysis of the GRF gene family was performed in poplar (a model tree species, Arabidopsis (a model plant for annual herbaceous dicots, grape (one model plant for perennial dicots, rice (a model plant for monocots and Chinese pear (one of the economical fruit crops. In total, 58 GRF genes were identified, 12 genes in rice (Oryza sativa, 8 genes in grape (Vitis vinifera, 9 genes in Arabidopsis thaliana, 19 genes in poplar (Populus trichocarpa and 10 genes in Chinese pear (Pyrus bretschneideri. The GRF genes were divided into five subfamilies based on the phylogenetic analysis, which was supported by their structural analysis. Furthermore, microsynteny analysis indicated that highly conserved regions of microsynteny were identified in all of the five species tested. And Ka/Ks analysis revealed that purifying selection play an important role in the maintenance of GRF genes. Our results provide basic information on GRF genes in five plant species and lay the foundation for future research on the functions of these genes.

  18. Identification of ‘safe harbor’ loci in indica rice genome by harnessing the property of zinc-finger nucleases to induce DNA damage and repair.

    Directory of Open Access Journals (Sweden)

    Christian eCantos

    2014-06-01

    Full Text Available Zinc-finger nucleases (ZFNs have proved to be successful tools for targeted genome manipulation in several organisms. Their main property is the induction of double-strand breaks (DSBs at specific sites, which are further repaired through homologous recombination (HR or non-homologous end joining (NHEJ. However, for the appropriate integration of genes at specific chromosomal locations, proper sites for gene integration need to be identified. These regions, hereby named safe harbor loci, must be localized in non-coding regions and possess high gene expression. In the present study, three different ZFN constructs (pZFN1, pZFN2, pZFN3, harboring β-glucuronidase (GUS as a reporter gene, were used to identify safe harbor loci regions on rice chromosomes. The constructs were delivered into IR64 rice by using an improved Agrobacterium-mediated transformation protocol, based on the use of immature embryos. Gene expression was measured by histochemical GUS activity and the flanking regions were determined through thermal-asymmetric interlaced polymerase chain reaction (TAIL PCR. Following sequencing, 28 regions were identified as putative sites for safe integration, but only one was localized in a non-coding region and it also possessed high GUS expression. These findings have significant applicability to create crops with new and valuable traits, since the site can be subsequently used to stably introduce one or more genes in a targeted manner.

  19. Identification and molecular characterization of tissue-preferred rice genes and their upstream regularly sequences on a genome-wide level.

    Science.gov (United States)

    Jiang, Shu-Ye; Vanitha, Jeevanandam; Bai, Yanan; Ramachandran, Srinivasan

    2014-11-27

    Gene upstream regularly sequences (URSs) can be used as one of the tools to annotate the biological functions of corresponding genes. In addition, tissue-preferred URSs are frequently used to drive the transgene expression exclusively in targeted tissues during plant transgenesis. Although many rice URSs have been molecularly characterized, it is still necessary and valuable to identify URSs that will benefit plant transformation and aid in analyzing gene function. In this study, we identified and characterized root-, seed-, leaf-, and panicle-preferred genes on a genome-wide level in rice. Subsequently, their expression patterns were confirmed through quantitative real-time RT-PCR (qRT-PCR) by randomly selecting 9candidate tissue-preferred genes. In addition, 5 tissue-preferred URSs were characterized by investigating the URS::GUS transgenic plants. Of these URS::GUS analyses, the transgenic plants harboring LOC_Os03g11350 URS::GUS construct showed the GUS activity only in young pollen. In contrast, when LOC_Os10g22450 URS was used to drive the reporter GUS gene, the GUS activity was detected only in mature pollen. Interestingly, the LOC_Os10g34360 URS was found to be vascular bundle preferred and its activities were restricted only to vascular bundles of leaves, roots and florets. In addition, we have also identified two URSs from genes LOC_Os02G15090 and LOC_Os06g31070 expressed in a seed-preferred manner showing the highest expression levels of GUS activities in mature seeds. By genome-wide analysis, we have identified tissue-preferred URSs, five of which were further characterized using transgenic plants harboring URS::GUS constructs. These data might provide some evidence for possible functions of the genes and be a valuable resource for tissue-preferred candidate URSs for plant transgenesis.

  20. Genomic insights into the glutathione S-transferase gene family of two rice planthoppers, Nilaparvata lugens (Stal and Sogatella furcifera (Horvath (Hemiptera: Delphacidae.

    Directory of Open Access Journals (Sweden)

    Wen-Wu Zhou

    Full Text Available BACKGROUND: Glutathione S-transferase (GST genes control crucial traits for the metabolism of various toxins encountered by insects in host plants and the wider environment, including insecticides. The planthoppers Nilaparvata lugens and Sogatella furcifera are serious specialist pests of rice throughout eastern Asia. Their capacity to rapidly adapt to resistant rice varieties and to develop resistance to various insecticides has led to severe outbreaks over the last decade. METHODOLOGY/PRINCIPAL FINDINGS: Using the genome sequence of N. lugens, we identified for the first time the complete GST gene family of a delphacid insect whilst nine GST gene orthologs were identified from the closely related species S. furcifera. Nilaparvata lugens has 11 GST genes belonging to six cytosolic subclasses and a microsomal class, many fewer than seen in other insects with known genomes. Sigma is the largest GST subclass, and the intron-exon pattern deviates significantly from that of other species. Higher GST gene expression in the N. lugens adult migratory form reflects the higher risk of this life stage in encountering the toxins of non-host plants. After exposure to a sub-lethal dose of four insecticides, chlorpyrifos, imidacloprid, buprofezin or beta-cypermethrin, more GST genes were upregulated in S. furcifera than in N. lugens. RNA interference targeting two N. lugens GST genes, NlGSTe1 and NlGSTm2, significantly increased the sensitivity of fourth instar nymphs to chlorpyrifos but not to beta-cypermethrin. CONCLUSIONS/SIGNIFICANCE: This study provides the first elucidation of the nature of the GST gene family in a delphacid species, offering new insights into the evolution of metabolic enzyme genes in insects. Further, the use of RNA interference to identify the GST genes induced by insecticides illustrates likely mechanisms for the tolerance of these insects.

  1. Genome-wide comparative analysis of NBS-encoding genes in four Gossypium species

    Science.gov (United States)

    Nucleotide binding site (NBS) genes encode a large family of disease resistance (R) proteins in plants. The availability of genomic data of the two diploid cotton species, Gossypium arboreum and Gossypium raimondii, and the two allotetraploid cotton species, Gossypium hirsutum (TM-1) and Gossypium ...

  2. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

    Science.gov (United States)

    Wheat (Triticum spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent over 10,000 years ago. Identifying genetic modifications underlying wheat's domestication requires knowledge of the genome of its allo-tetraploid proge...

  3. Identification and characterization of genomic regions on chromosomes 4 and 8 that control the rate of photosynthesis in rice leaves

    OpenAIRE

    2011-01-01

    DNA marker-assisted selection appears to be a promising strategy for improving rates of leaf photosynthesis in rice. The rate of leaf photosynthesis was significantly higher in a high-yielding indica variety, Habataki, than in the most popular Japanese variety, Koshihikari, at the full heading stage as a result of the higher level of leaf nitrogen at the same rate of application of nitrogen and the higher stomatal conductance even when the respective levels of leaf nitrogen were the same. The...

  4. Genome-wide identification and analysis of rice genes preferentially expressed in pollen at an early developmental stage.

    Science.gov (United States)

    Nguyen, Tien Dung; Moon, Sunok; Nguyen, Van Ngoc Tuyet; Gho, Yunsil; Chandran, Anil Kumar Nalini; Soh, Moon-Soo; Song, Jong Tae; An, Gynheung; Oh, Sung Aeong; Park, Soon Ki; Jung, Ki-Hong

    2016-09-01

    Microspore production using endogenous developmental programs has not been well studied. The main limitation is the difficulty in identifying genes preferentially expressed in pollen grains at early stages. To overcome this limitation, we collected transcriptome data from anthers and microspore/pollen and performed meta-expression analysis. Subsequently, we identified 410 genes showing preferential expression patterns in early developing pollen samples of both japonica and indica cultivars. The expression patterns of these genes are distinguishable from genes showing pollen mother cell or tapetum-preferred expression patterns. Gene Ontology enrichment and MapMan analyses indicated that microspores in rice are closely linked with protein degradation, nucleotide metabolism, and DNA biosynthesis and regulation, while the pollen mother cell or tapetum are strongly associated with cell wall metabolism, lipid metabolism, secondary metabolism, and RNA biosynthesis and regulation. We also generated transgenic lines under the control of the promoters of eight microspore-preferred genes and confirmed the preferred expression patterns in plants using the GUS reporting system. Furthermore, cis-regulatory element analysis revealed that pollen specific elements such as POLLEN1LELAT52, and 5659BOXLELAT5659 were commonly identified in the promoter regions of eight rice genes with more frequency than estimation. Our study will provide new sights on early pollen development in rice, a model crop plant.

  5. QTL analysis of novel genomic regions associated with yield and yield related traits in new plant type based recombinant inbred lines of rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    Marathi Balram

    2012-08-01

    Full Text Available Abstract Background Rice is staple food for more than half of the world’s population including two billion Asians, who obtain 60-70% of their energy intake from rice and its derivatives. To meet the growing demand from human population, rice varieties with higher yield potential and greater yield stability need to be developed. The favourable alleles for yield and yield contributing traits are distributed among two subspecies i.e., indica and japonica of cultivated rice (Oryza sativa L.. Identification of novel favourable alleles in indica/japonica will pave way to marker-assisted mobilization of these alleles in to a genetic background to break genetic barriers to yield. Results A new plant type (NPT based mapping population of 310 recombinant inbred lines (RILs was used to map novel genomic regions and QTL hotspots influencing yield and eleven yield component traits. We identified major quantitative trait loci (QTLs for days to 50% flowering (R2 = 25%, LOD = 14.3, panicles per plant (R2 = 19%, LOD = 9.74, flag leaf length (R2 = 22%, LOD = 3.05, flag leaf width (R2 = 53%, LOD = 46.5, spikelets per panicle (R2 = 16%, LOD = 13.8, filled grains per panicle (R2 = 22%, LOD = 15.3, percent spikelet sterility (R2 = 18%, LOD = 14.24, thousand grain weight (R2 = 25%, LOD = 12.9 and spikelet setting density (R2 = 23%, LOD = 15 expressing over two or more locations by using composite interval mapping. The phenotypic variation (R2 ranged from 8 to 53% for eleven QTLs expressing across all three locations. 19 novel QTLs were contributed by the NPT parent, Pusa1266. 15 QTL hotpots on eight chromosomes were identified for the correlated traits. Six epistatic QTLs effecting five traits at two locations were identified. A marker interval (RM3276-RM5709 on chromosome 4 harboring major QTLs for four traits was identified. Conclusions The present study reveals that favourable alleles for

  6. Epigenomic Modification and Epigenetic Regulation in Rice

    Institute of Scientific and Technical Information of China (English)

    Yu Zhao; Dao-Xiu Zhou

    2012-01-01

    Epigenomes including genome-wide histone modification and DNA methylation profiles are important for genome activity and for defining gene expression patterns of plant development and responses to various environmental conditions.Rice is the most important crop plant and serves as a model for cereal genomics.Rice epigenomic landscape is emerging and the function of chromatin modification regulators in gene expression,transposon repression and plant development is being characterized.Epigenomic variation that gives rise to stable or transgenerational heritable epialleles related to variation of important agronomical traits or stress responses is being characterized in rice.Implication of epigenomic variation in rice heterosis is being exploited.

  7. MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii.

    Science.gov (United States)

    Takagi, Hiroki; Uemura, Aiko; Yaegashi, Hiroki; Tamiru, Muluneh; Abe, Akira; Mitsuoka, Chikako; Utsushi, Hiroe; Natsume, Satoshi; Kanzaki, Hiroyuki; Matsumura, Hideo; Saitoh, Hiromasa; Yoshida, Kentaro; Cano, Liliana M; Kamoun, Sophien; Terauchi, Ryohei

    2013-10-01

    Next-generation sequencing allows the identification of mutations responsible for mutant phenotypes by whole-genome resequencing and alignment to a reference genome. However, when the resequenced cultivar/line displays significant structural variation from the reference genome, mutations in the genome regions missing from the reference (gaps) cannot be identified by simple alignment. Here we report on a method called 'MutMap-Gap', which involves delineating a candidate region harboring a mutation of interest using the recently reported MutMap method, followed by de novo assembly, alignment, and identification of the mutation within genome gaps. We applied MutMap-Gap to isolate the blast resistant gene Pii from the rice cv Hitomebore using mutant lines that have lost Pii function. MutMap-Gap should prove useful for cloning genes that exhibit significant structural variations such as disease resistance genes of the nucleotide-binding site-leucine rich repeat (NBS-LRR) class.

  8. Mapping QTLs for submergence tolerance during germination in rice

    African Journals Online (AJOL)

    STORAGESEVER

    2008-08-04

    Aug 4, 2008 ... The study was conducted at NG-01 greenhouse, Genome and. Mapping (GML), the ..... International Rice Genome Sequencing Project (IRGSP) (2005). The ... A high-resolution recombination map of the human genome. Nat.

  9. Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry

    Science.gov (United States)

    High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a commun...

  10. RICE CROSSES

    African Journals Online (AJOL)

    Spikelet sterility is the greatest barrier to rice hybridization. ... sterility, Hybridization, Duplicate recessive epis- tasis ' ... hybrid fertility of intra-subspecific crosses, i.e., indica by ..... 'Germ 59(1) 293$ ' ' male sterility and fertility restoration in rice.

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

    Science.gov (United States)

    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...

  12. Genome-wide analysis of rice ClpB/HSP100, ClpC and ClpD genes

    Directory of Open Access Journals (Sweden)

    Mittal Dheeraj

    2010-02-01

    Full Text Available Abstract Background ClpB-cyt/HSP100 protein acts as chaperone, mediating disaggregation of denatured proteins. Previous studies have shown that ClpB-cyt/HSP100 gene belongs to the group class I Clp ATPase proteins and ClpB-cyt/HSP100 transcript is regulated by heat stress and developmental cues. Results Nine ORFs were noted to constitute rice class I Clp ATPases in the following manner: 3 ClpB proteins (ClpB-cyt, Os05g44340; ClpB-m, Os02g08490; ClpB-c, Os03g31300, 4 ClpC proteins (ClpC1, Os04g32560; ClpC2, Os12g12580; ClpC3, Os11g16590; ClpC4, Os11g16770 and 2 ClpD proteins (ClpD1, Os02g32520; ClpD2, Os04g33210. Using the respective signal sequences cloned upstream to GFP/CFP reporter proteins and transient expression studies with onion epidermal cells, evidence is provided that rice ClpB-m and Clp-c proteins are indeed localized to their respective cell locations mitochondria and chloroplasts, respectively. Associated with their diverse cell locations, domain structures of OsClpB-c, OsClpB-m and OsClpB-cyt proteins are noted to possess a high-level conservation. OsClpB-cyt transcript is shown to be enriched at milk and dough stages of seed development. While expression of OsClpB-m was significantly less as compared to its cytoplasmic and chloroplastic counterparts in different tissues, this transcript showed highest heat-induced expression amongst the 3 ClpB proteins. OsClpC1 and OsClpC2 are predicted to be chloroplast-localized as is the case with all known plant ClpC proteins. However, the fact that OsClpC3 protein appears mitochondrial/chloroplastic with equal probability and OsClpC4 a plasma membrane protein reflects functional diversity of this class. Different class I Clp ATPase transcripts were noted to be cross-induced by a host of different abiotic stress conditions. Complementation assays of Δhsp104 mutant yeast cells showed that OsClpB-cyt, OsClpB-m, OsClpC1 and OsClpD1 have significantly positive effects. Remarkably, OsClpD1 gene

  13. Detection of Epistatic and Gene-Environment Interactions Underlying Three Quality Traits in Rice Using High-Throughput Genome-Wide Data

    Directory of Open Access Journals (Sweden)

    Haiming Xu

    2015-01-01

    Full Text Available With development of sequencing technology, dense single nucleotide polymorphisms (SNPs have been available, enabling uncovering genetic architecture of complex traits by genome-wide association study (GWAS. However, the current GWAS strategy usually ignores epistatic and gene-environment interactions due to absence of appropriate methodology and heavy computational burden. This study proposed a new GWAS strategy by combining the graphics processing unit- (GPU- based generalized multifactor dimensionality reduction (GMDR algorithm with mixed linear model approach. The reliability and efficiency of the analytical methods were verified through Monte Carlo simulations, suggesting that a population size of nearly 150 recombinant inbred lines (RILs had a reasonable resolution for the scenarios considered. Further, a GWAS was conducted with the above two-step strategy to investigate the additive, epistatic, and gene-environment associations between 701,867 SNPs and three important quality traits, gelatinization temperature, amylose content, and gel consistency, in a RIL population with 138 individuals derived from super-hybrid rice Xieyou9308 in two environments. Four significant SNPs were identified with additive, epistatic, and gene-environment interaction effects. Our study showed that the mixed linear model approach combining with the GPU-based GMDR algorithm is a feasible strategy for implementing GWAS to uncover genetic architecture of crop complex traits.

  14. Conditions in home and transplant soils have differential effects on the performance of diploid and allotetraploid anthericum species.

    Directory of Open Access Journals (Sweden)

    Lucie Černá

    Full Text Available Due to increased levels of heterozygosity, polyploids are expected to have a greater ability to adapt to different environments than their diploid ancestors. While this theoretical pattern has been suggested repeatedly, studies comparing adaptability to changing conditions in diploids and polyploids are rare. The aim of the study was to determine the importance of environmental conditions of origin as well as target conditions on performance of two Anthericum species, allotetraploid A. liliago and diploid A. ramosum and to explore whether the two species differ in the ability to adapt to these environmental conditions. Specifically, we performed a common garden experiment using soil from 6 localities within the species' natural range, and we simulated the forest and open environments in which they might occur. We compared the performance of diploid A. ramosum and allotetraploid A. liliago originating from different locations in the different soils. The performance of the two species was not affected by simulated shading but differed strongly between the different target soils. Growth of the tetraploids was not affected by the origin of the plants. In contrast, diploids from the most nutrient poor soil performed best in the richest soil, indicating that diploids from deprived environments have an increased ability to acquire nutrients when available. They are thus able to profit from transfer to novel nutrient rich environments. Therefore, the results of the study did not support the general expectation that the polyploids should have a greater ability than the diploids to adapt to a wide range of conditions. In contrast, the results are in line with the observation that diploids occupy a wider range of environments than the allotetraploids in our system.

  15. Conditions in home and transplant soils have differential effects on the performance of diploid and allotetraploid anthericum species.

    Science.gov (United States)

    Černá, Lucie; Münzbergová, Zuzana

    2015-01-01

    Due to increased levels of heterozygosity, polyploids are expected to have a greater ability to adapt to different environments than their diploid ancestors. While this theoretical pattern has been suggested repeatedly, studies comparing adaptability to changing conditions in diploids and polyploids are rare. The aim of the study was to determine the importance of environmental conditions of origin as well as target conditions on performance of two Anthericum species, allotetraploid A. liliago and diploid A. ramosum and to explore whether the two species differ in the ability to adapt to these environmental conditions. Specifically, we performed a common garden experiment using soil from 6 localities within the species' natural range, and we simulated the forest and open environments in which they might occur. We compared the performance of diploid A. ramosum and allotetraploid A. liliago originating from different locations in the different soils. The performance of the two species was not affected by simulated shading but differed strongly between the different target soils. Growth of the tetraploids was not affected by the origin of the plants. In contrast, diploids from the most nutrient poor soil performed best in the richest soil, indicating that diploids from deprived environments have an increased ability to acquire nutrients when available. They are thus able to profit from transfer to novel nutrient rich environments. Therefore, the results of the study did not support the general expectation that the polyploids should have a greater ability than the diploids to adapt to a wide range of conditions. In contrast, the results are in line with the observation that diploids occupy a wider range of environments than the allotetraploids in our system.

  16. Linkage mapping in tetraploid willows: segregation of molecular markers and estimation of linkage phases support an allotetraploid structure for Salix alba x Salix fragilis interspecific hybrids.

    Science.gov (United States)

    Barcaccia, G; Meneghetti, S; Albertini, E; Triest, L; Lucchin, M

    2003-02-01

    Salix alba-Salix fragilis complex includes closely related dioecious polyploid species, which are obligate outcrossers. Natural populations of these willows and their hybrids are represented by a mixture of highly heterozygous genotypes sharing a common gene pool. Since nothing is known about their genomic constitution, tetraploidy (2n=4x=76) in willow species makes basic and applied genetic studies difficult. We have used a two-way pseudotestcross strategy and single-dose markers (SDMs) to construct the first linkage maps for both pistillate and staminate willows. A total of 242 amplified fragment length polymorphisms (AFLPs) and 50 selective amplifications of microsatellite polymorphic loci (SAMPL) markers, which showed 1:1 segregation in the F(1) mapping populations, were used in linkage analysis. In S. alba, 73 maternal and 48 paternal SDMs were mapped to 19 and 16 linkage groups covering 708 and 339 cM, respectively. In S. fragilis, 13 maternal and 33 paternal SDMs were mapped in six and 14 linkage groups covering 98 and 321 cM, respectively. For most cosegregation groups, a comparable number of markers linked in coupling and repulsion was identified. This finding suggests that most of chromosomes pair preferentially as occurs in allotetraploid species exhibiting disomic inheritance. The detection of 10 pairs of marker alleles from single parents showing codominant inheritance strengthens this hypothesis. The fact that, of the 1122 marker loci identified in the two male and female parents, the vast majority (77.5%) were polymorphic and as few as 22.5% were shared between parental species highlight that S. alba and S. fragilis genotypes are differentiated. The highly difference between S. alba- and S. fragilis-specific markers found in both parental combinations (on average, 65.3 vs 34.7%, respectively) supports the (phylogenetic) hypothesis that S. fragilis is derived from S. alba-like progenitors.

  17. Methodology Study of Preparing High Quality Rice Genomic DNA for Shotgun Sequencing%Shotgun法测序制备高纯度水滔基因组DNA的方法探讨

    Institute of Scientific and Technical Information of China (English)

    杨继良; 王辉; 王庆华; 李军; 刘斌; 金德敏; 王斌

    2003-01-01

    在用散弹(shotgun)法测定水稻(Oryza sativa L.ssp. indica)基因组全序列的过程中,叶绿体和线粒体DNA的污染问题非常严峻.应用脉冲场电泳(PFGE)技术对水稻基因组DNA进行纯化,结果表明它能够有效去除叶绿体和线粒体DNA,使其污染率从3%降低到0.2%. 同时,比较了水稻绿苗和黄化苗的DNA得率,以及HB法和NIB法制备大分子质量(HMW)DNA的异同.最后提出一套制备水稻基因组DNA的方法,包括黄化苗培养; 细胞核的分离、包埋和裂解;脉冲场电泳纯化、回收聚集在低熔点(LMP)胶中的水稻HMW DNA.用该方法所得的水稻基因组DNA,纯度高(无叶绿体和线粒体DNA污染)、基因组完整(机械剪切和降解少)、回收率高(操作过程中DNA损失少). 另外,首次报道在融化的低熔点(LMP)胶中对水稻HMW DNA于38℃进行超声波处理,能够获得用于shotgun文库和梯度文库构建所需要的各种DNA片段(1.5~3 kb, 3~12 kb),并且效果优于在TE中进行操作.%The contamination of chloroplast and mitochondrial DNAs was a serious problem during genome sequencing of rice (Oryza sativa L.ssp.indica) by whole-genome shotgun strategy. Pulse field gel electrophoresis (PFGE) was utilized to purify rice genomic DNA, which could efficiently remove the organelles (chloroplast and mitochondrion) DNA and reduce the contamination ratio from 3% to 0.2%. At the same time, the rice DNAs yielded from yellow seedlings and green seedlings were compared, and the differences between HB method and NIB method in high molecular weight(HMW) DNA isolation were also studied. Finally, a set of methods for obtaining the whole and highly pure rice genomic DNAs were proposed, which included culturing rice yellow seedling; isolating, embedding and lysising rice nuclei, purifying and recovering rice genomic DNAs in low melting point (LMP) agarose gel by PFGE. Ultrasonic treatment on HMW DNAs in the melting LMP gel at 38℃ was reported at first time

  18. Rice mutant resources for gene discovery

    NARCIS (Netherlands)

    Hirochika, H.; Guiderdoni, E.; An, G.; Hsing, Y.I.; Eun, M.Y.; Han, C.D.; Upadhyaya, N.; Ramachandran, S.; Zhang, Q.F.; Pereira, A.B.; Sundaresan, V.; Leung, H.

    2004-01-01

    With the completion of genomic sequencing of rice, rice has been firmly established as a model organism for both basic and applied research. The next challenge is to uncover the functions of genes predicted by sequence analysis. Considering the amount of effort and the diversity of disciplines requi

  19. Cloning and Analysis of a cDNA Encoding psbL and psbJ Gene in Rice Chloroplast Genome%水稻叶绿体基因组中一个编码psbL 和psbJ基因cDNA的克隆与分析

    Institute of Scientific and Technical Information of China (English)

    顾克余; 罗林广; 苏昌潮; 翟虎渠

    2001-01-01

    A 505 bp cDNA was cloned from the leaves of rice (Oryza sativaL.) Shanyou 63 combination. DNA sequence analysis showed that it is a part of rice chloroplast genome. Its homology comparison with those known in GenBank found that it encodes 38 amino acid peptide deduced from psbL gene and 40 amino acid peptide deduced from psbJ gene in rice chloroplast PSⅡ. Northern hybridization showed that the cDNA was differentially displayed in hybrid F1 and its parental lines.

  20. Analysis of intron sequence variability of the conservative HMG-box of Sox9 genes in allotetraploids and their original parents

    Institute of Scientific and Technical Information of China (English)

    Liu Jifang; Liu Shaojun; Tao Min; Li Wei; Liu Yun

    2007-01-01

    The Sox genes of allotetraploids and their original maternal red crucian carp ( Carassius caassius red var. ) and original paternal common carp ( Cyprinus carpio L. ) were detected by PCR with the designed primers based on the conserved HMG-box sequence in different species. Sequencing of Sox genes indicated that two Sox9 genes (Atsox9a and Atsox9b ) existed in allotetraploids, while only one Sox9 gene existed in red crucian carp ( Rcsox9a ) and common carp ( Ccsox9b ). All of the four Sox9 genes contained an intron in the HMG-box, with the sizes of 413 bp, 703 bp, 401 bp and 714 bp, respectively. Moreover, the introns obeyed the rule of "GT-AG". A high similarity was observed between introns of Atsox9a and Rcsox9a (94.4 % ), Atsox9b and Ccsox9b (97.8 % ). Interestingly, the deduced amino acid sequences of their corresponding exons all shared 100 % identity. Thus, introns of the HMG-domain of Sox9s in allotetraploids and their original parents have not only the length polymorphism but also intron variability. Our results provide significant molecular evidence for the origin and evolution of allotetraploids.

  1. The Puzzle of Rice Domestication

    Institute of Scientific and Technical Information of China (English)

    Tao Sang; Song Ge

    2007-01-01

    The origin of cultivated rice has puzzled plant biologists for decades. This is due, at least in part, to the complex evolutionary dynamics in rice cultivars and wild progenitors, particularly rapid adaptive differentiation and continuous gene flow within and between cultivated and wild rice. The long-standing controversy over single versus multiple and annual versus perennial origins of cultivated rice has been brought into shaper focus with the rapid accumulation of genetic and phylogenetic data. Molecular phylogenetic analyses revealed ancient genomic differentiation between rice cultivars, suggesting that they were domesticated from divergent wild populations. However, the recently cloned domestication gene sh4, responsible for the reduction of grain shattering from wild to cultivated rice, seems to have originated only once. Herein, we propose two models to reconcile apparently conflicting evidence regarding rice domestication. The snow-balling model considers a single origin of cultivated rice. In this model, a core of critical domestication alleles was fixed in the founding cultivar and then acted to increase the genetic diversity of cultivars through hybridization with wild populations. The combination model considers multiple origins of cultivated rice. In this model, initial cultivars were domesticated from divergent wild populations and fixed different sets of domestication alleles. Subsequent crosses among these semi-domesticated cultivars resulted in the fixation of a similar set of critical domestication alleles in the contemporary cultivars. In both models, introgression has played an important role in rice domestication. Recent and future introgression of beneficial genes from the wild gene pool through conventional and molecular breeding programs can be viewed as the continuation of domestication.

  2. Translational Genomics for the Improvement of Switchgrass

    Energy Technology Data Exchange (ETDEWEB)

    Carpita, Nicholas; McCann, Maureen

    2014-05-07

    Our objectives were to apply bioinformatics and high throughput sequencing technologies to identify and classify the genes involved in cell wall formation in maize and switchgrass. Targets for genetic modification were to be identified and cell wall materials isolated and assayed for enhanced performance in bioprocessing. We annotated and assembled over 750 maize genes into gene families predicted to function in cell wall biogenesis. Comparative genomics of maize, rice, and Arabidopsis sequences revealed differences in gene family structure. In addition, differences in expression between gene family members of Arabidopsis, maize and rice underscored the need for a grass-specific genetic model for functional analyses. A forward screen of mature leaves of field-grown maize lines by near-infrared spectroscopy yielded several dozen lines with heritable spectroscopic phenotypes, several of which near-infrared (nir) mutants had altered carbohydrate-lignin compositions. Our contributions to the maize genome sequencing effort built on knowledge of copy number variation showing that uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. For example, although about 25% of all duplicated genes remain genome-wide, all of the cellulose synthase (CesA) homologs were retained. We showed that guaiacyl and syringyl lignin in lignocellulosic cell-wall materials from stems demonstrate a two-fold natural variation in content across a population of maize Intermated B73 x Mo7 (IBM) recombinant inbred lines, a maize Association Panel of 282 inbreds and landraces, and three populations of the maize Nested Association Mapping (NAM) recombinant inbred lines grown in three years. We then defined quantitative trait loci (QTL) for stem lignin content measured using pyrolysis molecular-beam mass spectrometry, and glucose and xylose yield measured using an enzymatic hydrolysis assay. Among five multi-year QTL for lignin

  3. Induced resistance in rice against insects.

    Science.gov (United States)

    Karban, R; Chen, Y

    2007-08-01

    Vaccinations are the mainstay of western preventive medicine, and they have been used to protect some crops against disease and insect pests. We consider rice as a model for protection using induced resistance since it is one of the most important staple crops and there have been significant new developments in: cross-resistance among rice insects, chemical pathways involved in induced resistance, sequencing the rice genome and expression of genes conferring resistance against rice insect pests. Insect attack has been found to cause lesions that kill planthopper eggs and early stages of gall midges. Damaged plants released volatiles that made them less likely to be chosen by planthoppers and more attractive to parasitoids. Chemical elicitors have been developed for dicotyledonous plants and these can induce resistance in rice, although rice does not fit models developed to explain signalling in dicots. For example, salicylic acid did not increase in rice after infection by pathogens and did not appear to be the mobile signal for induced resistance against pathogens although it was involved in induced responses to phloem-feeding insects. Jasmonic acid acted as a signal in some induced responses to pathogens as well as chewing insects. Many of the genes associated with induced resistance in rice have recently been mapped, and techniques are being developed to incorporate them into the genome of cultivated varieties. Attempts to control insect pests of rice will affect interactions with pathogens, predators and parasites, and other organisms in this agroecosystem.

  4. Information Commons for Rice (IC4R).

    Science.gov (United States)

    Hao, Lili; Zhang, Huiyong; Zhang, Zhang; Hu, Songnian; Xue, Yu

    2016-01-04

    Rice is the most important staple food for a large part of the world's human population and also a key model organism for plant research. Here, we present Information Commons for Rice (IC4R; http://ic4r.org), a rice knowledgebase featuring adoption of an extensible and sustainable architecture that integrates multiple omics data through community-contributed modules. Each module is developed and maintained by different committed groups, deals with data collection, processing and visualization, and delivers data on-demand via web services. In the current version, IC4R incorporates a variety of rice data through multiple committed modules, including genome-wide expression profiles derived entirely from RNA-Seq data, resequencing-based genomic variations obtained from re-sequencing data of thousands of rice varieties, plant homologous genes covering multiple diverse plant species, post-translational modifications, rice-related literatures and gene annotations contributed by the rice research community. Unlike extant related databases, IC4R is designed for scalability and sustainability and thus also features collaborative integration of rice data and low costs for database update and maintenance. Future directions of IC4R include incorporation of other omics data and association of multiple omics data with agronomically important traits, dedicating to build IC4R into a valuable knowledgebase for both basic and translational researches in rice. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Rice epigenomics and epigenetics: challenges and opportunities.

    Science.gov (United States)

    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. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Genome-wide analysis of autophagy-associated genes in foxtail millet (Setaria italica L.) and characterization of the function of SiATG8a in conferring tolerance to nitrogen starvation in rice.

    Science.gov (United States)

    Li, Weiwei; Chen, Ming; Wang, Erhui; Hu, Liqin; Hawkesford, Malcolm J; Zhong, Li; Chen, Zhu; Xu, Zhaoshi; Li, Liancheng; Zhou, Yongbin; Guo, Changhong; Ma, Youzhi

    2016-10-12

    Autophagy is a cellular degradation process that is highly evolutionarily-conserved in yeast, plants, and animals. In plants, autophagy plays important roles in regulating intracellular degradation and recycling of amino acids in response to nutrient starvation, senescence, and other environmental stresses. Foxtail millet (Setaria italica) has strong resistance to stresses and has been proposed as an ideal material for use in the study of the physiological mechanisms of abiotic stress tolerance in plants. Although the genome sequence of foxtail millet (Setaria italica) is available, the characteristics and functions of abiotic stress-related genes remain largely unknown for this species. A total of 37 putative ATG (autophagy-associated genes) genes in the foxtail millet genome were identified. Gene duplication analysis revealed that both segmental and tandem duplication events have played significant roles in the expansion of the ATG gene family in foxtail millet. Comparative synteny mapping between the genomes of foxtail millet and rice suggested that the ATG genes in both species have common ancestors, as their ATG genes were primarily located in similar syntenic regions. Gene expression analysis revealed the induced expression of 31 SiATG genes by one or more phytohormone treatments, 26 SiATG genes by drought, salt and cold, 24 SiATG genes by darkness and 25 SiATG genes by nitrogen starvation. Results of qRT-PCR showing that among 37 SiATG genes, the expression level of SiATG8a was the highest after nitrogen starvation treatment 24 h, suggesting its potential role in tolerance to nutrient starvation. Moreover, the heterologous expression of SiATG8a in rice improved nitrogen starvation tolerance. Compared to wild type rice, the transgenic rice performed better and had higher aboveground total nitrogen content when the plants were grown under nitrogen starvation conditions. Our results deepen understanding about the characteristics and functions of ATG genes in

  7. 细胞质雄性不育水稻线粒体基因组的RFLP分析%RFLP Analysis for Mitochondrial Genome of CMS-Rice

    Institute of Scientific and Technical Information of China (English)

    黄威; 汪莉; 易平; 谭学林; 张雪梅; 张再君; 李阳生; 朱英国

    2006-01-01

    Restriction fragment length polymorphism (RFLP) was used to analyze mitochondrial (mt) genome of cytoplasmic male sterility (CMS) rice. Differences were observed among mitochondrial genomes of the sterile line (A) and maintain line (B) of nine types of CMS rice; Mitochondrial genomic differences were also detected between A and B in many functional gene regions. Even the materials with the same nucleic background have differences in their mtDNA. This provides molecular evidence for the cytoplasmic heterogeneity and the CMS mechanism research.%利用RFLP技术,比较研究了在农业生产上广泛应用的9种细胞质雄性不育体系的线粒体基因组,结果表明:1)9种水稻雄性不育细胞质的遗传相似性变化范围为0.615~1.000.所有配子体雄性不育细胞质的遗传相似性变化范围为0.643~1.000,其中QXA,DY1A和YM15A这3种细胞质的遗传相似性为1.000.所有孢子体雄性不育细胞质的遗传相似性为1.000:2)在配子体细胞质雄性不育水稻中,用3个探针(atpA,atp9+nad6,cox2)与2种内切酶(HindⅢ,BamH Ⅰ)的组合未发现不育系与保持系之间的多态性,但在探针atp6,cob,和nad2的杂交带型中找到了不育系和保持系之间的一些差异.YTA和YTB在5个探针-内切酶组合(atp6/HindⅢ,cob/HindⅢ,atp6/BamH Ⅰ,cob/BamH Ⅰ,nad2/BamH Ⅰ)中存在差异.3种细胞质(QX,SJ,DY1)的不育系和保持系之间的差异是相同的,都出现在atp6/HindⅢ,atp6/BamH Ⅰ,cob/BamHⅠ等3个组合中.YM15A和YM15B在4个组合(atp6/HindⅢ,atp6/BamH Ⅰ,cob/BamH Ⅰ,nad2/BamH Ⅰ)中存在差异.LYA和LYB的差异出现在cob/HindⅢ,cob/BamH Ⅰ,nad2/BamH Ⅰ这3个组合中;3)在孢子体细胞质雄性不育水稻中,所有不育系的带型是一样的,所有保持系的带型也一样.不育系和保持系的差异出现在atp6/HindⅢ,cob/HindⅢ,atp6/EcoRⅠ,cob/EcoR Ⅰ,cox1/EcoR Ⅰ,atp6/BamH Ⅰ,cob/BamH Ⅰ,cox1/BamH Ⅰ,cox2/BamH Ⅰ等9个组合中.这些结

  8. The role of momilactones in rice allelopathy.

    Science.gov (United States)

    Kato-Noguchi, Hisashi; Peters, Reuben J

    2013-02-01

    Large field screening programs and laboratory experiments in many countries have indicated that rice is allelopathic and releases allelochemical(s) into its environment. A number of compounds, such as phenolic acids, fatty acids, phenylalkanoic acids, hydroxamic acids, terpenes, and indoles, have been identified as potential rice allelochemicals. However, the studies reviewed here demonstrate that the labdane-related diterpenoid momilactones are the most important, with momilactone B playing a particularly critical role. Rice plants secrete momilactone B from their roots into the neighboring environments over their entire life cycle at phytotoxic levels, and momilactone B seems to account for the majority of the observed rice allelopathy. In addition, genetic studies have shown that selective removal of the momilactones only from the complex mixture found in rice root exudates significantly reduces allelopathy, demonstrating that these serve as allelochemicals, the importance of which is reflected in the presence of a dedicated momilactone biosynthetic gene cluster in the rice genome.

  9. High-density Linkage Map of Cultivated Allotetraploid Cotton Based on SSR, TRAP, SRAP and AFLP Markers

    Institute of Scientific and Technical Information of China (English)

    Jiwen Yu; Shuxun Yu; Cairui Lu; Wu Wang; Shuli Fan; Meizhen Song; Zhongxu Lin; Xianlong Zhang; Jinfa Zhang

    2007-01-01

    A high-density linkage map was constructed for an F2 population derived from an interspecific cross of cultivated allotetraploid species between Gossyplum hirsutum L. and G. barbadense L. A total of 186 F2 individuals from the interspecific cross of "CRI 36 × Hai 7124" were genotyped at 1 252 polymorphic loci including a novel marker system,target region amplification polymorphism (TRAP). The map consists of 1 097 markers, including 697 simple sequence repeats (SSRs), 171 TRAPs, 129 sequence-related amplified polymorphisms, 98 amplified fragment length polymorphisms, and two morphological markers, and spanned 4 536.7 cM with an average genetic distance of 4.1 cM per marker. Using 45 duplicated SSR loci among chromosomes, 11 of the 13 pairs of homologous chromosomes were identified in tetraplold cotton. This map will provide an essential resource for high resolution mapping of quantitative trait loci and molecular breeding in cotton.

  10. [Major domestication traits in Asian rice].

    Science.gov (United States)

    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.

  11. 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

    Directory of Open Access Journals (Sweden)

    Maria Camila Rebolledo

    2016-09-01

    Full Text Available 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-values ≤ 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

  12. A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes

    Directory of Open Access Journals (Sweden)

    Lin Ye

    2008-06-01

    Full Text Available Abstract Background Xanthomonas oryzae pv. oryzae (Xoo and X. oryzae pv. oryzicola (Xoc are bacterial pathogens of the worldwide staple and grass model, rice. Xoo and Xoc are closely related but Xoo invades rice vascular tissue to cause bacterial leaf blight, a serious disease of rice in many parts of the world, and Xoc colonizes the mesophyll parenchyma to cause bacterial leaf streak, a disease of emerging importance. Both pathogens depend on hrp genes for type III secretion to infect their host. We constructed a 50–70 mer oligonucleotide microarray based on available genome data for Xoo and Xoc and compared gene expression in Xoo strains PXO99A and Xoc strain BLS256 grown in the rich medium PSB vs. XOM2, a minimal medium previously reported to induce hrp genes in Xoo strain T7174. Results Three biological replicates of the microarray experiment to compare global gene expression in representative strains of Xoo and Xoc grown in PSB vs. XOM2 were carried out. The non-specific error rate and the correlation coefficients across biological replicates and among duplicate spots revealed that the microarray data were robust. 247 genes of Xoo and 39 genes of Xoc were differentially expressed in the two media with a false discovery rate of 5% and with a minimum fold-change of 1.75. Semi-quantitative-RT-PCR assays confirmed differential expression of each of 16 genes each for Xoo and Xoc selected for validation. The differentially expressed genes represent 17 functional categories. Conclusion We describe here the construction and validation of a two-genome microarray for the two pathovars of X. oryzae. Microarray analysis revealed that using representative strains, a greater number of Xoo genes than Xoc genes are differentially expressed in XOM2 relative to PSB, and that these include hrp genes and other genes important in interactions with rice. An exception was the rax genes, which are required for production of the host resistance elicitor AvrXa21

  13. 转青鱼生长激素基因异源四倍体鲫鲤%Black Carp GH Gene Transgenic Allotetraploid Hybrids of Carassius auratus red var.(♀) × Cyprinus carpio (♂)

    Institute of Scientific and Technical Information of China (English)

    冯浩; 傅永明; 骆剑; 吴慧; 刘筠; 刘少军

    2011-01-01

    The ecological risk is the “bottleneck” for commercialization of transgenic fish. The sterile transgenic triploid fish derived from hydrating the transgenic tetraploid fish and transgenic diploid fish is one of the keys to solve this problem.The “all fish” gene construct (pbcAbcGHc) containing Black Carp B-actin gene promoter and cDNA of growth hormone (GH) gene from the same species was introduced into the fertilized eggs of the allotetroploid fish through microinjection. The contrast cultivation results show that the weight and body length of PO of the transgenic allotetraploid fish of 150 days were much larger than those of the controls. PCR assay was applied among 60 transgenic allotetraploid fish of 150 days and the integration ratio of the exogenous transplant gene in the genome of the caudal fin is 90%. The transplant gene could be detected in 13 of 20 samples from the sperm of the male transgenic tetraploid fish.The RT-PCR result demonstrates that the transcription of exogenous GH gene could be found in the muscle, liver,kidney and oval of the biggest transgenic allotetraploid fish. This study has developed PO of the Black Carp GH gene transgenic tetraploid fish with outstanding growth rate, which made the solid foundation for the pure line establishment of the transgenic tetraploid fish and for developing the sterile transgenic triploid fish.%生态安全性是转基因鱼走向市场的瓶颈,通过转基因四倍体鱼同转基因二倍体鱼杂交获得不育的转基因三倍体鱼是解决该问题的有效途径之一.本研究构建了青鱼β-actin基因启动子和青鱼生长激素(GH)基因精确连接的"金鱼"基因pbcAbcGHc;并采用显微注射法将pbcAbcGHc 导入异源四倍体鲫鲤受精卵.对照养殖结果表明,150日龄的转基因异源四倍体鲫鲤原代(P0)的体重及体长明显大于对照组.选择60尾P0代转基因异源四倍体鲫鲤,采用PCR方法检测出外源青鱼GH基因在P0代转基因四倍体尾

  14. Characterization of paralogous protein families in rice

    Directory of Open Access Journals (Sweden)

    Zhu Wei

    2008-02-01

    Full Text Available Abstract Background High gene numbers in plant genomes reflect polyploidy and major gene duplication events. Oryza sativa, cultivated rice, is a diploid monocotyledonous species with a ~390 Mb genome that has undergone segmental duplication of a substantial portion of its genome. This, coupled with other genetic events such as tandem duplications, has resulted in a substantial number of its genes, and resulting proteins, occurring in paralogous families. Results Using a computational pipeline that utilizes Pfam and novel protein domains, we characterized paralogous families in rice and compared these with paralogous families in the model dicotyledonous diploid species, Arabidopsis thaliana. Arabidopsis, which has undergone genome duplication as well, has a substantially smaller genome (~120 Mb and gene complement compared to rice. Overall, 53% and 68% of the non-transposable element-related rice and Arabidopsis proteins could be classified into paralogous protein families, respectively. Singleton and paralogous family genes differed substantially in their likelihood of encoding a protein of known or putative function; 26% and 66% of singleton genes compared to 73% and 96% of the paralogous family genes encode a known or putative protein in rice and Arabidopsis, respectively. Furthermore, a major skew in the distribution of specific gene function was observed; a total of 17 Gene Ontology categories in both rice and Arabidopsis were statistically significant in their differential distribution between paralogous family and singleton proteins. In contrast to mammalian organisms, we found that duplicated genes in rice and Arabidopsis tend to have more alternative splice forms. Using data from Massively Parallel Signature Sequencing, we show that a significant portion of the duplicated genes in rice show divergent expression although a correlation between sequence divergence and correlation of expression could be seen in very young genes. Conclusion

  15. Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice

    Directory of Open Access Journals (Sweden)

    Panaud Olivier

    2008-12-01

    Full Text Available Abstract 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 si

  16. Stamen specification and anther development in rice

    Institute of Scientific and Technical Information of China (English)

    ZHANG DaBing; WILSON Zoe A

    2009-01-01

    Male reproductive development is a complex biological process which includes the formation of the stamen with differentiated anther tissues, in which microspores/pollens are generated, then anther dehiscence and subsequently pollination. Stamen specification and anther development involve a number of extraordinary events such as meristem transition, cell division and differentiation, cell to cell communication, etc., which need the cooperative interaction of sporophytic and gametophytic genes. The advent of various tools for rice functional gene identification, such as complete genome sequence, genome-wide microarrays, collections of mutants, has greatly facilitated our understanding of mechanisms of rice stamen specification and anther development. Male sterile lines are critical for hybrid rice breeding, therefore understanding these processes will not only contribute greatly to the basic knowledge of crop developmental biology, but also to the development of new varieties for hybrid rice breeding in the future.

  17. Genome-wide expression analysis of rice aquaporin genes and development of a functional gene network mediated by aquaporin expression in roots.

    Science.gov (United States)

    Nguyen, Minh Xuan; Moon, Sunok; Jung, Ki-Hong

    2013-10-01

    The world population continually faces challenges of water scarcity for agriculture. A common strategy called water-balance control has evolved to adapt plant growth to these challenges. Aquaporins are a family of integral membrane proteins that play a central role in water-balance control. In this study, we identified 34 members of the rice aquaporin gene family, adding a novel member to the previous list. A combination of phylogenetic tree and anatomical meta-expression profiling data consisting of 983 Affymetrix arrays and 209 Agilent 44 K arrays was used to identify tissue-preferred aquaporin genes and evaluate functional redundancy among aquaporin family members. Eight aquaporins showed root-preferred expression in the vegetative growth stage, while 4 showed leaf/shoot-preferred expression. Integrating stress-induced expression patterns into phylogenetic tree and semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR) analyses revealed that 3 rice aquaporin genes were markedly downregulated and 4 were upregulated by water deficiency in the root, suggesting that these candidate genes are key regulators of water uptake from the soil. Finally, we constructed a functional network of genes mediated by water stress and refined the network by confirming the differential expression using RT-PCR and real-time PCR. Our data will be useful to elucidate the molecular mechanism of water-balance control in rice root.

  18. Introduction of cryIB-cryIAa Hybrid Gene Into Rice (Oryza sativa Genom cv. Rojolele using Agrobacterium-Mediated Transformation

    Directory of Open Access Journals (Sweden)

    SYAMSIDAH RAHMAWATI

    2006-03-01

    Full Text Available Rojolele is one of Indonesian local variety from Javanica group that susceptible to yellow stem borer (Scirpophaga incertulas. Previous study showed that Rojolele can be cultured and regenerated in vitro. Two cry genes, cryIB-cryIAa were fused and introduced into rice cv. Rojolele in an attempt to improve resistance and to obtain durable resistance rice against the yellow stem borer. Two-week old embryogenic calli of Rojolele rice were inoculated with Agrobacterium tumefaciens harbored with binary vector pCAMBIA 1301, 1303, or 1304 carrying cryIB-cryIAa hybrid gene, hygromycin resistant gene (hpt, and -glucuronidase (gus gene interrupted with an intron. The transformed calli were selected gradually on medium containing hygromycin (50, 100 mg/l and regenerated on medium containing 0.5 mg/l IAA and 0.3 mg/l BAP. GUS activity in infected calli was detected by histochemical assay 3 days after inoculation. The highest (100% transformation efficiency were obtained from calli transformed with pCAMBIA 1303 and 1304. Thirty four out of 77 transformed shoots were tested positive for the cryIB-cryIAa gene using PCR analysis. These shoots were grown in the soil to maturity and to collect the seeds. PCR analysis of the T1 progeny revealed that two out of six lines tested showed a Mendelian segregation pattern. These two lines were also potentially resistant to yellow stem borer based on bioassay in planta.

  19. Investigation of possible horizontal gene transfer from transgenic rice to soil microorganisms in paddy rice field.

    Science.gov (United States)

    Kim, Sung Eun; Moon, Jae Sun; Kim, Jung Kyu; Choi, Won Sik; Lee, Sang Han; Kim, Sung Uk

    2010-01-01

    In order to monitor the possibility of horizontal gene transfer between transgenic rice and microorganisms in paddy rice field, the gene flow from bifunctional fusion (TPSP) rice containing trehalose-6-phosphate synthase and phosphatase to microorganisms in soils was investigated. The soil samples collected every month from the paddy rice field during June, 2004 to March, 2006 were investigated by multiplex PCR, Southern hybridization, and amplified fragment length polymorphism (AFLP). The TPSP gene from soil genomics DNAs was not detected by PCR. Soil genomic DNAs were not shown its homologies on the Southern blotting data, indicating that gene-transfer did not occur during the last two years in paddy rice field. In addition, the AFLP band patterns produced by both soil genomic DNAs extracted from transgenic and non-transgenic rice field appeared similar to each other when analyzed by NTSYSpc program. Thus, these data suggest that transgenic rice does not give a significant impact on the communities of soil microorganisms although long-term observation may be needed.

  20. Toward closing rice telomere gaps: mapping and sequence characterization of rice subtelomere regions.

    NARCIS (Netherlands)

    Yang, T.J.; Yu, Y.; Chang, S.B.; Jong, de J.H.S.G.M.; Oh, C.S.; Ahn, S.N.; Fang, E.; Wing, R.A.

    2005-01-01

    Despite the collective efforts of the international community to sequence the complete rice genome, telomeric regions of most chromosome arms remain uncharacterized. In this report we present sequence data from subtelomere regions obtained by analyzing telomeric clones from two 8.8 × genome equivale

  1. The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species.

    Science.gov (United States)

    Wing, Rod A; Ammiraju, Jetty S S; Luo, Meizhong; Kim, Hyeran; Yu, Yeisoo; Kudrna, Dave; Goicoechea, Jose L; Wang, Wenming; Nelson, Will; Rao, Kiran; Brar, Darshan; Mackill, Dave J; Han, Bin; Soderlund, Cari; Stein, Lincoln; SanMiguel, Phillip; Jackson, Scott

    2005-09-01

    The wild species of the genus Oryza offer enormous potential to make a significant impact on agricultural productivity of the cultivated rice species Oryza sativa and Oryza glaberrima. To unlock the genetic potential of wild rice we have initiated a project entitled the 'Oryza Map Alignment Project' (OMAP) with the ultimate goal of constructing and aligning BAC/STC based physical maps of 11 wild and one cultivated rice species to the International Rice Genome Sequencing Project's finished reference genome--O. sativa ssp. japonica c. v. Nipponbare. The 11 wild rice species comprise nine different genome types and include six diploid genomes (AA, BB, CC, EE, FF and GG) and four tetrapliod genomes (BBCC, CCDD, HHKK and HHJJ) with broad geographical distribution and ecological adaptation. In this paper we describe our strategy to construct robust physical maps of all 12 rice species with an emphasis on the AA diploid O. nivara--thought to be the progenitor of modern cultivated rice.

  2. Genome-Wide Analysis of the AP2/ERF Gene Family in Physic Nut and Overexpression of the JcERF011 Gene in Rice Increased Its Sensitivity to Salinity Stress.

    Science.gov (United States)

    Tang, Yuehui; Qin, Shanshan; Guo, Yali; Chen, Yanbo; Wu, Pingzhi; Chen, Yaping; Li, Meiru; Jiang, Huawu; Wu, Guojiang

    2016-01-01

    The AP2/ERF transcription factors play crucial roles in plant growth, development and responses to biotic and abiotic stresses. A total of 119 AP2/ERF genes (JcAP2/ERFs) have been identified in the physic nut genome; they include 16 AP2, 4 RAV, 1 Soloist, and 98 ERF genes. Phylogenetic analysis indicated that physic nut AP2 genes could be divided into 3 subgroups, while ERF genes could be classed into 11 groups or 43 subgroups. The AP2/ERF genes are non-randomly distributed across the 11 linkage groups of the physic nut genome and retain many duplicates which arose from ancient duplication events. The expression patterns of several JcAP2/ERF duplicates in the physic nut showed differences among four tissues (root, stem, leaf, and seed), and 38 JcAP2/ERF genes responded to at least one abiotic stressor (drought, salinity, phosphate starvation, and nitrogen starvation) in leaves and/or roots according to analysis of digital gene expression tag data. The expression of JcERF011 was downregulated by salinity stress in physic nut roots. Overexpression of the JcERF011 gene in rice plants increased its sensitivity to salinity stress. The increased expression levels of several salt tolerance-related genes were impaired in the JcERF011-overexpressing plants under salinity stress.

  3. Origin, dispersal, cultivation and variation of rice.

    Science.gov (United States)

    Khush, G S

    1997-09-01

    There are two cultivated and twenty-one wild species of genus Oryza. O. sativa, the Asian cultivated rice is grown all over the world. The African cultivated rice, O. glaberrima is grown on a small scale in West Africa. The genus Oryza probably originated about 130 million years ago in Gondwanaland and different species got distributed into different continents with the breakup of Gondwanaland. The cultivated species originated from a common ancestor with AA genome. Perennial and annual ancestors of O. sativa are O. rufipogon and O. nivara and those of O. glaberrima are O. longistaminata, O. breviligulata and O. glaberrima probably domesticated in Niger river delta. Varieties of O. sativa are classified into six groups on the basis of genetic affinity. Widely known indica rices correspond to group I and japonicas to group VI. The so called javanica rices also belong to group VI and are designated as tropical japonicas in contrast to temperate japonicas grown in temperate climate. Indica and japonica rices had a polyphyletic origin. Indicas were probably domesticated in the foothills of Himalayas in Eastern India and japonicas somewhere in South China. The indica rices dispersed throughout the tropics and subtropics from India. The japonica rices moved northward from South China and became the temperate ecotype. They also moved southward to Southeast Asia and from there to West Africa and Brazil and became tropical ecotype. Rice is now grown between 55 degrees N and 36 degrees S latitudes. It is grown under diverse growing conditions such as irrigated, rainfed lowland, rainfed upland and floodprone ecosystems. Human selection and adaptation to diverse environments has resulted in numerous cultivars. It is estimated that about 120,000 varieties of rice exist in the world. After the establishment of International Rice Research Institute in 1960, rice varietal improvement was intensified and high yielding varieties were developed. These varieties are now planted to 70

  4. Comparison of four methods of DNA extraction from rice

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    @@ Polyphenols, teroens, and resins make it difficult to obtain high quality genomic DNA from rice. Four extraction methods were compared in our study, and CTAB precipitation was the most practical one.

  5. The genome of Chenopodium quinoa

    KAUST Repository

    Jarvis, David E.

    2017-02-08

    Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

  6. The genome of Chenopodium quinoa.

    Science.gov (United States)

    Jarvis, David E; Ho, Yung Shwen; Lightfoot, Damien J; Schmöckel, Sandra M; Li, Bo; Borm, Theo J A; Ohyanagi, Hajime; Mineta, Katsuhiko; Michell, Craig T; Saber, Noha; Kharbatia, Najeh M; Rupper, Ryan R; Sharp, Aaron R; Dally, Nadine; Boughton, Berin A; Woo, Yong H; Gao, Ge; Schijlen, Elio G W M; Guo, Xiujie; Momin, Afaque A; Negrão, Sónia; Al-Babili, Salim; Gehring, Christoph; Roessner, Ute; Jung, Christian; Murphy, Kevin; Arold, Stefan T; Gojobori, Takashi; Linden, C Gerard van der; van Loo, Eibertus N; Jellen, Eric N; Maughan, Peter J; Tester, Mark

    2017-02-16

    Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

  7. Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica.

    Science.gov (United States)

    Paape, Timothy; Hatakeyama, Masaomi; Shimizu-Inatsugi, Rie; Cereghetti, Teo; Onda, Yoshihiko; Kenta, Tanaka; Sese, Jun; Shimizu, Kentaro K

    2016-11-01

    Allopolyploidization combines parental genomes and often confers broader species distribution. However, little is known about parentally transmitted gene expression underlying quantitative traits following allopolyploidization because of the complexity of polyploid genomes. The allopolyploid species Arabidopsis kamchatica is a natural hybrid of the zinc hyperaccumulator Arabidopsis halleri and of the nonaccumulator Arabidopsis lyrata We found that A. kamchatica retained the ability to hyperaccumulate zinc from A. halleri and grows in soils with both low and high metal content. Hyperaccumulation of zinc by A. kamchatica was reduced to about half of A. halleri, but is 10-fold greater than A. lyrata Homeologs derived from A. halleri had significantly higher levels of expression of genes such as HEAVY METAL ATPASE4 (HMA4), METAL TRANSPORTER PROTEIN1 and other metal ion transporters than those derived from A. lyrata, which suggests cis-regulatory differences. A. kamchatica has on average about half the expression of these genes compared with A. halleri due to fixed heterozygosity inherent in allopolyploids. Zinc treatment significantly changed the ratios of expression of 1% of homeologous pairs, including genes putatively involved in metal homeostasis. Resequencing data showed a significant reduction in genetic diversity over a large genomic region (290 kb) surrounding the HMA4 locus derived from the A. halleri parent compared with the syntenic A. lyrata-derived region, which suggests different evolutionary histories. We also estimated that three A. halleri-derived HMA4 copies are present in A. kamchatica Our findings support a transcriptomic model in which environment-related transcriptional patterns of both parents are conserved but attenuated in the allopolyploids. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  8. Rice domestication: histories and mysteries.

    Science.gov (United States)

    Gross, Briana L

    2012-09-01

    Domesticated rice (Oryza sativa) is one of the world's most important food crops, culturally, nutritionally and economically (Khush 1997). Thus, it is no surprise that there is intense curiosity about its genetic and geographical origins, its response to selection under domestication, and the genetic structure of its wild relative, Oryza rufipogon. Studies of Oryza attempting to answer these questions have accompanied each stage of the development of molecular markers, starting with allozymes and continuing to genome sequencing. While many of these studies have been restricted to small sample sizes, in terms of either the number of markers used or the number and distribution of the accessions, costs are now low enough that researchers are including large numbers of molecular markers and accessions. How will these studies relate to previous findings and long-held assumptions about rice domestication and evolution? If the paper in this issue of Molecular Ecology (Huang et al. 2012) is any indication, there will be some considerable surprises in store. In this study, a geographically and genomically thorough sampling of O. rufipogon and O. sativa revealed two genetically distinct groups of wild rice and also indicated that only one of these groups appears to be related to domesticated rice. While this fits well with previous studies indicating that there are genetic subdivisions within O. rufipogon, it stands in contrast to previous findings that the two major varieties of O. sativa (indica and japonica) were domesticated from two (or more) subpopulations of wild rice.

  9. Impact of SNPs on Protein Phosphorylation Status in Rice (Oryza sativa L.

    Directory of Open Access Journals (Sweden)

    Shoukai Lin

    2016-11-01

    Full Text Available Single nucleotide polymorphisms (SNPs are widely used in functional genomics and genetics research work. The high-quality sequence of rice genome has provided a genome-wide SNP and proteome resource. However, the impact of SNPs on protein phosphorylation status in rice is not fully understood. In this paper, we firstly updated rice SNP resource based on the new rice genome Ver. 7.0, then systematically analyzed the potential impact of Non-synonymous SNPs (nsSNPs on the protein phosphorylation status. There were 3,897,312 SNPs in Ver. 7.0 rice genome, among which 9.9% was nsSNPs. Whilst, a total 2,508,261 phosphorylated sites were predicted in rice proteome. Interestingly, we observed that 150,197 (39.1% nsSNPs could influence protein phosphorylation status, among which 52.2% might induce changes of protein kinase (PK types for adjacent phosphorylation sites. We constructed a database, SNP_rice, to deposit the updated rice SNP resource and phosSNPs information. It was freely available to academic researchers at http://bioinformatics.fafu.edu.cn. As a case study, we detected five nsSNPs that potentially influenced heterotrimeric G proteins phosphorylation status in rice, indicating that genetic polymorphisms showed impact on the signal transduction by influencing the phosphorylation status of heterotrimeric G proteins. The results in this work could be a useful resource for future experimental identification and provide interesting information for better rice breeding.

  10. Genome-wide transcriptome analysis reveals that cadmium stress signaling controls the expression of genes in drought stress signal pathways in rice.

    Directory of Open Access Journals (Sweden)

    Youko Oono

    Full Text Available Plant growth is severely affected by toxic concentrations of the non-essential heavy metal cadmium (Cd. Comprehensive transcriptome analysis by RNA-Seq following cadmium exposure is required to further understand plant responses to Cd and facilitate future systems-based analyses of the underlying regulatory networks. In this study, rice plants were hydroponically treated with 50 µM Cd for 24 hours and ∼60,000 expressed transcripts, including transcripts that could not be characterized by microarray-based approaches, were evaluated. Upregulation of various ROS-scavenging enzymes, chelators and metal transporters demonstrated the appropriate expression profiles to Cd exposure. Gene Ontology enrichment analysis of the responsive transcripts indicated the upregulation of many drought stress-related genes under Cd exposure. Further investigation into the expression of drought stress marker genes such as DREB suggested that expression of genes in several drought stress signal pathways was activated under Cd exposure. Furthermore, qRT-PCR analyses of randomly selected Cd-responsive metal transporter transcripts under various metal ion stresses suggested that the expression of Cd-responsive transcripts might be easily affected by other ions. Our transcriptome analysis demonstrated a new transcriptional network linking Cd and drought stresses in rice. Considering our data and that Cd is a non-essential metal, the network underlying Cd stress responses and tolerance, which plants have developed to adapt to other stresses, could help to acclimate to Cd exposure. Our examination of this transcriptional network provides useful information for further studies of the molecular mechanisms of plant adaptation to Cd exposure and the improvement of tolerance in crop species.

  11. Transcriptome response to nitrogen starvation in rice

    Indian Academy of Sciences (India)

    Hongmei Cai; Yongen Lu; Weibo Xie; Tong Zhu; Xingming Lian

    2012-09-01

    Nitrogen is an essential mineral nutrient required for plant growth and development. Insufficient nitrogen (N) supply triggers extensive physiological and biochemical changes in plants. In this study, we used Affymetrix GeneChip rice genome arrays to analyse the dynamics of rice transcriptome under N starvation. N starvation induced or suppressed transcription of 3518 genes, representing 10.88% of the genome. These changes, mostly transient, affected various cellular metabolic pathways, including stress response, primary and secondary metabolism, molecular transport, regulatory process and organismal development. 462 or 13.1% transcripts for N starvation expressed similarly in root and shoot. Comparative analysis between rice and Arabidopsis identified 73 orthologous groups that responded to N starvation, demonstrated the existence of conserved N stress coupling mechanism among plants. Additional analysis of transcription profiles of microRNAs revealed differential expression of miR399 and miR530 under N starvation, suggesting their potential roles in plant nutrient homeostasis.

  12. Global Information Resources on Rice for Research and Development

    Institute of Scientific and Technical Information of China (English)

    Shri RAM; N.LAXMAN RAO

    2012-01-01

    Various issues concerning the progress of rice research are related to ambiguous germplasm identification,difficulty in tracing pedigree information,and lack of integration between genetic resources,characterization,breeding,evaluation and utilization data.These issues are the constraints in developing knowledge-intensive crop improvement programs.The rapid growth,development and the global spread of modern information and communication technology allow quick adoption in fundamental research.Thus,there is a need to provide an opportunity for the establishment of services which describe the rice information for better accessibility to information resources used by researchers to enhance the competitiveness.This work reviews some of available resources on rice bioinformatics and their roles in elucidating and propagating biological and genomic information in rice research.These reviews will also enable stakeholders to understand and adopt the change in research and development and share knowledge with the global community of agricultural scientists.The establishment like International Rice Information System,Rice Genome Research Project and Integrated Rice Genome Explorer are major initiatives for the improvement of rice.Creation of databases for comparative studies of rice and other cereals are major steps in further improvement of genetic compositions.This paper will also highlight some of the initiatives and organizations working in the field of rice improvement and explore the availability of the various web resources for the purpose of research and development of rice.We are developing a meta web server for integration of online resources such as databases,web servers and journals in the area of bioinformatics.This integrated platform,with acronym /BIRA,is available online at http://ibiranet.in.The resources reviewed here are the excerpts from the resources integrated in /BIRA.

  13. Draft Genome Sequence of Bacillus amyloliquefaciens EBL11, a New Strain of Plant Growth-Promoting Bacterium Isolated from Rice Rhizosphere

    Science.gov (United States)

    Wang, Yinghuan; Greenfield, Paul; Jin, Decai

    2014-01-01

    Bacillus amyloliquefaciens strain EBL11 is a bacterium that can promote plant growth by inhibiting the growth of fungi on plant surfaces and providing nutrients as a nonchemical biofertilizer. The estimated genome of this strain is 4.05 Mb in size and harbors 3,683 coding genes (CDSs). PMID:25059875

  14. Establishment of a Gene Expression System in Rice Chloroplast and Obtainment of PPT-Resistant Rice Plants

    Institute of Scientific and Technical Information of China (English)

    LI Yi-nü; SUN Bing-yao; SU Ning; MENG Xiang-xun; ZHANG Zhi-fang; SHEN Gui-fang

    2009-01-01

    In contrast to the situation of random integration of foreign genes in nuclear transformation,the introduction of genes via chloroplast genetic engineering is characterized by site-specific pattern via homologous recombination.To establish an expression system for alien genes in rice chloroplast,the intergenic region of ndhF and trnL was selected as target for sitespecific integration of PPT-resistant bar gene in this study.Two DNA fragments suitable for homologous recombination were cloned from rice chloroplast genome DNA using PCR technique,and the chloroplast-specific expression vector pRB was constructed by fusing a modified 16S rRNA gene promoter to bar gene together with terminator of psbA gene 3'sequence.Chloroplast transformation was carried out by biolistic bombardment of sterile rice calli with the pRB construct.Subsequently,the regenerated plantlets and seeds of progeny arising from reciprocal cross to the wild-type lines were obtained.Molecular analysis suggested that the bar gene has been integrated into rice chloroplast genome.Genetic analysis revealed that bar gene could be transmitted and expressed normally in chloroplast genome.Thus,the bar gene conferred not only selection pressure for the transformation of rice chloroplast genome,but PPT-resistant trait for rice plants as well.It is suggested that an efficient gene expression system in the rice chloroplast has been established by chloroplast transformation technique.

  15. Special rice in China

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Xianggu Rice: The rice originated from Jiangyong County, Hunan Province. Its characteristics were: even in grain shape, white in color, special fragrant in taste, and sticky in quality. Handongzao: It was from Wannian County, Jiangxi Province. The rice had big, fertile, and white grain, which was soft with fragrant smell, and it had high head rice rate. So, the local peasants liked to plant it. It was one of the "Tribute rice " in old time. Shizhu "Imperial Rice": The rice was also called "Fragrant Rice", was from Siyuan Village, Yuelai Town, Shizhu County, Sichuan Province. It was the treasure among the rices. The grain was bright in color. When it was cooked, the smell was fragrant. It was said that the rice was from "Han Dynasty", and has become the "Tribute Rice " since then. Blood Glutinous Rice: Originated from Changshu City, Jiangsu Province, the rice has been cultivated more than one hundred years. It had high nutrition value. Among the people, the Blood Glutinous Rice was often used as health food for lying-in women and patients. Qufu Fragrant Rice: Its characteristics were: clean, bright, and translucent in grain color, sticky in quality. It was suitable for cooking gruel and was also called "Fragrant Rice" in the local due to its strong fragrance. It was one of the "Tribute Rice" in old time. Taihu Lake Fragrant Japonica: The rice was from the Region of Taihu Lake, Jiangsu Province. The characteristics were: even and big in grain shape, soft in quality, white in color, fragrant in taste. The local people liked to plant and eat it.□ (To be continued) Translated by CHEN Wenhua, From "China Rice",No.1,1994

  16. 基于叶绿体基因多样性的中国水稻起源进化研究%Origin and Evolution of Cultivated Rice (O.sativa L.) in China Based on Gene Diversity of Chloroplast Genome

    Institute of Scientific and Technical Information of China (English)

    王荣升; 魏鑫; 曹立荣; 乔卫华; 张万霞; 杨庆文

    2011-01-01

    选择原产中国的98份亚洲栽培稻和125份普通野生稻为材料,对叶绿体中atpA序列、rps16内含子序列、trnP-rp133间隔区、trnG-trnfM序列、trnT-trnL间隔区序列的5段高突变序列进行测序,利用生物信息学方法进行比对分析,绘制Network网络图,构建系统发育树.结果表明,普通野生稻的Indel和SNP数目均比亚洲栽培稻多,序列多样性丰富;基于单倍型的Network网络图和系统发育树可将所有参试材料归为3个类群,类群Ⅰ主要为粳稻与普通野生稻,类群Ⅱ主要为籼稻,类群Ⅲ主要为普通野生稻,而类群Ⅱ和类群Ⅲ亲缘关系较近,提示粳、籼两个亚种可能由偏粳、偏籼的普通野生稻分别进化而来,支持二次起源学说;所有与亚洲栽培稻亲缘关系较近的普通野生稻均来源于华南地区,支持华南地区为我国亚洲栽培稻起源中心的论点.%To study the origin and evolution of Asian cultivated rice ( Oryza sativa L. ) ,98 accessions of Asian cultivated rice and 125 accessions of common wild rice {Oryza rufipogon) were selected for sequencing analysis. Through sequencing the atpA gene,rpsl6 intron,trnP-rpl33 inter spacer,trnG-trnfM inter spacer and trnT-trnL inter spacer in chloroplast genome in rice, the haplotype network and phylogenetic tree were made with bio-information software. The results showed that common wild rice had more Indels and SNPs compared with the Asian cultivated rice. Both the haplotype network and phylogenetic tree divided all test materials into three groups. Group I consisted by accessions from the Japonica subspecies and the common wild rice, Group II included mainly accessions of Indi-ca subspecies, while Group III were as the accessions of the common wild rice. Importantly, Group II and Group HI had a close relationship, which indicated that the Japonica and Indica Subspecies were originated from Japonica-like and Indica-like common wild rice separately, supporting the Double

  17. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication.

    Science.gov (United States)

    Avni, Raz; Nave, Moran; Barad, Omer; Baruch, Kobi; Twardziok, Sven O; Gundlach, Heidrun; Hale, Iago; Mascher, Martin; Spannagl, Manuel; Wiebe, Krystalee; Jordan, Katherine W; Golan, Guy; Deek, Jasline; Ben-Zvi, Batsheva; Ben-Zvi, Gil; Himmelbach, Axel; MacLachlan, Ron P; Sharpe, Andrew G; Fritz, Allan; Ben-David, Roi; Budak, Hikmet; Fahima, Tzion; Korol, Abraham; Faris, Justin D; Hernandez, Alvaro; Mikel, Mark A; Levy, Avraham A; Steffenson, Brian; Maccaferri, Marco; Tuberosa, Roberto; Cattivelli, Luigi; Faccioli, Primetta; Ceriotti, Aldo; Kashkush, Khalil; Pourkheirandish, Mohammad; Komatsuda, Takao; Eilam, Tamar; Sela, Hanan; Sharon, Amir; Ohad, Nir; Chamovitz, Daniel A; Mayer, Klaus F X; Stein, Nils; Ronen, Gil; Peleg, Zvi; Pozniak, Curtis J; Akhunov, Eduard D; Distelfeld, Assaf

    2017-07-07

    Wheat (Triticum spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat's domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer (T. turgidum ssp. dicoccoides). We report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity. With this fully assembled polyploid wheat genome, we identified the causal mutations in Brittle Rachis 1 (TtBtr1) genes controlling shattering, a key domestication trait. A study of genomic diversity among wild and domesticated accessions revealed genomic regions bearing the signature of selection under domestication. This reference assembly will serve as a resource for accelerating the genome-assisted improvement of modern wheat varieties. Copyright © 2017, American Association for the Advancement of Science.

  18. Comparative Proteomic, Physiological, Morphological, and Biochemical Analyses Reveal the Characteristics of the Diploid Spermatozoa of Allotetraploid Hybrids of Red Crucian Carp (Carassius auratus) and Common Carp (Cyprinus carpio).

    Science.gov (United States)

    Duan, Wei; Xu, Kang; Hu, Fangzhou; Zhang, Yi; Wen, Ming; Wang, Jing; Tao, Min; Luo, Kaikun; Zhao, Rurong; Qin, Qinbo; Zhang, Chun; Liu, Jinhui; Liu, Yun; Liu, Shaojun

    2016-02-01

    The generation of diploid spermatozoa is essential for the continuity of tetraploid lineages. The DNA content of diploid spermatozoa from allotetraploid hybrids of red crucian carp and common carp was nearly twice as great as that of haploid spermatozoa from common carp, and the durations of rapid and slow progressive motility were longer. We performed comparative proteomic analyses to measure variations in protein composition between diploid and haploid spermatozoa. Using two-dimensional electrophoresis followed by liquid chromatography tandem mass spectrometry, 21 protein spots that changed in abundance were analyzed. As the common carp and the allotetraploid hybrids are not fully sequenced organisms, we identified proteins by Mascot searching against the National Center for Biotechnology Information non-redundant (NR) protein database for the zebrafish (Danio rerio), and verified them against predicted homologous proteins derived from transcriptomes of the testis. Twenty protein spots were identified successfully, belonging to four gene ontogeny categories: cytoskeleton, energy metabolism, the ubiquitin-proteasome system, and other functions, indicating that these might be associated with the variation in diploid spermatozoa. This categorization of variations in protein composition in diploid spermatozoa will provide new perspectives on male polyploidy. Moreover, our approach indicates that transcriptome data are useful for proteomic analyses in organisms lacking full protein sequences.

  19. Genetic shift in local rice populations during rice breeding programs in the northern limit of rice cultivation in the world.

    Science.gov (United States)

    Fujino, Kenji; Obara, Mari; Ikegaya, Tomohito; Tamura, Kenichi

    2015-09-01

    The rapid accumulation of pre-existing mutations may play major roles in the establishment and shaping of adaptability for local regions in current rice breeding programs. The cultivated rice, Oryza sativa L., which originated from tropical regions, is now grown worldwide due to the concerted efforts of breeding programs. However, the process of establishing local populations and their origins remain unclear. In the present study, we characterized DNA polymorphisms in the rice variety KITAAKE from Hokkaido, one of the northern limits of rice cultivation in the world. Indel polymorphisms were attributed to transposable element-like insertions, tandem duplications, and non-TE deletions as the original mutation events in the NIPPONBARE and KITAAKE genomes. The allele frequencies of the KITAAKE alleles markedly shifted to the current variety types among the local population from Hokkaido in the last two decades. The KITAAKE alleles widely distributed throughout wild rice and cultivated rice over the world. These have accumulated in the local population from Hokkaido via Japanese landraces as the ancestral population of Hokkaido. These results strongly suggested that combinations of pre-existing mutations played a role in the establishment of adaptability. This approach using the re-sequencing of local varieties in unique environmental conditions will be useful as a genetic resource in plant breeding programs in local regions.

  20. The World of Rice

    Institute of Scientific and Technical Information of China (English)

    VALERIE SARTOR

    2010-01-01

    @@ Pilafs, risottos, soups, snacks, paellas,stuffing, vinegars, wines and desserts-rice is used all over the world in myriad ways as food and drink.Although rice is one of the world's most ancient foods and it is impossible to know exactly where and when cultivation of this marvelous grain began, China is popularly acknowledged as the homeland of rice. Chinese people have many legends about rice. Some describe a benevolent goddess in silk robes whose gown accidentally picked up stray rice grains, which she dropped from the heavens to humans below. It's also said that Shennong, the Divine Farmer in Chinese myth, sowed the first rice on earth.

  1. The B73 maize genome: complexity, diversity, and dynamics.

    Science.gov (United States)

    Schnable, Patrick S; Ware, Doreen; Fulton, Robert S; Stein, Joshua C; Wei, Fusheng; Pasternak, Shiran; Liang, Chengzhi; Zhang, Jianwei; Fulton, Lucinda; Graves, Tina A; Minx, Patrick; Reily, Amy Denise; Courtney, Laura; Kruchowski, Scott S; Tomlinson, Chad; Strong, Cindy; Delehaunty, Kim; Fronick, Catrina; Courtney, Bill; Rock, Susan M; Belter, Eddie; Du, Feiyu; Kim, Kyung; Abbott, Rachel M; Cotton, Marc; Levy, Andy; Marchetto, Pamela; Ochoa, Kerri; Jackson, Stephanie M; Gillam, Barbara; Chen, Weizu; Yan, Le; Higginbotham, Jamey; Cardenas, Marco; Waligorski, Jason; Applebaum, Elizabeth; Phelps, Lindsey; Falcone, Jason; Kanchi, Krishna; Thane, Thynn; Scimone, Adam; Thane, Nay; Henke, Jessica; Wang, Tom; Ruppert, Jessica; Shah, Neha; Rotter, Kelsi; Hodges, Jennifer; Ingenthron, Elizabeth; Cordes, Matt; Kohlberg, Sara; Sgro, Jennifer; Delgado, Brandon; Mead, Kelly; Chinwalla, Asif; Leonard, Shawn; Crouse, Kevin; Collura, Kristi; Kudrna, Dave; Currie, Jennifer; He, Ruifeng; Angelova, Angelina; Rajasekar, Shanmugam; Mueller, Teri; Lomeli, Rene; Scara, Gabriel; Ko, Ara; Delaney, Krista; Wissotski, Marina; Lopez, Georgina; Campos, David; Braidotti, Michele; Ashley, Elizabeth; Golser, Wolfgang; Kim, HyeRan; Lee, Seunghee; Lin, Jinke; Dujmic, Zeljko; Kim, Woojin; Talag, Jayson; Zuccolo, Andrea; Fan, Chuanzhu; Sebastian, Aswathy; Kramer, Melissa; Spiegel, Lori; Nascimento, Lidia; Zutavern, Theresa; Miller, Beth; Ambroise, Claude; Muller, Stephanie; Spooner, Will; Narechania, Apurva; Ren, Liya; Wei, Sharon; Kumari, Sunita; Faga, Ben; Levy, Michael J; McMahan, Linda; Van Buren, Peter; Vaughn, Matthew W; Ying, Kai; Yeh, Cheng-Ting; Emrich, Scott J; Jia, Yi; Kalyanaraman, Ananth; Hsia, An-Ping; Barbazuk, W Brad; Baucom, Regina S; Brutnell, Thomas P; Carpita, Nicholas C; Chaparro, Cristian; Chia, Jer-Ming; Deragon, Jean-Marc; Estill, James C; Fu, Yan; Jeddeloh, Jeffrey A; Han, Yujun; Lee, Hyeran; Li, Pinghua; Lisch, Damon R; Liu, Sanzhen; Liu, Zhijie; Nagel, Dawn Holligan; McCann, Maureen C; SanMiguel, Phillip; Myers, Alan M; Nettleton, Dan; Nguyen, John; Penning, Bryan W; Ponnala, Lalit; Schneider, Kevin L; Schwartz, David C; Sharma, Anupma; Soderlund, Carol; Springer, Nathan M; Sun, Qi; Wang, Hao; Waterman, Michael; Westerman, Richard; Wolfgruber, Thomas K; Yang, Lixing; Yu, Yeisoo; Zhang, Lifang; Zhou, Shiguo; Zhu, Qihui; Bennetzen, Jeffrey L; Dawe, R Kelly; Jiang, Jiming; Jiang, Ning; Presting, Gernot G; Wessler, Susan R; Aluru, Srinivas; Martienssen, Robert A; Clifton, Sandra W; McCombie, W Richard; Wing, Rod A; Wilson, Richard K

    2009-11-20

    We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

  2. Genome Polymorphisms Between Indica and Japonica Revealed by RFLP

    Institute of Scientific and Technical Information of China (English)

    WANG Song-wen; LIU Xia; XU Cai-guo; SHI Li-li; ZHANG Xin; DING De-liang; WANG Yong

    2007-01-01

    Revealing the genome polymorphisms between indica and japonica subspecies; RFLP markers, which are located across 12 chromosomes of rice, were used to analyze indica-japonica differentiation in different rice varieties. At the same time, genome sequence variations of screened loci were analyzed by bioinformatics method. Twenty-eight RFLP probes, which can classify indica-japonica rice, were confirmed. Subspecies genome polymorphisms of screened loci were found by analyzing the publication of the genome sequences data of rice. The study indicated that these screened markers can be used for classifying indica-japonica subspecies. With the publication of the genome sequences of rice, marker polymorphisms between indica and japonica subspecies can be revealed by genome differentiation.

  3. Photosynthetic Characteristics of Rice Transformed with Genomic DNA of Oryza minuta%转小粒野生稻基因组DNA水稻的光合性状研究

    Institute of Scientific and Technical Information of China (English)

    匡勇; 袁娇; 夏石头; 黄志远; 孙一丹; 赵炳然

    2011-01-01

    A new rice germplasm Yewei B was bred through transformed with genomic DNA of the distantly related species Oryza minuta into hybrid rice parent V20B by ear-stem injecting. Compared with V2OB, Yewei B has loose plant type, small and thin stem. The leaf area of the top 1st, top 2nd and top 3rd leaf is significantly smaller than that of V20B respectively. The content of chlorophyll of Yewei B and V20B decreased gradually from initial heading stage ( I ) to heading stage ( Ⅱ ), milk ripening stage ( Ⅲ ), wax ripening stage (Ⅳ) and yellow ripening stage ( V ), and there is no significant difference between these two varieties. However the photosynthetic rate of the top 1st, top 2nd and top 3rd leaf in Yewei B is significantly higher than that of V20B.%通过"穗茎注射法",将远缘物种小粒野生稻(Oryza minuta)的基因组DNA导入杂交水稻亲本V20B中,培育出转基因水稻新种质野威B.与亲本V20B相比,野威B的株型较松散,茎较细小,其倒1、倒2和倒3叶的叶面积均显著小于亲本的.从始穗期(Ⅰ期)、齐穗期(Ⅱ期)到乳熟期(Ⅲ期)再到黄熟期(Ⅳ期)和腊熟期(Ⅴ期),野威B和V20B的叶绿素含量逐渐降低,两者之间差异未达到显著水平,但野威B的倒1、倒2和倒3叶片的光合速率均极显著高于亲本V20B的光合速率.

  4. Molecular evolution of the rice blast resistance gene Pi-ta in invasive weedy rice in the USA.

    Directory of Open Access Journals (Sweden)

    Seonghee Lee

    Full Text Available The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. To investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus, which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH, suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta, not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing.

  5. Molecular evolution of the rice blast resistance gene Pi-ta in invasive weedy rice in the USA.

    Science.gov (United States)

    Lee, Seonghee; Jia, Yulin; Jia, Melissa; Gealy, David R; Olsen, Kenneth M; Caicedo, Ana L

    2011-01-01

    The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. To investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus), which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta) found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH), suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s) required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta), not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing.

  6. Genome evolution of Oryza

    Directory of Open Access Journals (Sweden)

    Tieyan Liu

    2014-01-01

    Full Text Available The genus Oryza is composed of approximately 24 species. Wild species of Oryza contain a largely untapped resource of agronomically important genes. As an increasing number of genomes of wild rice species have been or will be sequenced, Oryza is becoming a model system for plant comparative, functional and evolutionary genomics studies. Comparative analyses of large genomic regions and whole-genome sequences have revealed molecular mechanisms involved in genome size variation, gene movement, genome evolution of polyploids, transition of euchromatin to heterochromatin and centromere evolution in the genus Oryza. Transposon activity and removal of transposable elements by unequal recombination or illegitimate recombination are two important factors contributing to expansion or contraction of Oryza genomes. Double-strand break repair mediated gene movement, especially non-homologous end joining, is an important source of non-colinear genes. Transition of euchromatin to heterochromatin is accompanied by transposable element amplification, segmental and tandem duplication of genic segments, and acquisition of heterochromatic genes from other genomic locations. Comparative analyses of multiple genomes dramatically improve the precision and sensitivity of evolutionary inference than single-genome analyses can provide. Further investigations on the impact of structural variation, lineage-specific genes and evolution of agriculturally important genes on phenotype diversity and adaptation in the genus Oryza should facilitate molecular breeding and genetic improvement of rice.

  7. Transformation of japonica rice with RHL gene and salt tolerance of the transgenic rice plant

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Overexpression of the yeast HAL2 gene increases salt tolerance of yeast and plant. Rice HAL2-like (RHL) gene was introduced into a japonica rice cultivar HJ19 with Agrobacterium tumefaciens-mediated transformation. Transgenic plants in R0 generation were selected on the principle of GUS-positive, RHL gene PCR-positive and normal growth. Hygromycin-resistant plants of some transgenic lines in R1 generation increased salt tolerance during the seedling and booting stage, being less damaged in the cytomembrane and stronger in leaf tissue viability under salt stress during booting period. Southern analysis of transgenic lines tolerant to salt in R1 generation showed that the RHL gene expression cassette had been successfully integrated into rice genome. Moreover, gene engineering breeding methodology and really salt-tolerant rice cultivar were discussed.

  8. Special rice in China

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@Mingshui Rice: It originated from Zhangqiu County, Shandong Province. The characteristics of Mingshui Rice were: absorbing more water, swelling up greatly after being soaked, and being sticky and smelling fragrant after cooked.

  9. Identification and Structural Analysis of a Class of Potentially Transposable Solo-LTR in Rice Genome%水稻基因组中一类具有潜在转座活性的S010-LTR的结构分析和鉴定

    Institute of Scientific and Technical Information of China (English)

    周波; 陈泽华; 韩斌; 洪国藩

    2001-01-01

    Two solo-LTRs, named SLTR1 and SLTR2, were found in BAC t17804 and q5343 on rice chromosome 4, respectively. SLTR1 is in a 18 S rRNA gene and $LTR2 is in a retrotransposon. They share sequence homology and show sequence similarity 89.1% and 70.1% to the LTR of rice retrotransposon RIRE8,respectively. SLTR1 and SLTR2 are of gypsy retrotransposons of rice. They are both highly repetitive sequences and widely distributed in the rice genome, as shown by hybridization with specific probes of SLTR1 and SLTR2. Using PCR amplication with primers on flanking sequences of SLTR1 and SLTR2, no bands corresponding to those of BACs were amplified using the rice genomic DNA as template. SLTR1 and SLTR2 did not locate in the relative loci of the rice genome, as supported by hybridization with specific probes of genes interrupted by them. Obviously, SLTR1 and SLTR2 reported here came from different loci of the genome by the transposition. These solo-LTRs may be useful for our rice genome studies.%在水稻4号染色体两个BAC克隆序列分析中,发现了两个solo-LTR,分别命名为SLTR1和SLTR2。它们分别位于水稻18 S rRNA基因和一逆转座子内部。序列比较发现,SLTR1和SLTR2存在着较高的同源性,并与水稻逆转座子RIRE8的LTR序列高度同源,分别为89.1%和70.1%,它们属于一类水稻gypsy类型逆转座子。利用SITR1和SLTR2与水稻DNA杂交,结果显示两者广泛分布于水稻基因组中,是一类高拷贝重复序列。分别利用SLTR1和SLTR2的两侧特异性序列设计引物进行PCR扩增,结果发现在基因组的相应位置并不存在SLTR1或SITR2;利用它们两侧被打断基因的特异性片段杂交基因组DNA,得到了同样的的结果。这意味着,SITR1和SLTR2来源于基因组的其它位置,并通过某种转座的过程进入18 S rRNA基因和另一逆转座子内部。Solo-LTR存在着这种潜在的转座活性,对于进一步研究solo-LTR的来源以及其在基因组

  10. Homoeologous chromosomes of Xenopus laevis are highly conserved after whole-genome duplication.

    Science.gov (United States)

    Uno, Y; Nishida, C; Takagi, C; Ueno, N; Matsuda, Y

    2013-11-01

    It has been suggested that whole-genome duplication (WGD) occurred twice during the evolutionary process of vertebrates around 450 and 500 million years ago, which contributed to an increase in the genomic and phenotypic complexities of vertebrates. However, little is still known about the evolutionary process of homoeologous chromosomes after WGD because many duplicate genes have been lost. Therefore, Xenopus laevis (2n=36) and Xenopus (Silurana) tropicalis (2n=20) are good animal models for studying the process of genomic and chromosomal reorganization after WGD because X. laevis is an allotetraploid species that resulted from WGD after the interspecific hybridization of diploid species closely related to X. tropicalis. We constructed a comparative cytogenetic map of X. laevis using 60 complimentary DNA clones that covered the entire chromosomal regions of 10 pairs of X. tropicalis chromosomes. We consequently identified all nine homoeologous chromosome groups of X. laevis. Hybridization signals on two pairs of X. laevis homoeologous chromosomes were detected for 50 of 60 (83%) genes, and the genetic linkage is highly conserved between X. tropicalis and X. laevis chromosomes except for one fusion and one inversion and also between X. laevis homoeologous chromosomes except for two inversions. These results indicate that the loss of duplicated genes and inter- and/or intrachromosomal rearrangements occurred much less frequently in this lineage, suggesting that these events were not essential for diploidization of the allotetraploid genome in X. laevis after WGD.

  11. Rice Price under Pressure

    Institute of Scientific and Technical Information of China (English)

    Liu Xinwen

    2008-01-01

    @@ Early in April, the FOB (Free on Board) value of rice exported from Bangkok, Thailand, the biggest rice exporter of the world, surged to a new high of US$730per ton, representing an increase of 70 percent in recent years, and setting a new record over the past 34 years of Thailand rice exports.

  12. Molecular Population Genetics of Rice Domestication

    Institute of Scientific and Technical Information of China (English)

    Tian Tang; Suhua Shi

    2007-01-01

    Domestication is a selection process that genetically modifies species to meet human needs. A most intriguing feature of domestication is the extreme phenotypic diversification among breeds. What could be the ultimate source of such genetic variations? Another notable outcome of artificial selection is the reduction in the fitness of domesticated species when they live in the wild without human assistance. The complete sequences of the two subspecies of rice cultivars provide an opportunity to address these questions. Between the two subspecies, we found much higher rates of non-synonymous (N) than synonymous (S) substitutions and the N/S ratios are higher between cultivars than between wild species. Most interestingly, substitutions of highly dissimilar amino acids that are deleterious and uncommon between natural species are disproportionately common between the two subspecies of rice. We suggest strong selection in the absence of effective recombination may be the driving force, which we called the domestication-associated Hill-Robertson effect. These hitchhiking mutations may contribute to some fitness reduction in cultivars. Comparisons of the two genomes also reveal the existence of highly divergent regions in the genomes. Haplotypes in these regions often form highly polymorphic linkage blocks that are much older than speciation between wild species. Genes from such regions could contribute to the differences between indica and japonica and are likely to be involved in the diversifying selection under domestication. Their existence suggests that the amount of genetic variation within the single progenitor species Oryza ruflpogon may be insufficient to account for the variation among rice cultivars, which may come from a more inclusive gene pool comprising most of the A-genome wild species. Genes from the highly polymorphic regions also provide strong support for the independent domestication of the two subspecies. The genomic variation in rice has revealing

  13. 基于线粒体基因片段核苷酸多态性的亚洲栽培稻起源进化研究%Study on the Origin and Evolution of Asian Cultivated Rice Based on Gene Fragment Nucleotides Diversity of Mitochondrial Genome

    Institute of Scientific and Technical Information of China (English)

    曹立荣; 魏鑫; 黄娟; 乔卫华; 张万霞; 杨庆文

    2013-01-01

    亚洲栽培稻的祖先是普通野生稻,已成为世界公认的观点,然而亚洲栽培稻的2个亚种:粳稻和籼稻是一次起源还是二次起源仍存在很大争议,其起源地是国内还是国外依然是国际学者间争论的焦点.本文通过对184份亚洲栽培稻和203份普通野生稻3段基因序列cox3、cox1、orf 224和2段基因间序列ssv-39/178、rps2-trnfM的多样性研究,验证了以下观点:1)粳稻起源于中国,籼稻起源于中国和国外;2)亚洲栽培稻的起源为二次起源,即普通野生稻存在偏籼和偏粳2种类型,亚洲栽培稻的2个亚种籼稻和粳稻在进化过程中分别由偏籼型的普通野生稻和偏粳型的普通野生稻进化而来.%Wild rice ( Oryza rufipogon ) has been recognized as the ancestor of Asian cultivated rice ( Oryza sati-va). However, where and how cultivated rice originated from wild rice has been debated for a long time in the world. Moreover,whether the two subspecies of Asian cultivated rice, indica and japonica, were domesticated with the ways of single origin or multiple origins was still considerably controversial, and whether they originated from China or aboard was still the focus of debate among international scholars. In this study, 184 accessions of Asian cultivated rice and 203 accessions of Oryza rufipogon to be sequenced with 3 gene fragments (cox3 ,coxl, orf 224) and two inter gene regions( ssv-39/178 ,rps2-trnfM) in mitochondrial genome of rice were collected. Through the study of gene diversity of the five fragments, the following propositions were verified. First,the origin of japonica was in China, and the origin of indica was not only in China but also in foreign countries. Second,the subspecies of Asian cultivated rice were domesticated with two origins. In other words,common wild rice contained the indica-like and japonica-like types, and the two subspecies were evolved from the indica -like wild rice and the japonica-like wild rice respectively.

  14. Rice peasants and rice research in Colombia

    NARCIS (Netherlands)

    Spijkers, P.A.N.M.

    1983-01-01

    Rice has been grown as a food crop in Latin America from early colonial times. In Colombia rice became a prominent subsistence crop especially on the north coast where it has been grown since the 17th century, sometimes also as a commercial crop. During the last twenty years there has been a sharp i

  15. Rice peasants and rice research in Colombia

    NARCIS (Netherlands)

    Spijkers, P.A.N.M.

    1983-01-01

    Rice has been grown as a food crop in Latin America from early colonial times. In Colombia rice became a prominent subsistence crop especially on the north coast where it has been grown since the 17th century, sometimes also as a commercial crop. During the last twenty years there has been a sharp

  16. Genome-wide analysis of disease resistance gene analogues in rice%水稻全基因组编码抗病基因同源序列分析

    Institute of Scientific and Technical Information of China (English)

    任鄄胜; 肖培村; 陈勇; 吕启明; 王玉平; 赵慧霞; 李仕贵

    2010-01-01

    利用模糊搜索的方法,在TIGR水稻日本晴基因组数据库(TIGR Rice Genome Annotation - Release 5)中识别出565个编码抗病蛋白质的同源序列;利用识别出565个编码抗病蛋白质序列分别与籼稻基因组数据库进行BLASTP联配,共确定320个对应的等位基因.通过在线生物信息学软件,识别了这565个抗病基因的保守结构域、保守模体和DNA序列内转座子元件,其中有14个抗病基因同源序列注释错误.同时绘出了这些基因的基因组分布,并基于这些基因的同源树分析和基因组物理分布,认为基因的原位和远程复制事件产生了抗病基因的现存分布和多样性,其中转座子在复制过程中扮演了重要角色.这些对抗病机制研究和抗病基因进化研究以及抗病基因的转育具有重要意义.

  17. Special rice in China

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Wushan Rice: It grew in hilly land around Wu Mountain in Wang City, Hunan Province. Its grain is bright and transparent, and the cooked rice is soft, sticky, fragrant, and sweet in taste. It was a "Tribute Rice" in old time. Indian Indica: Growing in Wuchang City, Hubei Province, it was also called" Red Flower Rice" . It was characterized by its thin pericarp and soft, sticky, and oily quality. Its taste was delicious. Fragrant Rice 1: It was from Xinxiang and Hui counties, Henan Province. Its characteristics were: long-round in grain shape, white in color, soft and sticky in quality, and agreeable to the taste. It was usually used as a gift in the local. Baiyutang Rice: It originated from Gaozhuang Village, Beijing suburban district. It had good quality due to the irrigation of the spring water. The rice had even grain shape, white color, hard enough quality to be cooked, fragrant and sweet taste. It was one of the "Tribute Rice" in old time. Tian′e Indica Rice: Xianning and Wuchang counties, Hubei Province were its growing area. It also called "Double Grain" because of its big grain. The hull was red, while the grain was white. When cooked, it needed more water than normal rice, and the rice was agreeable to the taste. Baiyan Rice: It originated from Jishou County, Hunan Province. The grain was even in shape, white in color, and sticky in quality. The rice was easy to be cooked and was fragrant and sweet in taste. It was also a " Tribute Rice" in old time. □ (To be continued) Translated by CHEN Wenhua, From "China Rice", No. 1, 1994

  18. Genome Sizes in Hepatica Mill: (Ranunculaceae Show a Loss of DNA, Not a Gain, in Polyploids

    Directory of Open Access Journals (Sweden)

    B. J. M. Zonneveld

    2010-01-01

    , and a possible pentaploid. The somatic nuclear DNA contents (2C-value, as measured by flow cytometry with propidium iodide, were shown to range from 33 to 80 pg. The Asiatic and American species, often considered subspecies of H. nobilis, could be clearly distinguished from European H. nobilis. DNA content confirmed the close relationships in the Asiatic species, and these are here considered as subspecies of H. asiatica. Parents for the allotetraploid species could be suggested based on their nuclear DNA content. Contrary to the increase in genome size suggested earlier for Hepatica, a significant (6%–14% loss of nuclear DNA in the natural allopolyploids was found.

  19. Status and Perspectives on the Researches of Rice Glutelin Mutants

    Institute of Scientific and Technical Information of China (English)

    ZHENG Tian-qing; SHEN Wen-biao; ZHU Su-song; ZHAI Hu-qu; WAN Jian-min

    2003-01-01

    Rice (Oryza sativa L. ) is one of the model plants for genomics research. As the raising offunctional rice breeding for special usage, glutelin mutants play a more and more important role in the func-tional rice breeding as well as eukaryotic gene expression and regulation research materials. For example, therice cultivar special for the patients suffering from kidney disease and diabetes could be developed from the riceglutelin mutants. In this paper, current researches on characterization, mutation mechanism and breeding us-age of various rice glutelin mutants, especially the low glutelin content cultivars, were all discussed with per-spectives on the trends of the glutelin mutant researches in the era of post-genomics.

  20. Special rice in China

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    @@Shanxi black rice It was originally from Yang County, Hanzhong Region.This rice was a world-famous rice variety developed in 140 BC. It had pitch-black surface with the protein and oil contents being 6.8% and 20% higher than that of common rice, respectively. It had 15 kinds of amino acids and many kinds of vitamins. It was praised as" Black pearl" and "The king of the world riee".DongnianThe other names for Dongnian were "Yellow rice" and "Oil rice". It was grown in E City and Huangmei County,Hubei Province. It was characterized by its long-slim shape, milky yellow in color, oily, solid, and sticky quality, fragrant smell, and easiness for digestion.Guizhou black pearl rice

  1. Conserved but attenuated parental gene expression in allopolyploids: constitutive zinc hyperaccumulation in the allotetraploidArabidopsis kamchatica

    OpenAIRE

    Paape, Timothy; Hatakeyama, Masaomi; Shimizu-Inatsugi, Rie; Cereghetti, Teo; Onda, Yoshihiko; Kenta, Tanaka; Sese, Jun; Kentaro K. Shimizu

    2016-01-01

    Allopolyploidization combines parental genomes and often confers broader species distribution. However, little is known about parentally transmitted gene expression underlying quantitative traits following allopolyploidization because of the complexity of polyploid genomes. The allopolyploid species Arabidopsis kamchatica is a natural hybrid of the zinc hyperaccumulator Arabidopsis halleri and of the nonaccumulator Arabidopsis lyrata. We found that A. kamchatica retained the ability to hypera...

  2. An efficient TALEN mutagenesis system in rice.

    Science.gov (United States)

    Chen, Kunling; Shan, Qiwei; Gao, Caixia

    2014-08-15

    Targeted gene mutagenesis is a powerful tool for elucidating gene function and facilitating genetic improvement in rice. TALENs (transcription activator-like effector nucleases), consisting of a custom TALE DNA binding domain fused to a nonspecific FokI cleavage domain, are one of the most efficient genome engineering methods developed to date. The technology of TALENs allows DNA double-strand breaks (DSBs) to be introduced into predetermined chromosomal loci. DSBs trigger DNA repair mechanisms and can result in loss of gene function by error-prone non-homologous end joining (NHEJ), or they can be exploited to modify gene function or activity by precise homologous recombination (HR). In this paper, we describe a detailed protocol for constructing TALEN expression vectors, assessing nuclease activities in vivo using rice protoplast-based assays, generating and introducing TALEN DNAs into embryogenic calluses of rice and identifying TALEN-generated mutations at targeted genomic sites. Using these methods, T0 rice plants resulting from TALEN mutagenesis can be produced within 4-5 months.

  3. Reconstructing the Evolution of Brachypodium Genomes Using Comparative Chromosome Painting.

    Directory of Open Access Journals (Sweden)

    Alexander Betekhtin

    Full Text Available Brachypodium distachyon is a model for the temperate cereals and grasses and has a biology, genomics infrastructure and cytogenetic platform fit for purpose. It is a member of a genus with fewer than 20 species, which have different genome sizes, basic chromosome numbers and ploidy levels. The phylogeny and interspecific relationships of this group have not to date been resolved by sequence comparisons and karyotypical studies. The aims of this study are not only to reconstruct the evolution of Brachypodium karyotypes to resolve the phylogeny, but also to highlight the mechanisms that shape the evolution of grass genomes. This was achieved through the use of comparative chromosome painting (CCP which hybridises fluorescent, chromosome-specific probes derived from B. distachyon to homoeologous meiotic chromosomes of its close relatives. The study included five diploids (B. distachyon 2n = 10, B. sylvaticum 2n = 18, B. pinnatum 2n = 16; 2n = 18, B. arbuscula 2n = 18 and B. stacei 2n = 20 three allotetraploids (B. pinnatum 2n = 28, B. phoenicoides 2n = 28 and B. hybridum 2n = 30, and two species of unknown ploidy (B. retusum 2n = 38 and B. mexicanum 2n = 40. On the basis of the patterns of hybridisation and incorporating published data, we propose two alternative, but similar, models of karyotype evolution in the genus Brachypodium. According to the first model, the extant genome of B. distachyon derives from B. mexicanum or B. stacei by several rounds of descending dysploidy, and the other diploids evolve from B. distachyon via ascending dysploidy. The allotetraploids arise by interspecific hybridisation and chromosome doubling between B. distachyon and other diploids. The second model differs from the first insofar as it incorporates an intermediate 2n = 18 species between the B. mexicanum or B. stacei progenitors and the dysploidic B. distachyon.

  4. Rice that Filipinos Grow and Eat

    OpenAIRE

    de Leon, John C.

    2005-01-01

    This paper introduces rice to the reader and analyzes the changes it has gone through these past 100 years in the shaping hands of varietal improvement science. Here, the richness of the crop as a genetic material and resource is revealed. Landrace rice, pureline selection rice, crossbred rice, semidwarf rice, hybrid rice, new plant type rice, designer rice - from the traditional to modern to futuristic - rice becomes all of these while traversing time in the Philippines. There is rice for th...

  5. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

    DEFF Research Database (Denmark)

    Xu, Xun; Liu, Xin; Ge, Song;

    2012-01-01

    Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 ...

  6. The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

    Science.gov (United States)

    Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

    2013-02-01

    Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

  7. Details of rice EST mapping results - RGP estmap2001 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available gel blot hybridization of YAC or rice genomic DNA with genetic markers or EST clones was conducted using the enhanced chemiluminesce...nce system (Amersham, Buckinghamshire, UK). Notes #; flo

  8. Determinants for grading Malaysian rice

    Science.gov (United States)

    ChePa, Noraziah; Yusoff, Nooraini; Ahmad, Norhayati

    2016-08-01

    Due to un-uniformity of rice grading practices in Malaysia, zones which actively producing rice in Malaysia are using their own way of grading rice. Rice grading is important in determining rice quality and its subsequent price in the market. It is an important process applied in the rice production industry with the purpose of ensuring that the rice produced for the market meets the quality requirements of consumer. Two important aspects that need to be considered in determining rice grades are grading technique and determinants to be used for grading (usually referred as rice attributes). This article proposes the list of determinants to be used in grading Malaysian rice. Determinants were explored through combination of extensive literature review and series of interview with the domain experts and practitioners. The proposed determinants are believed to be beneficial to BERNAS in improving the current Malaysian rice grading process.

  9. The Complex History of the Domestication of Rice

    Science.gov (United States)

    Sweeney, Megan; McCouch, Susan

    2007-01-01

    Background Rice has been found in archaeological sites dating to 8000 bc, although the date of rice domestication is a matter of continuing debate. Two species of domesticated rice, Oryza sativa (Asian) and Oryza glaberrima (African) are grown globally. Numerous traits separate wild and domesticated rices including changes in: pericarp colour, dormancy, shattering, panicle architecture, tiller number, mating type and number and size of seeds. Scope Genetic studies using diverse methodologies have uncovered a deep population structure within domesticated rice. Two main groups, the indica and japonica subspecies, have been identified with several subpopulations existing within each group. The antiquity of the divide has been estimated at more than 100 000 years ago. This date far precedes domestication, supporting independent domestications of indica and japonica from pre-differentiated pools of the wild ancestor. Crosses between subspecies display sterility and segregate for domestication traits, indicating that different populations are fixed for different networks of alleles conditioning these traits. Numerous domestication QTLs have been identified in crosses between the subspecies and in crosses between wild and domesticated accessions of rice. Many of the QTLs cluster in the same genomic regions, suggesting that a single gene with pleiotropic effects or that closely linked clusters of genes underlie these QTL. Recently, several domestication loci have been cloned from rice, including the gene controlling pericarp colour and two loci for shattering. The distribution and evolutionary history of these genes gives insight into the domestication process and the relationship between the subspecies. Conclusions The evolutionary history of rice is complex, but recent work has shed light on the genetics of the transition from wild (O. rufipogon and O. nivara) to domesticated (O. sativa) rice. The types of genes involved and the geographic and genetic distribution of

  10. Rice Transcriptome Analysis to Identify Possible Herbicide Quinclorac Detoxification Genes

    Directory of Open Access Journals (Sweden)

    Wenying eXu

    2015-09-01

    Full Text Available Quinclorac is a highly selective auxin-type herbicide, and is widely used in the effective control of barnyard grass in paddy rice fields, improving the world’s rice yield. The herbicide mode of action of quinclorac has been proposed and hormone interactions affect quinclorac signaling. Because of widespread use, quinclorac may be transported outside rice fields with the drainage waters, leading to soil and water pollution and environmental health problems.In this study, we used 57K Affymetrix rice whole-genome array to identify quinclorac signaling response genes to study the molecular mechanisms of action and detoxification of quinclorac in rice plants. Overall, 637 probe sets were identified with differential expression levels under either 6 or 24 h of quinclorac treatment. Auxin-related genes such as GH3 and OsIAAs responded to quinclorac treatment. Gene Ontology analysis showed that genes of detoxification-related family genes were significantly enriched, including cytochrome P450, GST, UGT, and ABC and drug transporter genes. Moreover, real-time RT-PCR analysis showed that top candidate P450 families such as CYP81, CYP709C and CYP72A genes were universally induced by different herbicides. Some Arabidopsis genes for the same P450 family were up-regulated under quinclorac treatment.We conduct rice whole-genome GeneChip analysis and the first global identification of quinclorac response genes. This work may provide potential markers for detoxification of quinclorac and biomonitors of environmental chemical pollution.

  11. Rice Yellow Mottle Virus stress responsive genes from susceptible and tolerant rice genotypes

    Directory of Open Access Journals (Sweden)

    Siré Christelle

    2008-03-01

    Full Text Available Abstract Background The effects of viral infection involve concomitant plant gene variations and cellular changes. A simple system is required to assess the complexity of host responses to viral infection. The genome of the Rice yellow mottle virus (RYMV is a single-stranded RNA with a simple organisation. It is the most well-known monocotyledon virus model. Several studies on its biology, structure and phylogeography have provided a suitable background for further genetic studies. 12 rice chromosome sequences are now available and provide strong support for genomic studies, particularly physical mapping and gene identification. Results The present data, obtained through the cDNA-AFLP technique, demonstrate differential responses to RYMV of two different rice cultivars, i.e. susceptible IR64 (Oryza sativa indica, and partially resistant Azucena (O. s. japonica. This RNA profiling provides a new original dataset that will enable us to gain greater insight into the RYMV/rice interaction and the specificity of the host response. Using the SIM4 subroutine, we took the intron/exon structure of the gene into account and mapped 281 RYMV stress responsive (RSR transcripts on 12 rice chromosomes corresponding to 234 RSR genes. We also mapped previously identified deregulated proteins and genes involved in partial resistance and thus constructed the first global physical map of the RYMV/rice interaction. RSR transcripts on rice chromosomes 4 and 10 were found to be not randomly distributed. Seven genes were identified in the susceptible and partially resistant cultivars, and transcripts were colocalized for these seven genes in both cultivars. During virus infection, many concomitant plant gene expression changes may be associated with host changes caused by the infection process, general stress or defence responses. We noted that some genes (e.g. ABC transporters were regulated throughout the kinetics of infection and differentiated susceptible and

  12. The Power of Inbreeding: NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication.

    Science.gov (United States)

    Wang, Hongru; Xu, Xun; Vieira, Filipe Garrett; Xiao, Yunhua; Li, Zhikang; Wang, Jun; Nielsen, Rasmus; Chu, Chengcai

    2016-07-01

    Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in humans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice (Oryza sativa L.), which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5× and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SNPs in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice, japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.

  13. Rice (Oryza) hemoglobins

    Science.gov (United States)

    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 sin...

  14. Super Rice Breeding in China

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@I. Demand for super high yield rice in China   Rice is one of the main staple food in China. The performance of rice sector in production and yield had been very impressive in the last four decades. However, rice production and yield has stagnated since 1990.

  15. Genetic and molecular dissection of naturally occurring variations in rice

    Energy Technology Data Exchange (ETDEWEB)

    Yano, Masahiro [National Institute of Agrobiological Sciences, Tsukuba, Ibaraki (Japan)

    2002-02-01

    The progress for structural analysis of the rice genome has allowed us to embark on the sequencing of the whole rice genome. Resources - genetic markers, sequence data, and genomic clones - derived from many efforts will be used for the functional analysis of rice genes in the next decade. Although artificially induced variations, such as mutants, have been used mainly for genetic and physiological studies in rice and other plant species, the development of DNA markers has made possible access to naturally occurring allelic variations underlying complex traits. Such analysis is often referred to as quantitative traits locus (QTL) analysis. Many QTLs have been mapped for many complex traits in rice. During the analyses of several quantitative traits by the DNA marker-assisted strategy, two questions about QTL analysis have been raised: 1) Does a QTL represent a single Mendelian locus or a cluster of multiple loci? 2) Is it possible to precisely map a QTL and identify QTLs at the molecular level using map-based or other strategies? To answer these questions, a series of analyses on heading date, including the identification of putative QTLs, characterization and fine mapping of QTLs using nearly isogenic lines (NILs), and identification of genes at QTLs for heading date by the map-based strategy has been performed. In addition, several primary permanent mapping populations and secondary genetic resources, such as chromosomal segmental substitution lines, have been developed to facilitate the genetic analysis of naturally occurring allelic variation. (M. Suetake)

  16. Construction of a Rice Glvcosvltransferase Phylogenomic Data base and Identification of Rice-Diverged Glvcosvltransferases

    Institute of Scientific and Technical Information of China (English)

    Pei-Jian Cao; Laura E.Bartley; Ki-Hong Jung; Pamela C.Ronald

    2008-01-01

    GlycosyItransferases(GTs;Ec 2.4.x.y)constitute a large group of enzymes that form glycosidic bonds through transfer of sugars from activated donor molecules to acceptor molecules.GTs are critical to the biosynthesis of plant cell walls,among other diverse functions.Based on the Carbohydrate-Active enZymes(CAZy)database and sequence similarity searches,we have identified 609 potentiaI GT genes(loci)corresponding to 769 transcripts(gene models)in rice (Oryza sativa),the reference monocotyledonous species.Using domain composition and sequence similarity,these rice GTs were classified into 40 CAZy families plus an additionaI unknown class.We found that two Pfam domains of unknown function,PF04577 and PF04646,are associated with GT families GT61 and GT31,respectively.To facilitate functional analysis of this important and large gene family,we created a phylogenomic Rice GT Database(http://ricephylogenomics.ucdavis.edu/cellwalls/gt/).Through the database.severaI classes of functionaI genomic data,including mutant lines and gene expression data,can be displayed for each rice GT in the context of a phylogenetic tree,allowing for comparative analysis both within and between GT families.Comprehensive digital expression analysis of public gene expression data revealed that most(~80%)rice GTs are expressed.Based on analysis with Inparanoid,we identified 282'rice-diverged'GTs that lack orthologs in sequenced dicots(Arabidopsis thaliana,Populus tricocarpa,Medicago truncatula.and Ricinus communis).Combining these analyses,we identified 33 rice-diverged GT genes(45 gene models)that are highly expressed in above-ground,vegetative tissues.From the literature and this analysis,21 of these Ioci are excellent targets for functional examination toward understanding and manipuIating grass cell wall qualities.Study of the remainder may reveal aspects of hormone and protein metabolism that are critical for rice biology.This list of 33 genes and the Rice GT Database will facilitate the

  17. Microarray and Proteomic Analysis of Brassinosteroid- and Gibberellin-Regulated Gene and Protein Expression in Rice

    Institute of Scientific and Technical Information of China (English)

    Guangxiao Yang; Setsuko Komatsu

    2004-01-01

    Brassinosteroid (BR) and gibberellin (GA) are two groups of plant growth regulators essential for normal plant growth and development. To gain insight into the molecular mechanism by which BR and GA regulate the growth and development of plants, especially the monocot plant rice, it is necessary to identify and analyze more genes and proteins that are regulated by them. With the availability of draft sequences of two major types, japonica and indica rice, it has become possible to analyze expression changes of genes and proteins at genome scale. In this review, we summarize rice functional genomic research by using microarray and proteomic approaches and our recent research results focusing on the comparison of cDNA microarray and proteomic analyses of BR- and GA-regulated gene and protein expression in rice. We believe our findings have important implications for understanding the mechanism by which BR and GA regulate the growth and development of rice.

  18. Rice Germplasm Resources in China

    Institute of Scientific and Technical Information of China (English)

    YINGCunshan

    1994-01-01

    China is one of the origin countries in Asia of cultiv ated rice (O. sativaL.), and rice is one of the aged-long food crops in the country. The results of the 14C evaluation on the carbonified rice grains unearthed from Hemudu in Yuyao County and Luojiajiao in Tongxiang County of Zhejiang Province indicated that rice in these area has been planted more than 7,000 yrs and indica (hsien) and japonica (keng) rices coexisted with each other.

  19. Structure, Function, and Evolution of Rice Centromeres

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Construction of a DNA library from chromosome 4 of rice (Oryza sativa) by microdissection

    Institute of Scientific and Technical Information of China (English)

    MAOYINGWEI; SIYUANLIANG; 等

    1998-01-01

    A simple method to create a chromosome-specific DNA librqary of rice,including microdissection,amplification,charterization and cloning,is described.Rice chromosome 4 from a metaphase cell has been isolated and amplified by the Linker Adapter PCR (LA-PCR).The PCR products were labeled as probes with DIG-11-dUTP using the random priming method.Southern blot analysis with rice genomic DNA and specific RFLP markers demonstrated that the PCR products were derived from rice chromosome 4.A large library comprising over 100,000 recombinant plasmid microclones from rice chromosome 4 was constructed.Colony hybridization showed that 58% of the clones contained single or low-copy sequences and 42% contained repetitive sequences.The size of inserts generated by PCR ranged from 140bp to 500bp.This method will facilitate cloning of the specific chromosome DNA markers and important genes of rice.

  1. Allogamy-Autogamy Switch Enhance Assortative Mating in the Allotetraploid Centaurea seridis L. Coexisting with the Diploid Centaurea aspera L. and Triggers the Asymmetrical Formation of Triploid Hybrids

    Science.gov (United States)

    Ferriol, María; Garmendia, Alfonso; Gonzalez, Ana; Merle, Hugo

    2015-01-01

    Hybridization between tetraploids and their related diploids is generally unsuccessful in Centaurea, hence natural formation of triploid hybrids is rare. In contrast, the diploid Centaurea aspera and the allotetraploid C. seridis coexist in several contact zones where a high frequency of triploid hybrids is found. We analyzed the floral biology of the three taxa to identify reproductive isolation mechanisms that allow their coexistence. Flowering phenology was recorded, and controlled pollinations within and between the three taxa were performed in the field. Ploidy level and germination of progeny were also assessed. There was a 50% flowering overlap which indicated a phenological shift. Diploids were strictly allogamous and did not display mentor effects, while tetraploids were found to be highly autogamous. This breakdown of self-incompatibility by polyploids is first described in Centaurea. The asymmetrical formation of the hybrid was also found: all the triploid intact cypselae came from the diploid mothers pollinated by the pollen of tetraploids. Pollen and eggs from triploids were totally sterile, acting as a strong triploid block. These prezygotic isolation mechanisms ensured higher assortative mating in tetraploids than in diploids, improving their persistence in the contact zones. However these mechanisms can also be the cause of the low genetic diversity and high genetic structure observed in C. seridis. PMID:26469271

  2. Efficient indica and japonica rice identification based on the InDel molecular method: Its implication in rice breeding and evolutionary research

    Institute of Scientific and Technical Information of China (English)

    Bao-Rong Lu; Xingxing Cai; Xin Jin

    2009-01-01

    An efficient molecular method for the accurate and efficient identification of indica and japonica rice was created based on the poly-morphisms of insertion/deletion (InDel) DNA fragments obtained from the basic local alignment search tool (BLAST) to the entire genomic sequences of indica (93-11) and japonica rice (Nipponbare). The 45 InDel loci were validated experimentally by the polymerase chain reaction (PCR) and polyacrylamide gel electrophoresis (PAGE) in 44 typical indica and japonica rice varieties, including 93-11 and Nipponbare. A neutrality test of the data matrix generated from electrophoretic banding patterns of various InDel loci indicated that 34 InDel loci were strongly associated with the differentiation of indica and japonica rice. More extensive analyses involving cultivated rice varieties from 11 Asian countries, and 12 wild Oryza species with various origins confirmed that indica and japonica characteristics could accurately be determined via calculating the average frequency of indica- or japonica-specific alleles on different InDel loci across the rice genome. This method was named as the "InDel molecular index" that combines molecular and statistical methods in determining the indica and japonica characteristics of rice varieties. Compared with the traditional methods based essentially on morphology, the InDel molecular index provides a very accurate, rapid, simple, and efficient method for identifying indica and japonica rice. In addition, the InDel index can be used to determine indica or japonica characteristics of wild Oryza species, which largely extends the utility of this method. The InDel molecular index provides a new tool for the effective selection of appropriate indica or japonica rice germplasm in rice breeding. It also offers a novel model for the study of the origin, evolution, and genetic differentiation of indica and japonica rice adapted to various environmental changes.

  3. Analysis on Genomic Structure Changes and Diversity of Introgression Lines in Dongxiang Wild Rice ( O.rufipogon Griff.)%东乡野生稻渐渗系基因组结构变化及多样性分析

    Institute of Scientific and Technical Information of China (English)

    邓晓娟; 罗向东; 谢建坤; 万勇; 胡标林; 曹娟芳; 戴亮芳

    2012-01-01

    [Objective] The aim of the study was to make research on genomic structure variation and variety analysis of Dongxiang wild rice. [Method] Introgression groups of BC1F6 were based on donor of O. Rufipogon Griff. And receptor of O. Sativa sp. Indica Kato. . Strains of 239 in the group were analyzed on Polymorphism with the help of 25 couples of SSR primers distributed in 12 pairs of chromosomes. [Result] Gene fragments of 0. Rufipogon Griff, were found penetrated in the 25 microsatellite sites and most of the groups kept the parents of Xieqinzao B or DNA sequence of 0. Rufipogon Griff. . The average rate of recurrent homozygous bands was 78. 13% in the Ils, but the highest was 94. 98% (amplified by primer RM131) and the lowest was 60. 25% ( RM171 ). The average rate of donor homozygous bands was 13. 37% , but the highest was 32. 64% (RM171) and the lowest was 2.93% ( RM1095 ). There were numerous heterozygous sites in the population and the average heterozygosis rate was 5.62% , while the highest was 10.04% (RM401). Moreover, we found that there were some parental fragments lost and some novel fragments which were not detected in either parent in BC1 F6 population. The average rate of lost bands was 2. 88% , while the highest was 13.39% (RM311) and the lowest was 0 (RM401). The average rate of new bands was 1%. The average of Nei's gene diversity (He) and Shannons Information index (I) were 0. 276 and 0.457 respectively in high generation of introgression lines. [Conclusion] The study demonstrated that distant hybridization led to extensive genetic and epigenetic variations in high generation of introgression lines, which expanded the base of genetic variation and laid an important foundation for rice improvement and germplasm innovation.%[目的]研究东乡野生稻渐渗系基因组结构变化及对其进行多样性分析.[方法]以东乡野生稻(O.rufipogon Grif,供体)和栽培稻协青早B(O.sativa sp.indica Kato.,受体)构建的BC1F6渐渗群体为研

  4. Iron homeostasis related genes in rice

    Directory of Open Access Journals (Sweden)

    Gross Jeferson

    2003-01-01

    Full Text Available Iron is essential for plants. However, excess iron is toxic, leading to oxidative stress and decreased productivity. Therefore, plants must use finely tuned mechanisms to keep iron homeostasis in each of their organs, tissues, cells and organelles. A few of the genes involved in iron homeostasis in plants have been identified recently, and we used some of their protein sequences as queries to look for corresponding genes in the rice (Oryza sativa genome. We have assigned possible functions to thirty-nine new rice genes. Together with four previously reported sequences, we analyzed a total of forty-three genes belonging to five known protein families: eighteen YS (Yellow Stripe, two FRO (Fe3+-chelate reductase oxidase, thirteen ZIP (Zinc regulated transporter / Iron regulated transporter Protein, eight NRAMP (Natural Resistance - Associated Macrophage Protein, and two Ferritin proteins. The possible cellular localization and number of potential transmembrane domains were evaluated, and phylogenetic analysis performed for each gene family. Annotation of genomic sequences was performed. The presence and number of homologues in each gene family in rice and Arabidopsis is discussed in light of the established iron acquisition strategies used by each one of these two plants.

  5. Modern elite rice varieties of the 'Green Revolution' have retained a large introgression from wild rice around the Pi33 rice blast resistance locus.

    Science.gov (United States)

    Ballini, Elsa; Berruyer, Romain; Morel, Jean-Benoît; Lebrun, Marc-Henri; Nottéghem, Jean-Loup; Tharreau, Didier

    2007-01-01

    During the breeding process of cultivated crops, resistance genes to pests and diseases are commonly introgressed from wild species. The size of these introgressions is predicted by theoretical models but has rarely been measured in cultivated varieties. By combining resistance tests with isogenic strains, genotyping and sequencing of different rice accessions, it was shown that, in the elite rice variety IR64, the resistance conferring allele of the rice blast resistance gene Pi33 was introgressed from the wild rice Oryza rufipogon (accession IRGC101508). Further characterization of this introgression revealed a large introgression at this locus in IR64 and the related variety IR36. The introgressed fragment represents approximately half of the short arm of rice chromosome 8. This is the first report of a large introgression in a cultivated variety of rice. Such a large introgression is likely to have been maintained during backcrossing only if a selection pressure was exerted on this genomic region. The possible traits that were selected are discussed.

  6. Comparative analysis of drought resistance genes in Arabidopsis and rice

    NARCIS (Netherlands)

    Trijatmiko, K.R.

    2005-01-01

    Keywords: rice, Arabidopsis, drought, genetic mapping,microarray, transcription factor, AP2/ERF, SHINE, wax, stomata, comparative genetics, activation tagging, Ac/Ds, En/IThis thesis describes the use of genomics information and tools from Arabidopsis and

  7. Genomic Signal Enhancement by Clustering

    Institute of Scientific and Technical Information of China (English)

    ZHENG Wei-Mou

    2003-01-01

    Weight matrix models for signal sequence motif are simple. A main limitation of the models is the assumption of independence between positions. Signal enhancement is achieved by taking the total likelihood as the objective function for maximization to cluster sequences into groups with different patterns. As an example, the initial and terminal signals for translation in rice genome are examined.

  8. ECONOMICS OF RICE PRODUCTION

    African Journals Online (AJOL)

    Fertilizer was the only variable that significantly influenced rice yields on ... cultural production in Ghana (MOFA, 2002), [n 2002, the agricultural sector em- ..... The rapid growth of the population has culminated in undue pressure on agricultural.

  9. Glutinous Rice in Pineapple

    Institute of Scientific and Technical Information of China (English)

    1998-01-01

    Ingredients: 50 grams glutinous rice, one pineapple, 20 grams dried fruits (raisins, walnuts. Chinese wolfberry, Chinese dates, lotus seeds, lily petals, kidney beans and peanuts) Seasonings: 5 grams rock sugar, 5 grams salad oil. Method:

  10. Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression

    Directory of Open Access Journals (Sweden)

    Li Xin

    2012-07-01

    Full Text Available Abstract Background DNA methylation plays important biological roles in plants and animals. To examine the rice genomic methylation landscape and assess its functional significance, we generated single-base resolution DNA methylome maps for Asian cultivated rice Oryza sativa ssp. japonica, indica and their wild relatives, Oryza rufipogon and Oryza nivara. Results The overall methylation level of rice genomes is four times higher than that of Arabidopsis. Consistent with the results reported for Arabidopsis, methylation in promoters represses gene expression while gene-body methylation generally appears to be positively associated with gene expression. Interestingly, we discovered that methylation in gene transcriptional termination regions (TTRs can significantly repress gene expression, and the effect is even stronger than that of promoter methylation. Through integrated analysis of genomic, DNA methylomic and transcriptomic differences between cultivated and wild rice, we found that primary DNA sequence divergence is the major determinant of methylational differences at the whole genome level, but DNA methylational difference alone can only account for limited gene expression variation between the cultivated and wild rice. Furthermore, we identified a number of genes with significant difference in methylation level between the wild and cultivated rice. Conclusions The single-base resolution methylomes of rice obtained in this study have not only broadened our understanding of the mechanism and function of DNA methylation in plant genomes, but also provided valuable data for future studies of rice epigenetics and the epigenetic differentiation between wild and cultivated rice.

  11. Validation of yield component traits identified by GWA mapping in a rice tropical japonica x tropical japonica RIL mapping population

    Science.gov (United States)

    The Rice Diversity Panel 1 (RDP1) was developed for genome-wide association (GWA) mapping to explore the five diverse rice (Oryza sativa) subpopulations (indica, aus, aromatic, temperate japonica and tropical japonica). RDP1 was evaluated for over 30 agronomic and morphological traits, most of whic...

  12. Structure and expression of a rice hsp70 gene

    Institute of Scientific and Technical Information of China (English)

    王群; 方荣祥

    1996-01-01

    A genomic hsp70 gene was isolated from a rice IR36 genomic library and 4 794 bp of the gene have been sequenoed. The 5’ flanking region of the gene contained a putative TATA box and a typical heat shock element sequence 5’-CTcgGAAccTTCgAG-3’. The amino acid sequence of the rice HSP70 deduced from the coding region shared 84%-92% homologies with those of HSP70s from other plant species. An intron 1939bp long was identified in the coding region at the codon specifying amino acid 72 (Asp), the similar position introns occurring in other intron-containing hsp70 genes. In addition, another intron of 57 bp was found in the 3’-untranslated region in the rice hsp70 gene. Southern blot hybridization showed that rice hsp70 gene family contained at least three members. Analysis of the RNA leveis with the gene-specific and non-specific probes revealed that the rice hsp70 gene expressed at normal temperature and the expression was enhanced by heat shock treatment.

  13. 基于短序列测序数据的四倍体拟南芥转录组研究%De Novo Assembly of Allotetraploid Arabidopsis suecica Transcriptome using Short Reads for Gene Discovery and Marker Identification

    Institute of Scientific and Technical Information of China (English)

    刘新星; 陈超

    2011-01-01

    为了促进对四倍体拟南芥(A.suecica)的研究,阐明多倍体植物在染色体加倍过程中遗传物质的变化,从而在分子层面上解释多倍体植物的环境适应和进化机制,描述了一套基于第二代测序技术的转录组短序列组装和生物信息学分析方法.通过对23 000 000条来至于Illumina测序平台的序列数据进行SOAPdenovo组装,以及后续的TGICL聚类和Phrap拼接,共得到125 953条非冗余的转录本序列,其N50和平均长度分别为550bp和331bp.通过BLASTX比对,共有96 057(76.3%)条转录本序列与Nr数据库中的植物蛋白序列具有高度同源性(e-value<10-5),对转录本序列的GO(gene ontology)要的蛋白功能.另外,将A.suecica转录组的GC含量与其相邻物种进行了比较分析,并对简单重复序列(SSRs)进行了鉴定.研究结果表明基于短序列测序数据的多重kmer组装对于转录组分析的可行性,并且为其他相关物种的转录组组装和基因表达分析提供了重要的参考价值.%To facilitate the research on Arabidopsis suecica (A. suecica), a method was presented for de novo assembly of A. suecica transcriptome using short reads produced by Illumina sequencing platform. 23 million sequencing reads were assembled into 125 953 unique sequences with the N50 length of 550 bp and mean size of 331 bp. At the protein level, a total of 96 057 (76. 3% ) A. suecica transcripts showed significant similarity with transcripts proteins from the other plants in the Nr database. Functional categorization revealed the conservation of genes involved in various biological processes in A. suecica. In addition, simple sequence repeats (SSRs) motifs in the A. suecica transcriptome was identified. The data provides a comprehensive sequence resource available for A. suecica study and demonstrates that the short pair-end reads sequencing allows de novo transcriptome assembly in a allotetraploid species lacking genome information. It is anticipated that

  14. Methodologies for in vitro cloning of small RNAs and application for plant genome(s).

    Science.gov (United States)

    Devor, Eric J; Huang, Lingyan; Abdukarimov, Abdusattor; Abdurakhmonov, Ibrokhim Y

    2009-01-01

    The "RNA revolution" that started at the end of the 20th century with the discovery of post-transcriptional gene silencing and its mechanism via RNA interference (RNAi) placed tiny 21-24 nucleotide long noncoding RNAs (ncRNAs) in the forefront of biology as one of the most important regulatory elements in a host of physiologic processes. The discovery of new classes of ncRNAs including endogenous small interfering RNAs, microRNAs, and PIWI-interacting RNAs is a hallmark in the understanding of RNA-dependent gene regulation. New generation high-throughput sequencing technologies further accelerated the studies of this "tiny world" and provided their global characterization and validation in many biological systems with sequenced genomes. Nevertheless, for the many "yet-unsequenced" plant genomes, the discovery of small RNA world requires in vitro cloning from purified cellular RNAs. Thus, reproducible methods for in vitro small RNA cloning are of paramount importance and will remain so into the foreseeable future. In this paper, we present a description of existing small RNA cloning methods as well as next-generation sequencing methods that have accelerated this research along with a description of the application of one in vitro cloning method in an initial small RNA survey in the "still unsequenced" allotetraploid cotton genome.

  15. Association Analysis of the Amino Acid Contents in Rice

    Institute of Scientific and Technical Information of China (English)

    Weiguo Zhao; Eun-Jin Park; Jong-Wook Chung; Yong-Jin Park; III-Min Chung; Joung-Kuk Ahn; Gwang-Ho Kim

    2009-01-01

    The main objective of the present study was to identify simple sequence repeat (SSR) markers associated with the amino acid content of rice (Oryza sativa L.). SSR markers were selected by prescreening for the relationship to amino acid content. Eighty-four rice landrace accessions from Korea were evaluated for 16 kinds of amino acids in brown rice and genotyped with 25 SSR markers. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r2 value for all intrachromosomal loci pairs was 0.033. LD between linked markers decreased with distance. Marker-trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). A total of 42 marker-trait associations with amino acids (P < 0.05) were identified using 15 different SSR markers covering three chromosomes and explaining more than 40% of the total variation. These results suggest that association analysis In rice is a viable alternative to quantitative trait loci mapping and should help rice breeders develop strategies for improving rice quality.

  16. 利用EcoTILLING简化技术进行水稻基因型鉴定及单核苷酸多态性(SNP)检测%Application of Simplified Ecotype Targeting Induced Local Lesions in Genomes (EcoTILLING) Technique for Genotyping and Single Nucleotide Polymorphism(SNP) Detection in Rice

    Institute of Scientific and Technical Information of China (English)

    滕斌; 李泽福; 罗志祥; 吴敬德; 朱学桂; 宣红; 张瑛

    2012-01-01

    Ecotype targeting induced local lesions in genomes (EcoTILLING) is a high-throughput method of detection and analysis of single nucleotide polymorphism (SNP) variations in natural populations. However, it requires a substantial investment in sophisticated equipment and costly fluorescence labeled primers to detect CELI - cut products that limit its use in laboratories with common financial resources. The technology of traditional EcoTILLING had been appropriately improved in this study. Here, we simplified extraction procedure of the CELI enzyme, prepared heteroduplex DNA products for CEL I digestion by use of natural cooling method, and detected the CEL I-cleaved products through general silver staining. The results of activities of crude CEL I enzyme extracts showed that the activity of CEL I was high enough for detection of mismatch bases. Using the simplified EcoTILLING technique, the G/T polymorphism at the first intron 5' splice site of the Wx gene among 18rice (Oryza saliva L.) accessions were successfully genotyped. In addition, CEL I digested bands of a 417 bp fragment within the Wx gene of the 18 rice accessions were distinguished into several types. On comparisons with sequencing results, CEL I cut bands could accurately reflect the SNP variations between the materials. The results suggested that the simplified EcoTILLING is an effective method for SNP discovery and genotyping in rice that will provide powerful tool for rice functional genomics research.%EcoTILLING(ecotype targeting induced local lesions in genomes)是一种高通量检测和分析自然群体中单核苷酸多态性(single nucleotide polymorphism,SNP)变异的研究方法.由于该技术需要高级、精密的仪器设备和昂贵的荧光标记引物来检测CEL(celery)I的酶切产物,极大地限制了该技术的应用.本研究对传统EcoTILLING技术做了适当改进,简化了CELI酶的抽提步骤,采用自然冷却方法制备异源双链产物,普通银染检测CELI酶切

  17. Rheological properties of rice-blackgram batter while replacing white rice with brown rice.

    Science.gov (United States)

    Manickavasagan, Annamalai; Al-Marhubi, Insaaf Mohd; Dev, Satyanarayan

    2014-06-01

    Rice-blackgram batter is a raw material for many traditional convenience foods in Asia. Reformulation of traditional convenience food by replacing white rice with whole rice (brown rice) is a novel method to reduce the consumption of refined grain and increase the intake of whole grain in our diet. In this study, rheological properties of rice-blackgram batter was investigated while replacing white rice with brown rice at five levels (T1--0% replacement (control), T2--25% replacement, T3--50% replacement, T4--75% replacement, and T5--100% replacement). The shear stress versus shear rate plot indicates that the rice-blackgram batter exhibited non-Newtonian fluid behavior (shear thinning property) even after 100% replacement of white rice with brown rice. The rheological characteristics of rice-blackgram batters fitted reasonably well in Cassan (r2 = 0.8521-0.9856) and power law (r2 = 0.8042-0.9823) models. Brown rice replacement at all levels did not affect the flow behavior index, yield stress, consistency coefficient, and apparent viscosity of batter at 25 degrees C. However, at higher temperature, the viscosity was greater for T4 and T5 (no difference between them) than T1, T2, and T3 (no difference between them) batters. Further research is required to determine the sensory attributes and acceptability of the cooked products with brown rice-blended batter.

  18. Designing climate-resilient rice with ideal grain quality suited for high-temperature stress.

    Science.gov (United States)

    Sreenivasulu, Nese; Butardo, Vito M; Misra, Gopal; Cuevas, Rosa Paula; Anacleto, Roslen; Kavi Kishor, Polavarpu B

    2015-04-01

    To ensure rice food security, the target outputs of future rice breeding programmes should focus on developing climate-resilient rice varieties with emphasis on increased head rice yield coupled with superior grain quality. This challenge is made greater by a world that is increasingly becoming warmer. Such environmental changes dramatically impact head rice and milling yield as well as increasing chalkiness because of impairment in starch accumulation and other storage biosynthetic pathways in the grain. This review highlights the knowledge gained through gene discovery via quantitative trait locus (QTL) cloning and structural-functional genomic strategies to reduce chalk, increase head rice yield, and develop stable lines with optimum grain quality in challenging environments. The newly discovered genes and the knowledge gained on the influence of specific alleles related to stability of grain quality attributes provide a robust platform for marker-assisted selection in breeding to design heat-tolerant rice varieties with superior grain quality. Using the chalkiness trait in rice as a case study, we demonstrate here that the emerging field of systems genetics can help fast-track the identification of novel alleles and gene targets that can be pyramided for the development of environmentally robust rice varieties that possess improved grain quality. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  19. Physical mapping, expression analysis and polymorphism survey of resistance gene analogues on chromosome 11 of rice

    Indian Academy of Sciences (India)

    Irfan A Ghazi; Prem S Srivastava; Vivek Dalal; Kishor Gaikwad; Ashok K Singh; Tilak R Sharma; Nagendra K Singh; Trilochan Mohapatra

    2009-06-01

    Rice is the first cereal genome with a finished sequence and a model crop that has important syntenic relationships with other cereal species. The objectives of our study were to identify resistance gene analogue (RGA) sequences from chromosome 11 of rice, understand their expression in other cereals and dicots by in silico analysis, determine their presence on other rice chromosomes, and evaluate the extent of polymorphism and actual expression in a set of rice genotypes. A total of 195 RGAs were predicted and physically localised. Of these, 91.79% expressed in rice, and 51.28% expressed in wheat, which was the highest among other cereals. Among monocots, sugarcane showed the highest (78.92%) expression, while among dicots, RGAs were maximally expressed in Arabidopsis (11.79%). Interestingly, two of the chromosome 11-specific RGAs were found to be expressing in all the organisms studied. Eighty RGAs of chromosome 11 had significant homology with chromosome 12, which was the maximum among all the rice chromosomes. Thirty-one per cent of the RGAs used in polymerase chain reaction (PCR) amplification showed polymorphism in a set of rice genotypes. Actual gene expression analysis revealed post-inoculation induction of one RGA in the rice line IRBB-4 carrying the bacterial blight resistance gene Xa-4. Our results have implications for the development of sequence-based markers and functional validation of specific RGAs in rice.

  20. Rice proteomics: a model system for crop improvement and food security.

    Science.gov (United States)

    Kim, Sun Tae; Kim, Sang Gon; Agrawal, Ganesh Kumar; Kikuchi, Shoshi; Rakwal, Randeep

    2014-03-01

    Rice proteomics has progressed at a tremendous pace since the year 2000, and that has resulted in establishing and understanding the proteomes of tissues, organs, and organelles under both normal and abnormal (adverse) environmental conditions. Established proteomes have also helped in re-annotating the rice genome and revealing the new role of previously known proteins. The progress of rice proteomics had recognized it as the corner/stepping stone for at least cereal crops. Rice proteomics remains a model system for crops as per its exemplary proteomics research. Proteomics-based discoveries in rice are likely to be translated in improving crop plants and vice versa against ever-changing environmental factors. This review comprehensively covers rice proteomics studies from August 2010 to July 2013, with major focus on rice responses to diverse abiotic (drought, salt, oxidative, temperature, nutrient, hormone, metal ions, UV radiation, and ozone) as well as various biotic stresses, especially rice-pathogen interactions. The differentially regulated proteins in response to various abiotic stresses in different tissues have also been summarized, indicating key metabolic and regulatory pathways. We envision a significant role of rice proteomics in addressing the global ground level problem of food security, to meet the demands of the human population which is expected to reach six to nine billion by 2040.

  1. Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture

    DEFF Research Database (Denmark)

    Li, Lei; Wang, Xiangfeng; Xia, Mian

    2005-01-01

    BACKGROUND: Sequencing and annotation of the genome of rice (Oryza sativa) have generated gene models in numbers that top all other fully sequenced species, with many lacking recognizable sequence homology to known genes. Experimental evaluation of these gene models and identification of new models...... definition of the heterochromatin and euchromatin domains. The heterochromatin domain appears to associate with distinct chromosome level transcriptional activities under normal and stress conditions. CONCLUSION: These results demonstrated the utility of genome tiling microarray in evaluating annotated rice...

  2. Agrobacterium-mediated transformation: rice transformation.

    Science.gov (United States)

    Slamet-Loedin, Inez H; Chadha-Mohanty, Prabhjit; Torrizo, Lina

    2014-01-01

    Agrobacterium is a common soil bacterium with natural capacity for trans-kingdom transfer of genetic information by transferring its T-DNA into the eukaryotic genome. In agricultural plant biotechnology, combination of non-phytopathogenic strain of Agrobacterium tumefaciens with modified T-DNA and vir-genes in a binary vector system is the most widely utilized system for genetic improvement in diverse plant species and for gene function validation. Here we have described a highly efficient A. tumefaciens-mediated transformation system for indica and japonica rice cultivars based on an immature embryo system.

  3. Amplification, analysis and chromosome mapping of novel homeobox-containing and homeobox-flanking sequences in rice

    Institute of Scientific and Technical Information of China (English)

    刘国振; 严长杰; 翟文学; 何平; 杨江; 李小兵; 朱立煌

    1999-01-01

    Homeobox genes, widely distributed among animal and plant kingdoms, play an important role in developmental process. Several homeobox conserved fragments were amplified by PCR and the flanking regions were also obtained by an LM-PCR procedure. Sequencing and Southern analysis showed that they belong to a homeobox gene family of rice. Six homeobox-containing fragments were mapped on the molecular linkage map of rice. They were located on chromosomes 3, 4 and 7 respectively. It is noteworthy that there are 4 homeobox fragments located on rice chromosome 3 and the result is also consistent with the comparative genomics between rice and maize.

  4. Gene enrichment in plant genomic shotgun libraries.

    Science.gov (United States)

    Rabinowicz, Pablo D; McCombie, W Richard; Martienssen, Robert A

    2003-04-01

    The Arabidopsis genome (about 130 Mbp) has been completely sequenced; whereas a draft sequence of the rice genome (about 430 Mbp) is now available and the sequencing of this genome will be completed in the near future. The much larger genomes of several important crop species, such as wheat (about 16,000 Mbp) or maize (about 2500 Mbp), may not be fully sequenced with current technology. Instead, sequencing-analysis strategies are being developed to obtain sequencing and mapping information selectively for the genic fraction (gene space) of complex plant genomes.

  5. Screening of Rice Genes Interacting with p5b of Rice Black-Streaked Dwarf Virus

    Institute of Scientific and Technical Information of China (English)

    LU Ying; YANG Jian; ZHANG Heng-mu; CHEN Jian-ping

    2013-01-01

    Rice black-streaked dwarf virus (RBSDV) is a recognized member of the genus Fijivirus,family Reoviridae.Its genome has ten double-stranded RNA (dsRNA) segments (S1-S10),in which the fifth genome segment (S5) contains two open reading frames (ORFs) with a partially overlapping region.The second ORF of RBSDV S5 encodes a viral nonstructural protein named p5b with unknown function.To reveal the function of p5b,its gene was ligated into the bait plasmid pGBKT7 and an expression library containing rice cDNAs was constructed using plasmid pGADT7 for yeast two-hybrid assay.The bait protein p5b was detected in yeast by western blot,and the result of an auto-activation test showed that p5b could not autonomously activate the expression of reporter genes in yeast.Then the bait protein p5b was used for screening the cDNA expression libraries of rice.Gene fragments of some pivotal enzymes involved in photosynthesis,respiration and other important metabolic processes,were identified to interact with p5b in yeast,suggesting that these interactions may play roles in symptom development in infected plants.

  6. Molecular Evolution of the TAC1 Gene from Rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    Jiahuan Jiang; Lubin Tan; Zuofeng Zhu; Yongcai Fu; Fengxia Liu; Hongwei Cai; Chuanqing Sun

    2012-01-01

    Tiller angle is a key feature of the architecture of cultivated rice (Oryza sativa),since it determines planting density and influences rice yield.Our previous work identified Tiller Angle Control 1 (TAC1) as a major quantitative trait locus that controls rice tiller angle.To further clarify the evolutionary characterization of the TAC1 gene,we compared a TAC1-containing 3164-bp genomic region among 113 cultivated varieties and 48 accessions of wild rice,including 43 accessions of O.rufipogon and five accessions of O.nivara.Only one single nucleotide polymorphism (SNP),a synonymous substitution,was detected in TAC1 coding regions of the cultivated rice varieties,whereas one synonymous and one nonsynonymous SNP were detected among the TAC1 coding regions of wild rice accessions.These data indicate that little natural mutation and modification in the TAC1 coding region occurred within the cultivated rice and its progenitor during evolution.Nucleotide diversities in the TAC1 gene regions of O.sativa and O.rufipogon of 0.00116 and 0.00112,respectively,further indicate that TAC1 has been highly conserved during the course of rice domestication.A functional nucleotide polymorphism (FNP) of TAC1 was only found in the japonica rice group.A neutrality test revealed strong selection,especially in the 3'-flanking region of the TAC1 coding region containing the FNP in the japonica rice group.However,no selection occurred in the indica and wild-rice groups.A phylogenetic tree derived from TAC1 sequence analysis suggests that the indica and japonica subspecies arose independently during the domestication of wild rice.

  7. Analysis of elite variety tag SNPs reveals an important allele in upland rice.

    Science.gov (United States)

    Lyu, Jun; Zhang, Shilai; Dong, Yang; He, Weiming; Zhang, Jing; Deng, Xianneng; Zhang, Yesheng; Li, Xin; Li, Baoye; Huang, Wangqi; Wan, Wenting; Yu, Yang; Li, Qiong; Li, Jun; Liu, Xin; Wang, Bo; Tao, Dayun; Zhang, Gengyun; Wang, Jun; Xu, Xun; Hu, Fengyi; Wang, Wen

    2013-01-01

    Elite crop varieties usually fix alleles that occur at low frequencies within non-elite gene pools. Dissecting these alleles for desirable agronomic traits can be accomplished by comparing the genomes of elite varieties with those from non-elite populations. Here we deep-sequence six elite rice varieties and use two large control panels to identify elite variety tag single-nucleotide polymorphism alleles (ETASs). Guided by this preliminary analysis, we comprehensively characterize one protein-altering ETAS in the 9-cis-epoxycarotenoid dioxygenase gene of the IRAT104 upland rice variety. This allele displays a drastic frequency difference between upland and irrigated rice, and a selective sweep is observed around this allele. Functional analysis indicates that in upland rice, this allele is associated with significantly higher abscisic acid levels and denser lateral roots, suggesting its association with upland rice suitability. This report provides a potential strategy to mine rare, agronomically important alleles.

  8. Role of LOX3 Gene in Alleviating Adverse Effects of Drought and Pathogens in Rice

    Institute of Scientific and Technical Information of China (English)

    LIU Nan-nan; JIANG Ling; ZHANG Wen-wei; LIU Ling-long; ZHAI Hu-qu; WAN Jian-min

    2008-01-01

    Lipoxygenase 3 (LOX3) is a major component of the LOX isozymes in mature rice seeds. To investigate the role of LOX3 gene under stresses, a plant expression vector containing antisense cDNA of LOX3 was constructed. Rice varieties Wuyunjing 7 and Kasalath were transformed by the Agrobacterium-mediated method and transgenic rice plants were generated. PCR and Southern blot results showed that the antisense LOX3 gene was integrated into the rice genome. Analyses of embryo LOX3 deletion and semi-quantitative RT-PCR confirmed the antisense suppression of LOX3 gene in transgenic plants. The T2 antisense plants of LOX3 were sensitive to drought stress, rice blast and bacterial blight compared with non-transgenic plants. These results suggest that the LOX3 gene might function in response to stresses.

  9. Construction of the Primary Physical Map of Rice Chromosome 12

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A primary physical map of rice chromosome 12 was constructed using marker-based chromosome landing and chromosome walking. A BAC library from IR64 was screened using 84 RFLP markers, 4 STS markers and 6 microsatellite markers on chromosome 12 by colony hybridization and polymerase chain reaction (PCR) amplification. A total of 59 contigs consisting of 419 BAC clones including 5 single-clones were physically aligned on rice chromosome 12 with the largest BAC contig covering 855 kb. The whole physical map had a size of ~16 Mb and covered about 52% of rice chromosome 12. This physical map will be certainly helpful for map-based gene cloning of agronomically and biological important genes and understanding the genome structure of the chromosome.

  10. Transgenic Expression of the Recombinant Phytase in Rice (Oryza sativa)

    Institute of Scientific and Technical Information of China (English)

    LIU Qiao-quan; LI Qian-feng; JIANG Li; ZHANG Da-jiang; WANG Hong-mei; GU Ming-hong; YAO Quan-hong

    2006-01-01

    In most of the cereal crop, phytic acid is the main storage form of phosphorus, which can decrease the bioavailability of phosphate. Transgenic expression of phytase is regarded as an efficient way to release phosphate from phytate in transgenic plants.In this study, a plant expression vector, containing the recombinant phytase gene driven by the maize ubiquitin (Ubi) promoter was constructed and introduced into an elite rice variety via Agrobacterium-mediated transformation. During the experiment, a total of 15 independent transgenic rice lines were regenerated. The results of PCR and Southern blot indicated that the target gene was integrated into the genome of transgenic rice plants. Moreover, the RT-PCR analysis of total RNAs extracted from the immature seeds of several transgenic lines showed that the recombinant phytase gene could be normally expressed. The inorganic phosphorus content, both in the mature seeds and the leaf was significantly higher in the transgenic plants than in the untransformed wild type.

  11. Rice Quality Improvement in China

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    @@ 1. Demand for high quality rice in China Rice is the leading cereal crop that contributes about 40% of the national grain production in China. The total output and areas rank the first and the second position in the world, respectively. In recent years, rice production grows steadily, but the quality improvement has been lagged and the quality becomes a limiting factor. As the grain supply exceeding the demand and the grain price plummeted, the State Council put forward expanding China′ s ongoing reform of the grain distribution system in 1998. Along with the foodstuff circulating system reform and market driving, the structure of rice production is adjusted,the planting acreage of early indica rice with poor quality decreased, and that of japonica rice in north China with good quality increased. With the challenge of China joining the WTO, Chinese government starts to pay premium on good quality rice.

  12. 棉花功能基因组研究用的突变体库构建%Establishment of Mutated Gene Bank for Cotton Functional Genomic Research

    Institute of Scientific and Technical Information of China (English)

    Ye-hua YANG; Xue-kui WANG; Zhen-bin WU; Hai-yan LIU

    2002-01-01

    @@ Upland cotton is one of the important cultivated allotetraploid species. From the point of functional genomic research, it is hard to obtain homozygous recessive mutants by applying of traditional mutagensis methods in this crop as its many traits are controlled by more than two pairs of alleles. Adopting of specific transposon tagging strategy which is widely used to induce and isolate mutated genes in various plant species can avoid isolating recessive mutants and is easy to find and characterize the mutated genes in the tetraploid cotton species.

  13. The genetic and molecular basis of cytoplasmic male sterility and fertility restoration in rice

    Institute of Scientific and Technical Information of China (English)

    GUO JingXin; LIU YaoGuang

    2009-01-01

    Cytoplasmic male sterility (CMS) is a maternally inherited characteristic found in many (>150) plant species. CMS/restoration systems are useful tools for hybrid seed production, and are ideal models for study of the interactions between nuclear and mitochondrial genomes. CMS/restoration systems in rice have been widely used for hybrid seed production, greatly contributing to the food supply. This article reviews the progress of the studies on the genetic and molecular basis of cytoplasmic male sterility and fertility restoration in rice.

  14. Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research

    Directory of Open Access Journals (Sweden)

    Rita eSharma

    2013-08-01

    Full Text Available Glycoside hydrolases (GH catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/. This database integrates multiple data types including the structural features, orthologous relationships, mutant availability and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four monocot genomes, we identified 138 GH genes that are highly diverged between monocots and dicots, 57 of which have diverged further in rice as compared with four monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification.

  15. Escape to Ferality: The Endoferal Origin of Weedy Rice from Crop Rice through De-Domestication

    Science.gov (United States)

    Gettler, Kyle A.; Burgos, Nilda R.; Fischer, Albert J.

    2016-01-01

    Domestication is the hallmark of evolution and civilization and harnesses biodiversity through selection for specific traits. In regions where domesticated lines are grown near wild relatives, congeneric sources of aggressive weedy genotypes cause major economic losses. Thus, the origins of weedy genotypes where no congeneric species occur raise questions regarding management effectiveness and evolutionary mechanisms responsible for weedy population success. Since eradication in the 1970s, California growers avoided weedy rice through continuous flood culture and zero-tolerance guidelines, preventing the import, presence, and movement of weedy seeds. In 2003, after decades of no reported presence in California, a weedy rice population was confirmed in dry-seeded fields. Our objectives were to identify the origins and establishment of this population and pinpoint possible phenotypes involved. We show that California weedy rice is derived from a different genetic source among a broad range of AA genome Oryzas and is most recently diverged from O. sativa temperate japonica cultivated in California. In contrast, other weedy rice ecotypes in North America (Southern US) originate from weedy genotypes from China near wild Oryza, and are derived through existing crop-wild relative crosses. Analyses of morphological data show that California weedy rice subgroups have phenotypes like medium-grain or gourmet cultivars, but have colored pericarp, seed shattering, and awns like wild relatives, suggesting that reversion to non-domestic or wild-like traits can occur following domestication, despite apparent fixation of domestication alleles. Additionally, these results indicate that preventive methods focused on incoming weed sources through contamination may miss burgeoning weedy genotypes that rapidly adapt, establish, and proliferate. Investigating the common and unique evolutionary mechanisms underlying global weed origins and subsequent interactions with crop relatives sheds

  16. Annotation and BAC/PAC localization of nonredundant ESTs from drought-stressed seedlings of an indica rice

    Indian Academy of Sciences (India)

    P. Ravindra Babu; A. Chandra Sekhar; Nagabhushana Ithal; G. Markandeya; Arjula R. Reddy

    2002-04-01

    To decipher the genes associated with drought stress response and to identify novel genes in rice, we utilized 1540 high-quality expressed sequence tags (ESTs) for functional annotation and mapping to rice genomic sequences. These ESTs were generated earlier by 3′-end single-pass sequencing of 2000 cDNA clones from normalized cDNA libraries constructed from drought-stressed seedlings of an indica rice. A rice UniGene set of 1025 transcripts was constructed from this collection through the BLASTN algorithm. Putative functions of 559 nonredundant ESTs were identified by BLAST similarity search against public databases. Putative functions were assigned at a stringency E value of 10-6 in BLASTN and BLASTX algorithms. To understand the gene structure and function further, we have utilized the publicly available finished and unfinished rice BAC/PAC (BAC, bacterial artificial chromosome; PAC, P1 artificial chromosome) sequences for similarity search using the BLASTN algorithm. Further, 603 nonredundant ESTs have been mapped to BAC/PAC clones. BAC clones were assigned by a homology of above 95% identity along 90% of EST sequence length in the aligned region. In all, 700 ESTs showed rice EST hits in GenBank. Of the 325 novel ESTs, 128 were localized to BAC clones. In addition, 127 ESTs with identified putative functions but with no homology in IRGSP (International Rice Genome Sequencing Program) BAC/PAC sequences were mapped to the Chinese WGS (whole genome shotgun contigs) draft sequence of the rice genome. Functional annotation uncovered about a hundred candidate ESTs associated with abiotic stress in rice and Arabidopsis that were previously reported based on microarray analysis and other studies. This study is a major effort in identifying genes associated with drought stress response and will serve as a resource to rice geneticists and molecular biologists.

  17. A novel gene OsAHL1 improves both drought avoidance and drought tolerance in rice

    OpenAIRE

    Liguo Zhou; Zaochang Liu; Yunhua Liu; Deyan Kong; Tianfei Li; Shunwu Yu; Hanwei Mei; Xiaoyan Xu; Hongyan Liu; Liang Chen; Lijun Luo

    2016-01-01

    A novel gene, OsAHL1, containing an AT-hook motif and a PPC domain was identified through genome-wide profiling and analysis of mRNAs by comparing the microarray of drought-challenged versus normally watered rice. The results indicated OsAHL1 has both drought avoidance and drought tolerance that could greatly improve drought resistance of the rice plant. Overexpression of OsAHL1 enhanced multiple stress tolerances in rice plants during both seedling and panicle development stages. Functional ...

  18. Tracing ancestor rice of Suriname Maroons back to its African origin.

    Science.gov (United States)

    van Andel, Tinde R; Meyer, Rachel S; Aflitos, Saulo A; Carney, Judith A; Veltman, Margaretha A; Copetti, Dario; Flowers, Jonathan M; Havinga, Reinout M; Maat, Harro; Purugganan, Michael D; Wing, Rod A; Schranz, M Eric

    2016-10-03

    African rice (Oryza glaberrima) and African cultivation practices are said to have influenced emerging colonial plantation economies in the Americas(1,2). However, the level of impact of African rice practices is difficult to establish because of limited written or botanical records(2,3). Recent findings of O. glaberrima in rice fields of Suriname Maroons bear evidence of the high level of knowledge about rice among African slaves and their descendants, who consecrate it in ancestor rituals(4,5). Here we establish the strong similarity, and hence likely origin, of the first extant New World landrace of O. glaberrima to landraces from the Upper Guinean forests in West Africa. We collected African rice from a Maroon market in Paramaribo, Suriname, propagated it, sequenced its genome(6) and compared it with genomes of 109 accessions representing O. glaberrima diversity across West Africa. By analysing 1,649,769 single nucleotide polymorphisms (SNPs) in clustering analyses, the Suriname sample appears sister to an Ivory Coast landrace, and shows no evidence of introgression from Asian rice. Whereas the Dutch took most slaves from Ghana, Benin and Central Africa(7), the diaries of slave ship captains record the purchase of food for provisions when sailing along the West African Coast(8), offering one possible explanation for the patterns of genetic similarity. This study demonstrates the utility of genomics in understanding the largely unwritten histories of crop cultures of diaspora communities.

  19. Workshop on hybrid rice

    Institute of Scientific and Technical Information of China (English)

    TANZhijun

    1994-01-01

    FAO, in collaboration with FEDEARROZ in Colombia and EMBRAPA / CNPAF in Brail, organized a workshop on the Establishment of a Coorperative Research Network on Hybrid Rice in Latin America and the Caribbean held from Mar 16 to 18, 1994 at EMBRAPA/CNPAF in Brazil. Dr MAO Changxiang,

  20. Glutinous Rice Cakes

    Institute of Scientific and Technical Information of China (English)

    1997-01-01

    CELEBRATING Spring Festival includes making glutinous rice cakes, or niangao in Chinese. Traditional and new methods of making niangao vary in taste according to different areas. No matter poor or rich. niangao is a must for every family during Spring Festival as it symbolizes auspiciousness. In Beijing, both northern and southernstyle niangao are available. After the Beginning of Autumn (13th solar term), the

  1. Exploring Japan through Rice.

    Science.gov (United States)

    Wojtan, Linda S.

    1998-01-01

    Explores the role of rice in Japanese culture by presenting historical background and teaching activities in a variety of categories, such as language, sociology, history, and contemporary politics. Suggests teachers create cross-cultural comparisons; for example, the role of corn in the United States. Provides a list of teacher resources. (CMK)

  2. Physiological, genomic and transcriptional diversity in responses to boron deficiency in rapeseed genotypes

    Science.gov (United States)

    Hua, Yingpeng; Zhou, Ting; Ding, Guangda; Yang, Qingyong; Shi, Lei; Xu, Fangsen

    2016-01-01

    Allotetraploid rapeseed (Brassica napus L. AnAnCnCn, 2n=4x=38) is highly susceptible to boron (B) deficiency, a widespread limiting factor that causes severe losses in seed yield. The genetic variation in the sensitivity to B deficiency found in rapeseed genotypes emphasizes the complex response architecture. In this research, a B-inefficient genotype, ‘Westar 10’ (‘W10’), responded to B deficiencies during vegetative and reproductive development with an over-accumulation of reactive oxygen species, severe lipid peroxidation, evident plasmolysis, abnormal floral organogenesis, and widespread sterility compared to a B-efficient genotype, ‘Qingyou 10’ (‘QY10’). Whole-genome re-sequencing (WGS) of ‘QY10’ and ‘W10’ revealed a total of 1 605 747 single nucleotide polymorphisms and 218 755 insertions/deletions unevenly distributed across the allotetraploid rapeseed genome (~1130Mb). Digital gene expression (DGE) profiling identified more genes related to B transporters, antioxidant enzymes, and the maintenance of cell walls and membranes with higher transcript levels in the roots of ‘QY10’ than in ‘W10’ under B deficiency. Furthermore, based on WGS and bulked segregant analysis of the doubled haploid (DH) line pools derived from ‘QY10’ and ‘W10’, two significant quantitative trait loci (QTLs) for B efficiency were characterized on chromosome C2, and DGE-assisted QTL-seq analyses then identified a nodulin 26-like intrinsic protein gene and an ATP-binding cassette (ABC) transporter gene as the corresponding candidates regulating B efficiency. This research facilitates a more comprehensive understanding of the differential physiological and transcriptional responses to B deficiency and abundant genetic diversity in rapeseed genotypes, and the DGE-assisted QTL-seq analyses provide novel insights regarding the rapid dissection of quantitative trait genes in plant species with complex genomes. PMID:27639094

  3. Comparative analysis of A, B,C and D genomes in the genus Oryza with C0t-1 DNA of C genome

    Institute of Scientific and Technical Information of China (English)

    LAN Weizhen; QIN Rui; LI Gang; HE Guangcun

    2006-01-01

    Fluorescence in situ hybridization (FISH)was applied to somatic chromosomes preparations of Oryza officinalis Wall. (CC), O. sativa L. (AA)×O. officinalis F1 hybrid (AC), backcross progenies BC1 (AAC and ACC), O. latifolia Desv. (CCDD), O. alta Swallen (CCDD) and O. punctata Kotschy (BBCC)with a labelled probe of Cot-1 DNA from O. officinalis.In O. officinalis, the homologous chromosomes showed similar signal bands probed by C0t-1 DNA and karyotype analysis was conducted based on the band patterns. Using no blocking DNA, the probe identified the chromosomes of C genome clearly, but detected few signals on chromosomes of A genome in the F1 hybrid and two backcross progenies of BC1.It is obvious that the highly and moderately repetitive DNA sequences were considerably different between C and A genomes. The chromosomes of C genome were also discriminated from the chromosomes of D-and B-genome in the tetraploid species O. latifolia, O.alta and O. punctata by C0t-1 DNA-FISH. Comparison of the fluorescence intensity on the chromosomes of B, C and D genomes in O. latifolia, O. alta,and O. punctata indicated that the differentiations between C and D genomes are less than that between C and B genomes. The relationship between C and D genomes in O. alta is closer than that of C and D genomes in O. latifolia. This would be one of the causes for the fact that both the genomes are of the same karyotype (CCDD) but belong to different species. The above results showed that the C0t-1 DNA had a high specificity of genome and species. In this paper, the origin of allotetraploid in genus Oryza is also discussed.

  4. OryzaGenome: Genome Diversity Database of Wild Oryza Species

    KAUST Repository

    Ohyanagi, Hajime

    2015-11-18

    The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a textbased browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tabdelimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/ scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.

  5. OryzaGenome: Genome Diversity Database of Wild Oryza Species.

    Science.gov (United States)

    Ohyanagi, Hajime; Ebata, Toshinobu; Huang, Xuehui; Gong, Hao; Fujita, Masahiro; Mochizuki, Takako; Toyoda, Atsushi; Fujiyama, Asao; Kaminuma, Eli; Nakamura, Yasukazu; Feng, Qi; Wang, Zi-Xuan; Han, Bin; Kurata, Nori

    2016-01-01

    The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a text-based browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tab-delimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.

  6. 7 CFR 868.310 - Grades and grade requirements for the classes Long Grain Milled Rice, Medium Grain Milled Rice...

    Science.gov (United States)

    2010-01-01

    ... Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice. (See also Â...) GRAIN INSPECTION, PACKERS AND STOCKYARD ADMINISTRATION (FEDERAL GRAIN INSPECTION SERVICE), DEPARTMENT OF... classes Long Grain Milled Rice, Medium Grain Milled Rice, Short Grain Milled Rice, and Mixed Milled Rice...

  7. Sequence variation and selection of small RNAs in domesticated rice

    Directory of Open Access Journals (Sweden)

    Cai Daguang

    2010-04-01

    Full Text Available Abstract Background Endogenous non-coding small RNAs (21-24 nt play an important role in post-transcriptional gene regulation in plants. Domestication selection is the most important evolutionary force in shaping crop genomes. The extent of polymorphism at small RNA loci in domesticated rice and whether small RNA loci are targets of domestication selection have not yet been determined. Results A polymorphism survey of 94 small RNA loci (88 MIRNAs, four TAS3 loci and two miRNA-like long hairpins was conducted in domesticated rice, generating 2 Mb of sequence data. Many mutations (substitution or insertion/deletion were observed at small RNA loci in domesticated rice, e.g. 12 mutation sites were observed in the mature miRNA sequences of 11 MIRNAs (12.5% of the investigated MIRNAs. Several small RNA loci showed significant signals for positive selection and/or potential domestication selection. Conclusions Sequence variation at miRNAs and other small RNAs is higher than expected in domesticated rice. Like protein-coding genes, non-coding small RNA loci could be targets of domestication selection and play an important role in rice domestication and improvement.

  8. Comparative proteomic analysis of indica and japonica rice varieties

    Directory of Open Access Journals (Sweden)

    Yanhua Yang

    2014-12-01

    Full Text Available Indica and japonica are two main subspecies of Asian cultivated rice (Oryza sativa L. that differ clearly in morphological and agronomic traits, in physiological and biochemical characteristics and in their genomic structure. However, the proteins and genes responsible for these differences remain poorly characterized. In this study, proteomic tools, including two-dimensional electrophoresis and mass spectrometry, were used to globally identify proteins that differed between two sequenced rice varieties (93-11 and Nipponbare. In all, 47 proteins that differed significantly between 93-11 and Nipponbare were identified using mass spectrometry and database searches. Interestingly, seven proteins were expressed only in Nipponbare and one protein was expressed specifically in 93-11; these differences were confirmed by quantitative real-time PCR and proteomic analysis of other indica and japonica rice varieties. This is the first report to successfully demonstrate differences in the protein composition of indica and japonica rice varieties and to identify candidate proteins and genes for future investigation of their roles in the differentiation of indica and japonica rice.

  9. Monitoring homologous recombination in rice (Oryza sativa L.)

    Energy Technology Data Exchange (ETDEWEB)

    Yang Zhuanying; Tang Li [Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631 (China); Li Meiru [South China Botanic Garden, Chinese Academy of Sciences, Guangzhou 510650 (China); Chen Lei; Xu Jie [Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631 (China); Wu Goujiang [South China Botanic Garden, Chinese Academy of Sciences, Guangzhou 510650 (China); Li Hongqing, E-mail: hqli@scnu.edu.cn [Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631 (China)

    2010-09-10

    Here we describe a system to assay homologous recombination during the complete life cycle of rice (Oryza sativa L.). Rice plants were transformed with two copies of non-functional GUS reporter overlap fragments as recombination substrate. Recombination was observed in all plant organs examined, from the seed stage until the flowering stage of somatic plant development. Embryogenic cells exhibited the highest recombination ability with an average of 3 x 10{sup -5} recombination events per genome, which is about 10-fold of that observed in root cells, and two orders of that observed in leaf cells. Histological analysis revealed that recombination events occurred in diverse cell types, but preferentially in cells with small size. Examples of this included embryogenic cells in callus, phloem cells in the leaf vein, and cells located in the root apical meristem. Steady state RNA analysis revealed that the expression levels of rice Rad51 homologs are positively correlated with increased recombination rates in embryogenic calli, roots and anthers. Finally, radiation treatment of plantlets from distinct recombination lines increased the recombination frequency to different extents. These results showed that homologous recombination frequency can be effectively measured in rice using a transgene reporter assay. This system will facilitate the study of DNA damage signaling and homologous recombination in rice, a model monocot.

  10. Study on red rice%赤米考

    Institute of Scientific and Technical Information of China (English)

    俞为洁

    2005-01-01

    'The red rice grain' recorded in the Chinese ancient books is neither a kind of good rice variety nor old rice grain or rotten rice grain, they are some rice varieties which have red-color grains and poor taste.

  11. Transcriptome analysis of rice root responses to potassium deficiency

    Directory of Open Access Journals (Sweden)

    Ma Tian-Li

    2012-09-01

    Full Text Available Abstract Background Potassium (K+ is an important nutrient ion in plant cells and plays crucial roles in many plant physiological and developmental processes. In the natural environment, K+ deficiency is a common abiotic stress that inhibits plant growth and reduces crop productivity. Several microarray studies have been conducted on genome-wide gene expression profiles of rice during its responses to various stresses. However, little is known about the transcriptional changes in rice genes under low-K+ conditions. Results We analyzed the transcriptomic profiles of rice roots in response to low-K+ stress. The roots of rice seedlings with or without low-K+ treatment were harvested after 6 h, and 3 and 5 d, and used for microarray analysis. The microarray data showed that many genes (2,896 were up-regulated or down-regulated more than 1.2-fold during low-K+ treatment. GO analysis indicated that the genes showing transcriptional changes were mainly in the following categories: metabolic process, membrane, cation binding, kinase activity, transport, and so on. We conducted a comparative analysis of transcriptomic changes between Arabidopsis and rice under low-K+ stress. Generally, the genes showing changes in transcription in rice and Arabidopsis in response to low-K+ stress displayed similar GO distribution patterns. However, there were more genes related to stress responses and development in Arabidopsis than in rice. Many auxin-related genes responded to K+ deficiency in rice, whereas jasmonic acid-related enzymes may play more important roles in K+ nutrient signaling in Arabidopsis. Conclusions According to the microarray data, fewer rice genes showed transcriptional changes in response to K+ deficiency than to phosphorus (P or nitrogen (N deficiency. Thus, transcriptional regulation is probably more important in responses to low-P and -N stress than to low-K+ stress. However, many genes in some categories (protein kinase and ion transporter

  12. Degradation of transgene DNA in genetically modified herbicide-tolerant rice during food processing.

    Science.gov (United States)

    Song, Shangxin; Zhou, Guanghong; Gao, Feng; Zhang, Wei; Qiu, Liangyan; Dai, Sifa; Xu, Xinglian; Xiao, Hongmei

    2011-12-01

    In order to assess the effect of food processing on the degradation of exogenous DNA components in sweet rice wine and rice crackers made from genetically modified (GM) rice (Oryza sativa L.), we developed genomic DNA extraction methods and compared the effect of different food processing procedures on DNA degradation. It was found that the purity, quantity and quality of DNA by alkaline lysis method were higher than by CTAB (cetyltrimethylammonium bromide) method. For sweet rice wine, CAMV35S (cauliflower mosaic virus 35S) promoter and NOS (nopaline synthase) terminator were degraded by the third day, whereas the exogenous gene Bar (bialaphos resistance) remained unaffected. For rice crackers, boiling, drying and microwaving contributed to the initial degradations of DNA. Baking resulted in further degradations, and frying led to the most severe changes. These results indicated that the stability of DNA in GM rice was different under different processing conditions. For sweet rice wine, Bar was most stable, followed by NOS, CAMV35S, and SPS. For rice crackers, CAMV35S was most stable, followed by SPS, NOS, and Bar.

  13. Review of Functional Markers for Improving Cooking, Eating and the Nutritional Qualities of Rice

    Directory of Open Access Journals (Sweden)

    Wendy Chui Phing Lau

    2015-10-01

    Full Text Available 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.

  14. Rice: Characterizing the Environmental Response of a Gibberellic Acid-Deficient Rice for Use as a Model Crop

    Science.gov (United States)

    Frantz, Jonathan M.; Pinnock, Derek; Klassen, Steve; Bugbee, Bruce

    2004-01-01

    Rice (Oryza sativa L.) is a useful model crop plant. Rice was the first crop plant to have its complete genome sequenced. Unfortunately, even semi-dwarf rice cultivars are 60 to 90 an tail, and large plant populations cannot be grown in the confined volumes of greenhouses and growth chambers. We recently identified an extremely short (20 em tall) rice line, which is an ideal model for larger rice cultivars. We called this line "Super Dwarf rice." Here we report the response of Super Dwarf to temperature, photoperiod, photosynthetic photon flux (PPF), and factors that can affect time to head emergence. Vegetative biomass increased 6% per degree Celsius, with increasing temperature from 27 to 31 C. Seed yield decreased by 2% per degree Celsius rise in temperature, and as a result, harvest index decreased from 60 to 54%. The time to heading increased by 2 d for every hour above a 12-h photoperiod. Yield increased with increasing PPF up to the highest level tested at 1800 micro-mol/sq m/s (12-h photoperiod; 77.8 mol/sq m/d). Yield efficiency (grams per mole of photons) increased to 900 micro-mol/sq m/s and then slightly decreased at 1800 micro-mol/sq m/s . Heading was delayed by addition of gibberellic acid 3 (GA,) to the root zone but was hastened under mild N stress. Overall, short stature, high yield, high harvest index, and no extraordinary environmental requirements make Super Dwarf rice an excellent model plant for yield studies in controlled environments.

  15. Successfully introduce maize DNA fragments into rice

    Institute of Scientific and Technical Information of China (English)

    WANGKaizhi

    1994-01-01

    The maize DNA fragments was successfully incorporated into rice by Associate Prof WAN Wenju's research team at Hunan Agricultural College, Changsha, China. The new gene transferring rice is named Genetic Engineered Rice (GER) line.

  16. Antisense expression of a rice cellular apoptosis susceptibility gene (OsCAS) alters the height of transgenic rice

    Institute of Scientific and Technical Information of China (English)

    XU Chunxiao; HE Chaozu

    2007-01-01

    Cellular apoptosis susceptibility (CAS) gene plays important roles in mitosis, development and export of importin αfrom the nucleus, but its function in plant is unknown. In this study, a rice CAS ortholog (OsCAS), which encodes a predicted protein of 983 amino acids with 62% similarity to human CAS, was identified. DNA gel blot analysis revealed a single copy of OsCAS in the rice genome. A 973 bp fragment at the 3' end of OsCAS cDNA was cloned from rice cDNA library and transferred into rice in the antisense direction under the control of CaMV 35S promoter via Agrobacterium-mediated transformation method, 105 transgenic lines were obtained. Expression of OsCAS was suppressed in the antisense transgenic lines as revealed by semi-quantitative RT-PCR. The antisense transgenic lines showed dwarf phenotypes. The results indicated that OsCAS was involved in culm development of rice.

  17. Overexpression of the rice carotenoid cleavage dioxygenase 1 gene in Golden Rice endosperm suggests apocarotenoids as substrates in planta.

    Science.gov (United States)

    Ilg, Andrea; Yu, Qiuju; Schaub, Patrick; Beyer, Peter; Al-Babili, Salim

    2010-08-01

    Carotenoids are converted by carotenoid cleavage dioxygenases that catalyze oxidative cleavage reactions leading to apocarotenoids. However, apocarotenoids can also be further truncated by some members of this enzyme family. The plant carotenoid cleavage dioxygenase 1 (CCD1) subfamily is known to degrade both carotenoids and apocarotenoids in vitro, leading to different volatile compounds. In this study, we investigated the impact of the rice CCD1 (OsCCD1) on the pigmentation of Golden Rice 2 (GR2), a genetically modified rice variety accumulating carotenoids in the endosperm. For this purpose, the corresponding cDNA was introduced into the rice genome under the control of an endosperm-specific promoter in sense and anti-sense orientations. Despite high expression levels of OsCCD1 in sense plants, pigment analysis revealed carotenoid levels and patterns comparable to those of GR2, pleading against carotenoids as substrates in rice endosperm. In support, similar carotenoid contents were determined in anti-sense plants. To check whether OsCCD1 overexpressed in GR2 endosperm is active, in vitro assays were performed with apocarotenoid substrates. HPLC analysis confirmed the cleavage activity of introduced OsCCD1. Our data indicate that apocarotenoids rather than carotenoids are the substrates of OsCCD1 in planta.

  18. Drought-tolerant rice germplasm developed from an Oryza officinalis transformation-competent artificial chromosome clone.

    Science.gov (United States)

    Liu, R; Zhang, H H; Chen, Z X; Shahid, M Q; Fu, X L; Liu, X D

    2015-10-29

    Oryza officinalis has proven to be a natural gene reservoir for the improvement of domesticated rice as it carries many desirable traits; however, the transfer of elite genes to cultivated rice by conventional hybridization has been a challenge for rice breeders. In this study, the conserved sequence of plant stress-related NAC transcription factors was selected as a probe to screen the O. officinalis genomic transformation-competent artificial chromosome library by Southern blot; 11 positive transformation-competent artificial chromosome clones were subsequently detected. By Agrobacterium-mediated transformation, an indica rice variety, Huajingxian 74 (HJX74), was transformed with a TAC clone harboring a NAC gene-positive genomic fragment from O. officinalis. Molecular analysis revealed that the O. officinalis genomic fragment was integrated into the genome of HJX74. The transgenic lines exhibited high tolerance to drought stress. Our results demonstrate that the introduction of stress-related transformation-competent artificial chromosome clones, coupled with a transgenic validation approach, is an effective method of transferring agronomically important genes from O. officinalis to cultivated rice.

  19. Study of Rice Marketing System in Iran

    OpenAIRE

    Feizabadi, Yaser

    2011-01-01

    Rice comes second after wheat in Iran`s food consumption economy. Rising population and recent growth in GDP has made Iran one of the greatest rice importer countries all over the world. That is why rice marketing has always been a controversial issue in Iran`s agricultural economics. To study rice marketing system in Iran, this paper aims to calculate rice marketing margin, market efficiency and marketing cost coefficient in seaside Mazandaran province( where 70 percent of domestic rice prod...

  20. Transcriptomic analysis of a psammophyte food crop, sand rice (Agriophyllum squarrosum) and identification of candidate genes essential for sand dune adaptation.

    Science.gov (United States)

    Zhao, Pengshan; Capella-Gutiérrez, Salvador; Shi, Yong; Zhao, Xin; Chen, Guoxiong; Gabaldón, Toni; Ma, Xiao-Fei

    2014-10-07

    Sand rice (Agriophyllum squarrosum) is an annual desert plant adapted to mobile sand dunes in arid and semi-arid regions of Central Asia. The sand rice seeds have excellent nutrition value and have been historically consumed by local populations in the desert regions of northwest China. Sand rice is a potential food crop resilient to ongoing climate change; however, partly due to the scarcity of genetic information, this species has undergone only little agronomic modifications through classical breeding during recent years. We generated a deep transcriptomic sequencing of sand rice, which uncovers 67,741 unigenes. Phylogenetic analysis based on 221 single-copy genes showed close relationship between sand rice and the recently domesticated crop sugar beet. Transcriptomic comparisons also showed a high level of global sequence conservation between these two species. Conservation of sand rice and sugar beet orthologs assigned to response to salt stress gene ontology term suggests that sand rice is also a potential salt tolerant plant. Furthermore, sand rice is far more tolerant to high temperature. A set of genes likely relevant for resistance to heat stress, was functionally annotated according to expression levels, sequence annotation, and comparisons corresponding transcriptome profiling results in Arabidopsis. The present work provides abundant genomic information for functional dissection of the important traits in sand rice. Future screening the genetic variation among different ecotypes and constructing a draft genome sequence will further facilitate agronomic trait improvement and final domestication of sand rice.

  1. Identification for Heat Tolerance in Backcross Recombinant Lines and Screening of Backcross Introgression Lines with Heat Tolerance at Milky Stage in Rice

    Institute of Scientific and Technical Information of China (English)

    LIAO Jiang-lin; ZHANG Hong-yu; SHAO Xue-lian; ZHONG Ping-an; HUANG Ying-jin

    2011-01-01

    The present study aimed at breeding new rice germplasms with similar genome but significantly differed in heat tolerance during the grain filling stage.A total of 791 BC1F8 backcross recombinant lines,derived from the cross of Xieqingzao B / N22∥Xieqingzao B,were used as materials.Each rice line was separated evenly into two groups,and the heat tolerance of all rice lines were evaluated at natural high temperature in fields.The rice lines with heat tolerant index higher than 90% or lower than 40% were selected to compare the phenotypic characters and further identify heat tolerance at the early milky stage in a phytotron.Rice lines with similar phenotypic characters but significantly differed in heat tolerance at the milky stage were analyzed by 887 simple sequence repeat markers that were evenly distributed on the 12 rice chromosomes.In the result,12 (6 pairs) rice lines with similar phenotypic characters but significantly differed in heat tolerance at the milky stage were obtained.Molecular marker analysis indicated that the genomic polymorphism between 703T and 704S was the smallest in the 6 pairs of rice lines,with only 16 polymorphic sites,including 22 different alleles.The application of these two backcross introgression rice lines for future study on the mechanisms of heat tolerance in rice at the milky stage will be theoretically beneficial in reducing the interference caused by genetic differences from experimental materials.

  2. Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

    Energy Technology Data Exchange (ETDEWEB)

    Schulman, Al

    2009-08-09

    Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops

  3. Nicaragua - Rice and Banana Farmers

    Data.gov (United States)

    Millennium Challenge Corporation — This report is an impact evaluation of two components of the Rural Business Development Program (RBD) in Nicaragua, specifically the components benefitting rice and...

  4. Genomic Signal Search by Dynamic Programming

    Institute of Scientific and Technical Information of China (English)

    ZHENG Wei-Mou

    2003-01-01

    A general and flexible multi-motif model is proposed based on dynamic programming. By extending theGibbs sampler to the dynamic programming and introducing temperature, an efficient algorithm is developed. Branchpoint signalsequences and translation initiation sequences extracted from the rice genome are then examined.

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

    Science.gov (United States)

    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.

  6. A new synthetic allotetraploid (A1A1G2G2 between Gossypium herbaceum and G. australe: bridging for simultaneously transferring favorable genes from these two diploid species into upland cotton.

    Directory of Open Access Journals (Sweden)

    Quan Liu

    Full Text Available Gossypium herbaceum, a cultivated diploid cotton species (2n = 2x = 26, A1A1, has favorable traits such as excellent drought tolerance and resistance to sucking insects and leaf curl virus. G. australe, a wild diploid cotton species (2n = 2x = 26, G2G2, possesses numerous economically valuable characteristics such as delayed pigment gland morphogenesis (which is conducive to the production of seeds with very low levels of gossypol as a potential food source for humans and animals and resistance to insects, wilt diseases and abiotic stress. Creating synthetic allotetraploid cotton from these two species would lay the foundation for simultaneously transferring favorable genes into cultivated tetraploid cotton. Here, we crossed G. herbaceum (as the maternal parent with G. australe to produce an F1 interspecific hybrid and doubled its chromosome complement with colchicine, successfully generating a synthetic tetraploid. The obtained tetraploid was confirmed by morphology, cytology and molecular markers and then self-pollinated. The S1 seedlings derived from this tetraploid gradually became flavescent after emergence of the fifth true leaf, but they were rescued by grafting and produced S2 seeds. The rescued S1 plants were partially fertile due to the existence of univalents at Metaphase I of meiosis, leading to the formation of unbalanced, nonviable gametes lacking complete sets of chromosomes. The S2 plants grew well and no flavescence was observed, implying that interspecific incompatibility, to some extent, had been alleviated in the S2 generation. The synthetic allotetraploid will be quite useful for polyploidy evolutionary studies and as a bridge for transferring favorable genes from these two diploid species into Upland cotton through hybridization.

  7. Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses.

    Directory of Open Access Journals (Sweden)

    Benjamin Schwessinger

    2015-03-01

    Full Text Available Plant plasma membrane localized pattern recognition receptors (PRRs detect extracellular pathogen-associated molecules. PRRs such as Arabidopsis EFR and rice XA21 are taxonomically restricted and are absent from most plant genomes. Here we show that rice plants expressing EFR or the chimeric receptor EFR::XA21, containing the EFR ectodomain and the XA21 intracellular domain, sense both Escherichia coli- and Xanthomonas oryzae pv. oryzae (Xoo-derived elf18 peptides at sub-nanomolar concentrations. Treatment of EFR and EFR::XA21 rice leaf tissue with elf18 leads to MAP kinase activation, reactive oxygen production and defense gene expression. Although expression of EFR does not lead to robust enhanced resistance to fully virulent Xoo isolates, it does lead to quantitatively enhanced resistance to weakly virulent Xoo isolates. EFR interacts with OsSERK2 and the XA21 binding protein 24 (XB24, two key components of the rice XA21-mediated immune response. Rice-EFR plants silenced for OsSERK2, or overexpressing rice XB24 are compromised in elf18-induced reactive oxygen production and defense gene expression indicating that these proteins are also important for EFR-mediated signaling in transgenic rice. Taken together, our results demonstrate the potential feasibility of enhancing disease resistance in rice and possibly other monocotyledonous crop species by expression of dicotyledonous PRRs. Our results also suggest that Arabidopsis EFR utilizes at least a subset of the known endogenous rice XA21 signaling components.

  8. Collection and comparative analysis of 1888 full-length cDNAs from wild rice Oryza rufipogon Griff. W1943.

    Science.gov (United States)

    Lu, Tingting; Yu, Shuliang; Fan, Danlin; Mu, Jie; Shangguan, Yingying; Wang, Zixuan; Minobe, Yuzo; Lin, Zhixin; Han, Bin

    2008-10-01

    A huge amount of cDNA and EST resources have been developed for cultivated rice species Oryza sativa; however, only few cDNA resources are available for wild rice species. In this study, we isolated and completely sequenced 1888 putative full-length cDNA (FLcDNA) clones from wild rice Oryza rufipogon Griff. W1943 for comparative analysis between wild and cultivated rice species. Two cDNA libraries were constructed from 3-week-old leaf samples under either normal or cold-treated conditions. Homology searching of these cDNA sequences revealed that >96.8% of the wild rice cDNAs were matched to the cultivated rice O. sativa ssp. japonica cv. Nipponbare genome sequence. However, sequence. The comparative analysis showed that O. rufipogon W1943 had greater similarity to O. sativa ssp. japonica than to ssp. indica cultivars. In addition, 17 novel rice cDNAs were identified, and 41 putative tissue-specific expression genes were defined through searching the rice massively parallel signature-sequencing database. In conclusion, these FLcDNA clones are a resource for further function verification and could be broadly utilized in rice biological studies.

  9. Systematic Identification of Rice ABC1 Gene Family and Its Response to Abiotic Stress

    Institute of Scientific and Technical Information of China (English)

    GAO Qing-song; ZHANG Dan; Xu Liang; XU Chen-wu

    2011-01-01

    Members of the activity of bc1 complex (ABC1) family are protein kinases that are widely found in prokaryotes and eukaryotes.Previous studies showed that several plant ABC1 genes participated in the abiotic stress response.Here,we present the systematic identification of rice and Arabidopsis ABC1 genes and the expression analysis of rice ABC1 genes.A total of 15 and 17 ABC1 genes from the rice and Arabidopsis genomes,respectively,were identified using a bioinformatics approach.Phylogenetic analyses of these proteins suggested that the divergence of this family had occurred and their main characteristics were established before the monocot-dicot split.Indeed,species-specific expansion contributed to the evolution of this family in rice and Arabidopsis after the monocot-dicot split.Intron/exon structure analysis indicated that most of the orthologous genes had similar exon sizes,but diverse intron sizes,and the rice genes contained larger introns,moreover,intron gain was an important event accompanying the recent evolution of the rice ABC1 family.Multiple sequence alignment revealed one conserved amino acid segment and four conserved amino acids in the ABC1 domain.Online subcellular localization predicted that nine rice ABC1 proteins were localized in chloroplasts.Real-time RT-PCR established that the rice ABC1 genes were primarily expressed in leaves and the expression could be modulated by a broad range of abiotic factors such as H2O2,abscisic acid,low temperature,drought,darkness and high salinity.These results reveal that the rice ABC1 gene family plays roles in the environmental stress response and specific biological processes of rice.

  10. Progress and Challenges in Improving the Nutritional Quality of Rice (Oryza sativa L.).

    Science.gov (United States)

    Birla, Deep Shikha; Malik, Kapil; Sainger, Manish; Chaudhary, Darshna; Jaiwal, Ranjana; Jaiwal, Pawan K

    2015-10-29

    Rice is a staple food for more than 3 billion people in more than 100 countries of the world but ironically it is deficient in many bioavailable vitamins, minerals, essential amino- and fatty-acids and phytochemicals that prevent chronic diseases like type 2 diabetes, heart disease, cancers and obesity. To enhance the nutritional and other quality aspects of rice, a better understanding of the regulation of the processes involved in the synthesis, uptake, transport and metabolism of macro-(starch, seed storage protein and lipid) and micronutrients (vitamins, minerals and phytochemicals) is required. With the publication of high quality genomic sequence of rice, significant progress has been made in identification, isolation and characterization of novel genes and their regulation for the nutritional and quality enhancement of rice. During the last decade, numerous efforts have been made to refine the nutritional and other quality traits either by using the traditional breeding with high through put technologies such as marker assisted selection and breeding, or by adopting the transgenic approach. A significant improvement in vitamins (A, folate and E), mineral (iron), essential amino acid (lysine) and flavonoids levels has been achieved in the edible part of rice, i. e. endosperm (biofortification) to meet the daily dietary allowance. However, studies on bioavailability and allergenicity on biofortified rice are still required. Despite the numerous efforts, the commercialization of biofortified rice has not yet been achieved. The present review summarizes the progress and challenges of genetic engineering and /or metabolic engineering technologies to improve rice grain quality, and presents the future prospects in developing nutrient dense rice to save the ever-increasing population, that depends solely on rice as the staple food, from widespread nutritional deficiencies.

  11. The Haitian Rice Tariff

    Directory of Open Access Journals (Sweden)

    Mats Lundahl

    2016-04-01

    Full Text Available Se ha argumentado que los problemas agríco-las de Haití derivan de la tarifa del arroz de a mediados de los años noventa. Antes, supues-tamente, Haití fue autosuficiente, abastecida por su producción doméstica. Después de la reducción, el mercado haitiano se inundó en importaciones de arroz barato de los EEUU, lo cual despojó a los campesinos de sus fincas, convirtiendolos en migrantes internos, hacia los empleos de bajo pago de las ciudades. El artículo rechaza ese argumento y demuestra que es falso. La malnutrición fue un fenómeno extendido en Haití mucho antes de la reducción de la tarifa del arroz, la cual tampoco tuvo un gran impacto en la importación y la producción doméstica del arroz. Lo que sí impulsó el aumento de las importaciones fue el crecimiento de la población. También el artículo argumenta que un aumento de la tarifa del arroz no solucionará el problema de la alimentación que sufre Haití. English: It has been argued that Haiti’s agricultural problems derive from the reduction of the rice tariff in the mid-1990s. Before that Haiti was allegedly able to meet its food needs by domestic production. After the reduction the Haitian market was swamped by imports of cheap American rice which drove the farmers off their lands and forced them to migrate to low-wage industrial jobs in the cities. The article demonstrates that the argument is false. Malnutrition was widespread in Haiti long before the rice tariff reduction, and the latter did not have much of an impact on rice imports and domestic production. Instead, the main driving force behind imports appears to be population growth. It is also shown that an increase of the rice tariff will not solve Haiti’s food problem.

  12. Impact of volunteer rice infestation on yield and grain quality of rice.

    Science.gov (United States)

    Singh, Vijay; Burgos, Nilda R; Singh, Shilpa; Gealy, David R; Gbur, Edward E; Caicedo, Ana L

    2017-03-01

    Volunteer rice (Oryza sativa L.) grains may differ in physicochemical traits from cultivated rice, which may reduce the quality of harvested rice grain. To evaluate the effect of volunteer rice on cultivated rice, fields were surveyed in Arkansas in 2012. Cropping history that included hybrid cultivars in the previous two years (2010 and 2011) had higher volunteer rice infestation (20%) compared with fields planted previously with inbred rice (5.5%). The total grain yield of rice was reduced by 0.4% for every 1% increase in volunteer rice density. The grain quality did not change in fields planted with the same cultivar for three years. Volunteer rice density of at least 7.6% negatively impacted the head rice and when infestation reached 17.7%, it also reduced the rice grain yield. The protein and amylose contents of rice were not affected until volunteer rice infestation exceeded 30%. Crop rotation systems that include hybrid rice are expected to have higher volunteer rice infestation than systems without hybrid rice. It is predicted that, at 8% infestation, volunteer rice will start to impact head rice yield and will reduce total yield at 18% infestation. It could alter the chemical quality of rice grain at >30% infestation. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  13. Water-wise Rice Production

    NARCIS (Netherlands)

    Bouman, B.A.M.; Hengsdijk, H.; Hardy, B.; Bindraban, P.S.; Tuong, T.P.; Ladha, J.K.

    2002-01-01

    Rice is a profligate user of water. It takes 3,000–5,000 liters to produce 1 kilogram of rice, which is about 2 to 3 times more than to produce 1 kilogram of other cereals such as wheat or maize. Until recently, this amount of water has been taken for granted. Now, however, the water crisis

  14. Hybrid Rice for Dry Regions

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Luo Lijun, director of the Shanghai Agrobiological Gene Center, recently announced that Hanyou No. 3 - a genetically modified rice capable of producing high yields in dry areas - has been developed at the center.The hybrid yields 7,571 kilograms per hectare, about the same as ordinary rice.

  15. BAC-end sequence-based SNP mining in Allotetraploid Cotton (Gossypium) utilizing re-sequencing data, phylogenetic inferences and perspectives for genetic mapping

    Science.gov (United States)

    A bacterial artificial chromosome (BAC) library and BAC-end sequences for Gossypium hirsutum L. have recently been developed. Here we report on genomic-based genome-wide SNP mining utilizing re-sequencing data with a BAC-end sequence reference for twelve G. hirsutum L. lines, one G. barbadense L. li...

  16. 21 CFR 137.350 - Enriched rice.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 2 2010-04-01 2010-04-01 false Enriched rice. 137.350 Section 137.350 Food and... Related Products § 137.350 Enriched rice. (a) The foods for which definitions and standards of identity are prescribed by this section are forms of milled rice (except rice coated with talc and glucose...

  17. Development of hybrid rice in China

    Institute of Scientific and Technical Information of China (English)

    Yuan Longping; Wu Xiaojin

    2004-01-01

    @@ Introduction The success achieved in development of hybrid rice isa great breakthrough in rice breeding which provides aneffective way to markedly enhance rice yield on a largescale. China is the first country in the world to exploit riceheterosis commercially. Research on hybrid rice was initiatedin 1964.

  18. Arsenic uptake in organic rice production systems

    Science.gov (United States)

    Arsenic in rice is known to be a problem in some rice-producing countries that have high levels of inorganic arsenic naturally occurring in water resources. However, it was never considered an issue for USA produced rice until international market surveys were published, indicating some USA rice sam...

  19. Establishment of a high efficiency Agrobacterium-mediated transformation system of rice (Oryza sativa L.).

    Science.gov (United States)

    Ozawa, Kenjirou

    2009-04-01

    Technologies for transformation of rice have been developed to meet the requirements of functional genomics in order to enable the production of transgenic rice plants with useful agricultural characters. However, many rice varieties are not efficiently transformed by Agrobacterium. We have succeeded in establishing a highly efficient transformation system in rice by co-cultivating rice calli with Agrobacterium on three filter papers moistened with enriched N6 or DKN media instead of using solid media. Rice calli immersed in Agrobacterium suspension (EHA101, Agrobacterium concentration of OD600=0.04) were co-cultured on three pieces of filter paper (9cm in diameter) moistened with 5.5mL of N6 or DKN liquid co-cultivation medium supplemented with 2,4-d (2mg/L), proline (10mM), casein hydrolysate (300mg/L), sucrose (30g/L), glucose (5g/L), l-cysteine (100mg/L) and acetosyringone (15mg/L) at 25°C for 3 days in the dark. Compared with the transformation efficiency of calli co-cultivated on solid media, transformation efficiency was increased by about fivefold by using the filter paper method for many varieties of rice, including those that previously yielded much poor transformation rates.

  20. Developing a matrix reference material for screening of transgenic rice.

    Science.gov (United States)

    Li, Jun; Wu, Yuhua; Li, Xiaofei; Wang, Yulei; Zhang, Li; Li, Yunjing; Wu, Gang

    2015-12-01

    Certified reference materials (CRMs) that are compatible with detection methods are needed to detect genetically modified organisms (GMOs). Screening is the first detection step in determining the possible presence of GMO ingredients in food or feed; however, screening has been hindered by the lack of GMO CRMs. In this study, transgenic rice materials were developed via the transformation of a construct harboring 11 commonly used screening elements. Digital PCR was utilized to identify a homozygous single-copy line termed SDrice. The qualitative detections of 11 elements in 21 transgenic materials demonstrated that the genomic DNA of the SDrice was suitable for use as a positive control in the screening of GMO ingredients. The suitability of SDrice as reference material was further checked by testing the sensitivity of 11 known conventional PCR assays, ranging from 10 to 50 copies of the SDrice genome. The standard curves that were created using SDrice DNA series as calibrators all exhibited good linearities in the relationships of the Ct values with the template copy numbers in these 11 real-time PCR assays. The LODs of the real-time PCR assays were estimated to be two to five copies of the SDrice genome. Comparisons of the SDrice with other GM rice revealed that significant differences existed in both the intercepts of the standard curves and the ΔCt values of the exogenous and reference genes for the P-35S, T-nos, HPT, T-35S, and Bar assays; the SDrice was not fit for quantification of other GM rice events. This study provided a matrix reference material (RM) that was suitable for screening GM rice, determination of sensitivity and a LOD of PCR assays, and overcame some of the drawbacks of plasmid DNA as reference material.

  1. A novel gene OsAHL1 improves both drought avoidance and drought tolerance in rice

    Science.gov (United States)

    Zhou, Liguo; Liu, Zaochang; Liu, Yunhua; Kong, Deyan; Li, Tianfei; Yu, Shunwu; Mei, Hanwei; Xu, Xiaoyan; Liu, Hongyan; Chen, Liang; Luo, Lijun

    2016-01-01

    A novel gene, OsAHL1, containing an AT-hook motif and a PPC domain was identified through genome-wide profiling and analysis of mRNAs by comparing the microarray of drought-challenged versus normally watered rice. The results indicated OsAHL1 has both drought avoidance and drought tolerance that could greatly improve drought resistance of the rice plant. Overexpression of OsAHL1 enhanced multiple stress tolerances in rice plants during both seedling and panicle development stages. Functional studies revealed that OsAHL1 regulates root development under drought condition to enhance drought avoidance, participates in oxidative stress response and also regulates the content of chlorophyll in rice leaves. OsAHL1 specifically binds to the A/T rich sequence region of promoters or introns, and hence directly regulates the expression of many stress related downstream genes. PMID:27453463

  2. Over-Expression of ICE1 Gene in Transgenic Rice Improves Cold Tolerance

    Institute of Scientific and Technical Information of China (English)

    XIANG Dian-jun; HU Xiang-yang; ZHANG Yu; YIN Kui-de

    2008-01-01

    ICE1, an Arabidopsis thaliana transcription factor gene, was cloned by RT-PCR and successfully transformed into rice variety Kenjiandao 10 by the Agrobacterium-mediated transformation method. PCR amplification and Southern blot analysis indicated that ICE1 had been integrated into rice genome. Compared with the non-transgenic plants, the transgenic plants exhibited high resistance to hygromycin B and were consistent with the Mendelian inheritance of a single copy of the transgenic ICE1. Under the low temperature stress, the transgenic plants showed the lower mortality rate and the increased proline content. These results suggest that the Arabidopsis ICE1 is functional in rice and the over-expression of ICE1 improves the tolerance to cold stress in rice.

  3. Characterization of enhancer trap and gene trap harboring Ac/Ds transposon in transgenic rice

    Institute of Scientific and Technical Information of China (English)

    金维正; 汪少敏; 徐敏; 段瑞君; 吴平

    2004-01-01

    Insertion mutagenesis has become one of the most popular methods for gene functions analysis.Here we report a two-element Ac/Ds transposon system containing enhancer trap and gene trap for gene tagging in rice.The excision of Ds element was examined by PCR amplification.The excision frequency of Ds element varied from 0% to 40% among 20 F2 populations derived from 11 different Ds parents.Southern blot analysis revealed that more than 70% of excised Ds elements reinserted into rice genome and above 70% of the reinserted Ds elements were located at different positions of the chromosome in rice.The result of histochemical GUS analysis indicated that 28% of enhancer trap and 22% of gene trap tagging plants displayed GUS activity in leaves, roots,flowers or seeds.The GUS positive lines will be useful for identifying gene function in rice.

  4. The Chinese Market and Thai Fragrant Jasmine Rice: Why does China, the world's largest rice producer, import rice from Thailand? (Japanese)

    OpenAIRE

    Miyata, Toshiyuki

    2011-01-01

    In 2008, the world experienced a sharp increase in rice prices due to destabilization of international rice demand and supply. Under these circumstances, rice exports from Thailand—the world's top rice exporter—and Thai rice export prices increased dramatically, but the amount of high-quality fragrant Jasmine rice exported to China decreased by some 30% over the previous year. This paper examines why, amidst increasing world rice prices and expansion of the Thai rice export market overall, th...

  5. Uruguayan rice (Oritza sativa L.) oils characterization

    OpenAIRE

    Cecilia Rodríguez; Grabiela Subúru; Marina Torres; Laura Olazabal; Alejandra Torre

    2011-01-01

    The rice crop is one of the most developed agricultural activities in Uruguay, having become the third item of export. Although the main product of the rice chain is the elaborated rice, in the recent years several industries have begun to produce co-products of rice: crude rice oil and refined oil, rice flour and cookies. The production of crude oil begins with ground, peeled and polished rice grain. This product can be used in animal nourishment or in oil extraction. Refinement from the cru...

  6. Rice industrial economy and its development strategy

    Institute of Scientific and Technical Information of China (English)

    Qing Xianguo

    2003-01-01

    On the basis of the analysis of the present situation of food grain and rice production in China,countering the beginning tendency to neglect rice production because of rice grain structural surplus and low market price after China's agriculture entering the new development stage,this paper putsforward the concept of rice industrial economy,explains its attribute,connotation,key factors,etc,forms the basic idea of developing the rice industrial economy,and suggests some strategic measures such as regionalized layout of rice production,etc.to develop the rice industrial economy.

  7. Current status and prospects for the study of Nicotiana genomics, genetics, and nicotine biosynthesis genes.

    Science.gov (United States)

    Wang, Xuewen; Bennetzen, Jeffrey L

    2015-02-01

    Nicotiana, a member of the Solanaceae family, is one of the most important research model plants, and of high agricultural and economic value worldwide. To better understand the substantial and rapid research progress with Nicotiana in recent years, its genomics, genetics, and nicotine gene studies are summarized, with useful web links. Several important genetic maps, including a high-density map of N. tabacum consisting of ~2,000 markers published in 2012, provide tools for genetics research. Four whole genome sequences are from allotetraploid species, including N. benthamiana in 2012, and three N. tabacum cultivars (TN90, K326, and BX) in 2014. Three whole genome sequences are from diploids, including progenitors N. sylvestris and N. tomentosiformis in 2013 and N. otophora in 2014. These and additional studies provide numerous insights into genome evolution after polyploidization, including changes in gene composition and transcriptome expression in N. tabacum. The major genes involved in the nicotine biosynthetic pathway have been identified and the genetic basis of the differences in nicotine levels among Nicotiana species has been revealed. In addition, other progress on chloroplast, mitochondrial, and NCBI-registered projects on Nicotiana are discussed. The challenges and prospects for genomic, genetic and application research are addressed. Hence, this review provides important resources and guidance for current and future research and application in Nicotiana.

  8. Bridging the Rice Yield Gaps under Drought: QTLs, Genes, and their Use in Breeding Programs

    Directory of Open Access Journals (Sweden)

    Nitika Sandhu

    2017-04-01

    Full Text Available Rice is the staple food for more than half of the world’s population. Although rice production has doubled in the last 30 years as a result of the development of high-yield, widely adaptable, resource-responsive, semi-dwarf varieties, the threat of a food crisis remains as severe as it was 60 years ago due to the ever-increasing population, water scarcity, labor scarcity, shifting climatic conditions, pest/diseases, loss of productive land to housing, industries, rising sea levels, increasing incidences of drought, flood, urbanization, soil erosion, reduction in soil nutrient status, and environmental issues associated with high-input agriculture. Among these, drought is predicted to be the most severe stress that reduces rice yield. Systematic research on drought over the last 10 years has been conducted across institutes on physiology, breeding, molecular genetics, biotechnology, and cellular and molecular biology. This has provided a better understanding of plant drought mechanisms and has helped scientists to devise better strategies to reduce rice yield losses under drought stress. These include the identification of quantitative trait loci (QTLs for grain yield under drought as well as many agronomically important traits related to drought tolerance, marker-assisted pyramiding of genetic regions that increase yield under drought, development of efficient techniques for genetic transformation, complete sequencing and annotation of rice genomes, and synteny studies of rice and other cereal genomes. Conventional and marker-assisted breeding rice lines containing useful introgressed genes or loci have been field tested and released as varieties. Still, there is a long way to go towards developing drought-tolerant rice varieties by exploiting existing genetic diversity, identifying superior alleles for drought tolerance, understanding interactions among alleles for drought tolerance and their interaction with genetic backgrounds, and

  9. Amylose content of rice marketed in Portugal

    OpenAIRE

    2014-01-01

    Amylose content is considered to be the most important parameter of cooking quality in rice. Presently, rice cultivars are categorized according to amylose content into three groups: low, medium and high amylose content cultivars. The specific objective of this work is to evaluate the grain amylose content of 77 cultivars, which cover Índica and Japónica subspecies, and different types of commercial rice like, aromatic (basmati and thay), wild rice, medium rice (carlose and risotto), glutinou...

  10. Sensory evaluation of rice fortified with iron

    OpenAIRE

    Beinner,Mark Anthony; Soares,Anne Danieli Nascimento; Barros,Ana Laura Antunes; Monteiro,Marlene Azevedo Magalhães

    2010-01-01

    The objective of this study was to examine sensory differences between conventional rice and iron-fortified Ultra Rice rice (UR) and determine consumer acceptance. Differences between both types of rice were analyzed using the Duo-Trio Test on 37 non-trained judges. The Acceptance Test evaluated general rice appearance, color, aroma and taste by 43 non-trained judges, using a 7-point hedonic scale with extremes ranging from "really disliked" and "really liked." There were no significant diffe...

  11. Differential regulation of genes by retrotransposons in rice promoters.

    Science.gov (United States)

    Dhadi, Surendar Reddy; Xu, Zijun; Shaik, Rafi; Driscoll, Kyle; Ramakrishna, Wusirika

    2015-04-01

    Rice genome harbors genes and promoters with retrotransposon insertions. There is very little information about their function. The effect of retrotransposon insertions in four rice promoter regions on gene regulation, was investigated using promoter-reporter gene constructs with and without retrotransposons. Differences in expression levels of gus and egfp reporter genes in forward orientation and rfp in reverse orientation were evaluated in rice plants with transient expression employing quantitative RT-PCR analysis, histochemical GUS staining, and eGFP and RFP fluorescent microscopy. The presence of SINE in the promoter 1 (P1) resulted in higher expression levels of the reporter genes, whereas the presence of LINE in P2 or gypsy LTR retrotransposon in P3 reduced expression of the reporter genes. Furthermore, the SINE in P1 acts as an enhancer in contrast with the LINE in P2 and the gypsy LTR retrotransposon in P3 which act as silencers. CTAA and CGG motifs in these retrotransposons are the likely candidates for the downregulation compared to TCTT motif (SINE) which is a candidate for the upregulation of gene expression. The effect of retrotransposons on gene regulation correlated with the earlier investigation of conservation patterns of these four retrotransposon insertions in several rice accessions implying their evolutionary significance.

  12. Performance of Autoregulatory Senescence-inhibition Gene in Rice

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The performance of autoregulatory senescence-inhibition gene PSAG12--IPT in rice has been investigated in the study. 422 transgenic plants from 134 independent resistant calli were obtained from 4 rice varieties through Agrobacterium-mediated transformation. Among them, 233were positive PSAG12-IPT transgenic plants identified by GUS histochemical assay and PCR analysis.Southern analysis showed the transgene was randomly integrated into rice genome, of which 42.29 % was single copy. Investigations on photosynthesis function and agronomic characters of R1 generation showed that chlorophy Ⅱ content and photosynthesis rate of flag leaves in transgenic plants, were 41.23 96 and 60.24 % higher than the control wild-type rice, respectively. The growth duration and plant height of the transgenic plants were similar to the control. Variations of other characters were dependent on the varieties. For the variety Millin with significant aging phenomenon in China, its total grains per hill, its seed setting rate and 1000-grain weight were increased by 40.44%, 8.05% and 8.32% respectively. The results indicated that after leaf senescence of varieties liable to age was delayed, the seed setting rate and the filling degree of seeds were improved, which finally resulted in significantly increased seed yield and biomass per hill. The new variety Wuyujing 2 without serious aging problem, was also increased in the panicles per hill, the total grains per hill, the seed yield per hill and biomass in different degrees.

  13. Overexpression of glutamine synthetases confers transgenic rice herbicide resistance

    Institute of Scientific and Technical Information of China (English)

    Sun Hui; Huang Qiman; Su Jin

    2005-01-01

    Glutamine synthetase (GS, E.C.6.3.1.2) is a key enzyme involved in the assimilation of inorganic nitrogen in higher plants and gram-negative microorganisms. GS is the targeting enzyme of a herbicide phosphinothricin (PPT) or Basta. In order to generate PPT-resistant transgenic rice via overexpression of GS, we constructed a plant expression vector p2GS harboring two different isoenzymes GS1 and GS2 cDNAs under the control of constitutive promoters of rice Act1 and maize Ubiquitin(Ubi) genes. The p2GS was introduced into rice genome by Agrobacterium-mediated transformation and confirmed by PCR and Southern blot hybridization. GS-transgene expression was first detected by Northern blot analyses. Results from Basta test indicated that GS-transgenic plants can tolerate as high as 0.3% Basta solution. In addition, our results also demonstrated that GS overexpression conferred transformed rice calli PPT resistance. Thus, GS cassette can serve as a selective marker gene instead of bar cassette for selection of PPT transformants.

  14. Quantitative trait loci for phyllochron and tillering in rice.

    Science.gov (United States)

    Miyamoto, N; Goto, Y; Matsui, M; Ukai, Y; Morita, M; Nemoto, K

    2004-08-01

    Morphogenetic processes in sequentially growing leaves and tiller buds are highly synchronized in rice ( Oryza sativa L.). Consequently, the appearance of successive leaves in the main tiller acts as the "pacemaker" for the whole shoot system development. The time interval between the appearance of successive leaves (days/leaf) in the main tiller is called the 'phyllochron'. The objectives of the investigation reported here were: (1) to identify quantitative trait loci (QTLs) that control rice phyllochron and (2) to understand the roles of phyllochron QTLs as an underlying developmental factor for rice tillering. For this purpose we developed a set of recombinant inbred lines derived from a cross between IR36 ( indica) and Genjah Wangkal (tropical japonica). Composite interval mapping detected three phyllochron QTLs located on chromosomes 4, 10 and 11, where the presence of a Genjah Wangkal allele increased phyllochron. The largest QTL (on chromosome 4) was located on the genomic region syntenic to the vicinity of the maize Teopod 2 mutation, while the QTL on chromosome 10 was close to the rice plastochron 1 mutation. These three phyllochron QTLs failed to coincide with major tiller number QTLs. However, one tiller number QTL was associated with small LOD peaks for phyllochron and tiller-bud dormancy that were linked in coupling phase, suggesting that linked small effects of phyllochron and tiller-bud dormancy might result in a multiplicative effect on tiller number.

  15. Transcriptomic and metabolomic shifts in rice roots in response to Cr (VI stress

    Directory of Open Access Journals (Sweden)

    Tripathi Preeti

    2010-11-01

    Full Text Available Abstract Background Widespread use of chromium (Cr contaminated fields due to careless and inappropriate management practices of effluent discharge, mostly from industries related to metallurgy, electroplating, production of paints and pigments, tanning, and wood preservation elevates its concentration in surface soil and eventually into rice plants and grains. In spite of many previous studies having been conducted on the effects of chromium stress, the precise molecular mechanisms related to both the effects of chromium phytotoxicity, the defense reactions of plants against chromium exposure as well as translocation and accumulation in rice remain poorly understood. Results Detailed analysis of genome-wide transcriptome profiling in rice root is reported here, following Cr-plant interaction. Such studies are important for the identification of genes responsible for tolerance, accumulation and defense response in plants with respect to Cr stress. Rice root metabolome analysis was also carried out to relate differential transcriptome data to biological processes affected by Cr (VI stress in rice. To check whether the Cr-specific motifs were indeed significantly over represented in the promoter regions of Cr-responsive genes, occurrence of these motifs in whole genome sequence was carried out. In the background of whole genome, the lift value for these 14 and 13 motifs was significantly high in the test dataset. Though no functional role has been assigned to any of the motifs, but all of these are present as promoter motifs in the Database of orthologus promoters. Conclusion These findings clearly suggest that a complex network of regulatory pathways modulates Cr-response of rice. The integrated matrix of both transcriptome and metabolome data after suitable normalization and initial calculations provided us a visual picture of the correlations between components. Predominance of different motifs in the subsets of genes suggests the involvement

  16. Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy.

    Directory of Open Access Journals (Sweden)

    Ki-Hong Jung

    Full Text Available 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.

  17. Structure, expression pattern and chromosomal localization of the rice Osgrp-2 gene

    Institute of Scientific and Technical Information of China (English)

    LIU; Zongzhi; (刘宗旨); WANG; Jianlong; (王建龙); WANG; Qun; (王群); HUANG; Xun; (黄勋); XU; Weihui; (徐卫辉); ZHU; Lihuang; (朱立煌); HE; Ping; (何平); FANG; Rongxiang; (方荣祥)

    2003-01-01

    Glycine-rich proteins (GRPs) belong to a kind of important structural proteins of plant cell walls. The expression of GRP genes is regulated spatially and developmentally as well as by various environmental stresses, thus providing a good model for the study of plant gene expression. We obtained the genomic sequence of a new GRP gene (Osgrp-2) from a rice genomic library. The transcription start site of Osgrp-2 was determined by 5'-rapid amplification of cDNA ends (RACE) and a 2.4-kb promoter sequence was thus delimited. The spatial and developmental expression pattern as well as the wound-inducible character of Osgrp-2 in rice plants was analyzed in detail. Furthermore, the gene was mapped onto rice chromosome 10 by analysis of restriction fragment length polymorphism (RFLP).

  18. Classificati,Expression Patter,and E3 Ligase Activity Assay of Rice U-Box-Containing Proteins

    Institute of Scientific and Technical Information of China (English)

    Li-Rong Zeng; Chan Ho Park; R.C.Venu; Julian Gough; Guo-Liang Wang

    2008-01-01

    Ubiquitin ligases play a central role in determining the specificity of the ubiquitination system by selecting a myriad of appropriate candidate proteins for modification.The U-box is a recently identified,ubiquitin ligase activityrelated protein domain that shows greater presence in plants than in other organisms.In this study,we identified 77 putative U-box proteins from the rice genome using a battery of whole genome analysis algorithms.Most of the U-box protein genes are expressed,as supported by the identification of their corresponding expressed sequence tags (ESTs),full-length cDNAs,or massively parallel signature sequencing(MPSS)tags.Using the same algorithms,we identified 61 U-box proteins from the Arabidopsis genome.The rice and Arabidopsis U-box proteins were classified into nine major classes based on their domain compositions.Comparison between rice and Arabidopsis U-box proteins indicates that the majority of rice and Arabidopsis U-box proteins have the same domain organizations.The inferred phylogeny established the homology between rice and Arabidopsis U-box/ARM proteins.Cell death assay using the rice protoplast system suggests that one rice U-box gene,OsPU851,might act as a negative regulator of cell death signaling.In addition,the selected U-box proteins were found to be functional E3 ubiquitin ligases.The identification and analysis of rice U-box proteins hereby at the genomic level will help functionally characterize this class of E3 ubiquitin ligase in the future.

  19. Ultrastructural morphologic description of the wild rice species Oryza latifolia (Poaceae in Costa Rica

    Directory of Open Access Journals (Sweden)

    Ethel Sánchez

    2003-06-01

    Full Text Available The wild rice species Oryza latifolia is endemic to Tropical America, allotetraploid and has a CCDD genome type. It belongs to the officinalis group of the genus Oryza. This species is widely distributed through-out the lowlands of Costa Rica and it is found on different life zones, having great morphologic diversity. The purpose of this research is to perform a morphologic description of O. latifolia samples of three Costa Rican localities (Carara, Liberia and Cañas and to see if the phenotypic diversity of the species is reflected at the ultra-structure level. Structures such as the leaf blade, ligule, auricles and spikelet were analyzed. Leaf blade morphology of the specimens from the three localities is characterized by the presence of diamond-shaped stomata with papillae, zipper-like rows of silica cells; a variety of evenly distributed epicuticular wax papillae and bulky prickle trichomes. The central vein of the leaf blade from the Cañas populations is glabrous, while those from Carara and Liberia have abundant papillae. There are also differences among the borders of the leaf blade between these locations. Cañas and Liberia present alternating large and small prickle trichomes ca. 81 and 150 µm, while Carara exhibits even sized prickle trichomes of ca. 93 µm. Auricles from Cañas are rectangular and present long trichomes along the surface ca. 1.5 mm, while those of Liberia and Carara wrap the culm and exhibit trichomes only in the borders. The ligule from the plants of Carara has an acute distal tip, while that of Cañas and Liberia is blunt. The Liberia spikelet has large lignified spines while Cañas and Carara show flexible trichomes.La especie silvestre Oryza latifolia es endémica de América, tetraploide y de genoma CCDD. Pertenece a las especies del género Oryza del grupo officinalis. Presenta una amplia distribución en las tierras bajas de Costa Rica y se le encuentra en varias zonas de vida, mostrando una gran diversidad

  20. Salt tolerance of transgenic rice (Oryza sativa L.) with mtlD gene and gutD gene

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Southern blot analysis indicated that mtlD gene (encoding mannitol-1-phosphate dehydrogenase) and gutD gene (encoding glucitol-6-phosphate dehydrogenase) had been integrated into the rice genome mediated by Agrobacterium tumefaciens LBA4404(pBIGM). The expression of the above two genes in transgenic rice plants was demonstrated by Northern blot analysis and enzymatic activity assay. Analysis of sugar alcohol showed that transgenic rice plants could produce and accumulate mannitol and sorbitol. The salt tolerance of transgenic plants was much higher than that of their controls.

  1. 异源四倍体棉花栽培品种分子连锁遗传图谱的构建%Construction of Molecular Linkage Map of Cultivated Allotetraploid Cotton (Gossypium hirsutum L.×G. Barbadense L. )with SSR and RAPD Markers

    Institute of Scientific and Technical Information of China (English)

    Jun ZHANG; Wang-zhen GUO; Tian-zhen ZHANG

    2002-01-01

      A permanent doubled haploid population from the crossing of G. hirsutum × G. barbadense were developed by means of Vsg, virescently marked semigamy line in sea island cotton,which was characterized by a cytological mechanism for developing haploids with certain convenience, and thus constructed an allotetraploid cotton molecular genetic linkage map with the high level polymorphic SSR and RAPD markers.……

  2. Rice8987 Array: PCR check - RMOS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available There are independent 8979 cDNA clones that were selected from about 40,000 cDNA clones isolated in the first research... stage of the rice genome research project. Those 8979 cDNA clones were

  3. A Rapid DNA Mini-prep Method for Large-Scale Rice Mutant Screening

    Institute of Scientific and Technical Information of China (English)

    QIU Fu-lin; WANG He-he; CHEN Jie; ZHUANG Jie-yun; Hei LEUNG; CHENG Shi-hua; Wu Jian-li

    2006-01-01

    A high throughput rice DNA mini-preparation method was developed. The method is suitable for large-scale mutant bank screening as well as large mapping populations with characteristics of maintaining relatively high level of DNA purity and concentration. The extracted DNA was tested and suitable for regular PCR amplification (SSR) and for Targeting Induced Local Lesion in Genome (TILLING) analysis.

  4. Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection.

    Directory of Open Access Journals (Sweden)

    Xianfa Xie

    Full Text Available Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa--indica and tropical japonica--as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups.

  5. Fine mapping and candidate gene analysis of purple pericarp gene Pb in rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Purple rice is a type of rice with anthocyanins deposited in its grain pericarp. The rice Pb gene controlling purple pericarp character is known to be on chromosome 4, and the purple color is dominant over white color. In this study, we fine mapped the Pb gene using two F2 segregating populations, i.e. Pei'ai 64S (white) × Yunanheixiannuo (purple) and Pei'ai 64S × Chuanheinuo (purple). In the first-pass mapping, the Pb gene was located in the region downstream the SSR marker RM3820. In the fine mapping, the candidate region was saturated with InDel and CAPS markers developed specifically for this study. Eventually, the Pb gene was mapped within the 25-kb region delimited by the upstream marker RID3 and the downstream marker RID4. The delimited region contained two annotated genes, Ra and bhlh16 (TIGR Rice Genome, R.5). The former is a homologue of the Myc transcription factor Lc controlling anthocyanin biosynthesis in maize, and the latter is a homologue of the TT8 gene, which is also an Myc transcription factor gene controlling the pericarp pigmentation in Arabidopsis thaliana. Sequence analysis showed that the exon 7 of the Ra gene of Yunanheixiannuo and Chuanheinuo had a 2-bp (GT) deletion compared with those of the white rice varieties Pei'ai 64S, 9311 and Nipponbare. A CAPS marker, CAPSRa, was developed according to the GT deletion for analysis of the two F2 segregating populations and 106 rice lines. The results showed that all F2 plants with white pericarp, and all non-purple rice lines (63 white and 22 red) contained no GT deletion, but all 20 purple rice lines contained the GT deletion. These results suggested that the Ra gene may be the Pb gene and the purple pericarp characteristic of rice is caused by the GT deletion within exon 7 of the Ra gene.

  6. Maize genome sequencing by methylation filtration.

    Science.gov (United States)

    Palmer, Lance E; Rabinowicz, Pablo D; O'Shaughnessy, Andrew L; Balija, Vivekanand S; Nascimento, Lidia U; Dike, Sujit; de la Bastide, Melissa; Martienssen, Robert A; McCombie, W Richard

    2003-12-19

    Gene enrichment strategies offer an alternative to sequencing large and repetitive genomes such as that of maize. We report the generation and analysis of nearly 100,000 undermethylated (or methylation filtration) maize sequences. Comparison with the rice genome reveals that methylation filtration results in a more comprehensive representation of maize genes than those that result from expressed sequence tags or transposon insertion sites sequences. About 7% of the repetitive DNA is unmethylated and thus selected in our libraries, but potentially active transposons and unmethylated organelle genomes can be identified. Reverse transcription polymerase chain reaction can be used to finish the maize transcriptome.

  7. Absorption and Cooked Rice Quality

    Institute of Scientific and Technical Information of China (English)

    LinJialianetal

    2001-01-01

    Abstract: Using glucono-8-1actone, sodiumcyclodextrin and proteinase as mainrice under different conditions and theadditivepolyphosphate, emulsifier, 13-the water-absorbing quality ofmethods to improve the edible quality ofcooked rice are systematically investigated. The experimental result indicatesthat the water-absorbing ability of rice at room temperature can be increasedsignificantly by soaking it in a 1:2 mixture of sodium polyphosphate andglucono-8-1actone. The cooked rice quality can be apparently improved bysoaking in a mixture of sodium polyphosphate, glucono-8-1actone, emulsifier, 13-cyclodextrin and protease.

  8. Development of Commercial Thermo-sensitive Genic Male Sterile Rice Accelerates Hybrid Rice Breeding Using the CRISPR/Cas9-mediated TMS5 Editing System

    OpenAIRE

    2016-01-01

    Hybrid rice breeding offers an important strategy to improve rice production, in which the cultivation of a male sterile line is the key to the success of cross-breeding. CRISPR/Cas9 systems have been widely used in target-site genome editing, whereas their application for crop genetic improvement has been rarely reported. Here, using the CRISPR/Cas9 system, we induced specific mutations in TMS5, which is the most widely applied thermo-sensitive genic male sterility (TGMS) gene in China, and ...

  9. Agromorphological characterization of some rice species in the main ...

    African Journals Online (AJOL)

    International Journal of Biological and Chemical Sciences ... of the samples of the prospection-collection from October 2005 to Mars 2006 revealed the existence of three types of rice in the zone: wild rice, adventitious rice and cultivated rice.

  10. Determinants of rice output among ADP contact farmers in mining ...

    African Journals Online (AJOL)

    Determinants of rice output among ADP contact farmers in mining and non mining ... The sample size was 120 rice farmers (60 mining area rice farmers and 60 non ... contacts significantly affected rice output at given levels of probability.

  11. Construction and characterization of a normalized whole-life-cycle cDNA library of rice

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    A cDNA library with genomic complete coverage is a powerful tool for functional genomic studies. For studying the functions of rice genes on a large scale, a normalized whole-life-cycle cDNA library is constructed based on the strategy of saturation hybridization with genomic DNA using rice cultivar Minghui 63, an elite restorer line for a number of rice hybrids that are widely cultivated in China. This library consists of cDNA from 15 directionally cloned cDNA libraries constructed with different tissues from 9 developmental stages. For normalization, the denatured plasmids purified from the 15 directionally cloned libraries are mixed and hybridized with saturated genomic DNA labeled with magnetic beads in two complementary systems. Well-matched plasmids are captured from the hybridized genomic DNA and electroporated into competent DH10B E. coli for construction of the normalized whole-life-cycle cDNA library. This library consists of 62000 clones with an average insert length about 1.4 kb. Inverse Northern blotting shows that this cDNA library included many rarely expressed genes and tissue-specific genes. Sequencing of 10750 cDNA clones of this library reveals 6399 unique ESTs (expressed sequence tags), indicating that the non-redundancy of the library is about 59.5%. This library has been used to make cDNA microarrays for functional genomic studies.

  12. Construction of Oryza Sativa genome contigs by fingerprint strategy

    Institute of Scientific and Technical Information of China (English)

    TAOQUAZHOU; GUOFANHONG; 等

    1995-01-01

    We described the construction of BAC contigs of the genome of a indica variety of Oryza sativa.Guang Lu Ai 4. An entire representative(Sixfold coverage of rice chromosomes)and genetically stable BAC library of rice genome constructed in this lab has been systematically analysed by restriction enzyme fragmentation and polyacrylamide gel electrophoresis.And all the images thus obtained were subject to image-processing,which consisted of preliminary location of bands,cooperative tracking of lanes by correlation of adjacent bads.a precise densitometric pass,alignment at the marker bands with the standard,optional interactive editing,and normalization of the accepted bands.The contigs were generated based on the Computer Software specially designed for genome mapping.The number of contigs with 600 kb in length on average was 464.of contigs with 1000kb in length on average was 107; of contigs with 1500 kb in length on average was Construction of Oryza Sativa genome contigs.23.Therefor,all the contigs we have obtained ampunted up to 420 megabases in length.Considering the size of rice genome(430 megabased),the contigs generated in this lab have covered nearly 98% of the rice genome.We are now in the process of mapping the contigs to chromosomes.

  13. Reticulate evolution of the rye genome.

    Science.gov (United States)

    Martis, Mihaela M; Zhou, Ruonan; Haseneyer, Grit; Schmutzer, Thomas; Vrána, Jan; Kubaláková, Marie; König, Susanne; Kugler, Karl G; Scholz, Uwe; Hackauf, Bernd; Korzun, Viktor; Schön, Chris-Carolin; Dolezel, Jaroslav; Bauer, Eva; Mayer, Klaus F X; Stein, Nils

    2013-10-01

    Rye (Secale cereale) is closely related to wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to its large genome (~8 Gb) and its regional importance, genome analysis of rye has lagged behind other cereals. Here, we established a virtual linear gene order model (genome zipper) comprising 22,426 or 72% of the detected set of 31,008 rye genes. This was achieved by high-throughput transcript mapping, chromosome survey sequencing, and integration of conserved synteny information of three sequenced model grass genomes (Brachypodium distachyon, rice [Oryza sativa], and sorghum [Sorghum bicolor]). This enabled a genome-wide high-density comparative analysis of rye/barley/model grass genome synteny. Seventeen conserved syntenic linkage blocks making up the rye and barley genomes were defined in comparison to model grass genomes. Six major translocations shaped the modern rye genome in comparison to a putative Triticeae ancestral genome. Strikingly dissimilar conserved syntenic gene content, gene sequence diversity signatures, and phylogenetic networks were found for individual rye syntenic blocks. This indicates that introgressive hybridizations (diploid or polyploidy hybrid speciation) and/or a series of whole-genome or chromosome duplications played a role in rye speciation and genome evolution.

  14. The Use of Rice Varietal Diversity for Rice Blast Control

    Institute of Scientific and Technical Information of China (English)

    ZHU You-yong; LI Zuo-shen; LU Bao-rong; CHEN Hai-ru; FAN Jing-hua; WANG Yun-yue; LI Yan; FAN Jin-xiang; YANG Shi-sheng; MA Guan-liang; CHEN Jian-bin

    2003-01-01

    Field experiments of mixed- (intercropping) and pure-planting (monoculture) of four rice vari-eties, representing improved hybrid varieties (Shanyou63 and Shanyou22) and high-quality traditional varie-ties (Huangkenuo and Zigu) from Yunnan Province, were conducted based on their differences in genetic back-ground and agro-economical characteristics. The results demonstrated that the mixed-planting of the hybridrice and high-quality traditional rice varieties had a significantly greater effect on controlling rice blast diseasethan the monocuiture of these varieties, particularly the traditional ones. It is evident for the highly suscepti-ble traditional varieties in mixed-planting to achieve disease control, with significant decreases in blast inci-dences and severity indexes. The blast control efficiency reached up to 83 - 98 % under such planting model.This suggests that an appropriate mixed-planting of rice varieties with diverse genetic background and agro-e-conomical characteristics is an effective approach for rice blast control. In addition, resistance of the tradi-tional rice varieties to lodging was considerably increased in the plots with mixed-planting, compared with theplots with monoculture. The average rate of grain-yield increase ranged from 6.5 to 9.7 % in the plots withmixed-planting.

  15. RNA-sequencing reveals previously unannotated protein- and microRNA-coding genes expressed in aleurone cells of rice seeds.

    Science.gov (United States)

    Watanabe, Kenneth A; Ringler, Patricia; Gu, Lingkun; Shen, Qingxi J

    2014-01-01

    The rice genome annotation has been greatly improved in recent years, largely due to the availability of full length cDNA sequences derived from many tissues. Among those yet to be studied is the aleurone layer, which produces hydrolases for mobilization of seed storage reserves during seed germination and post germination growth. Herein, we report transcriptomes of aleurone cells treated with the hormones abscisic acid, gibberellic acid, or both. Using a comprehensive approach, we identified hundreds of novel genes. To minimize the number of false positives, only transcripts that did not overlap with existing annotations, had a high level of expression, and showed a high level of uniqueness within the rice genome were considered to be novel genes. This approach led to the identification of 553 novel genes that encode proteins and/or microRNAs. The transcriptome data reported here will help to further improve the annotation of the rice genome.

  16. Soil Incorporation of Silica-Rich Rice Husk Decreases Inorganic Arsenic in Rice Grain.

    Science.gov (United States)

    Seyfferth, Angelia L; Morris, Andrew H; Gill, Rattandeep; Kearns, Kelli A; Mann, Jessica N; Paukett, Michelle; Leskanic, Corey

    2016-05-18

    Arsenic decreases rice yield, and inorganic grain As threatens human health; thus, strategies to decrease rice As are critically needed. Increased plant-available silica (Si) can decrease rice As, yet the source of Si matters. Rice husk, an underutilized and Si-rich byproduct of rice production that contains less labile C and an order of magnitude less As than rice straw, may be an economically viable Si resource to decrease rice As, yet the impact of rice husk incorporation on As in the rice-soil nexus has not been reported. This proof-of-concept study shows that rice husk incorporation to soil (1% w/w) decreases inorganic grain As by 25-50% without negatively affecting grain Cd, yield, or dissolved CH4 levels. Rice husk is a critical yet perhaps overlooked resource to improve soil quality through enhanced nutrient availability and attenuate human health risks through consumption of As-laden grain.

  17. Rice vaikib salavanglaist / Tõnis Erilaid

    Index Scriptorium Estoniae

    Erilaid, Tõnis, 1943-

    2005-01-01

    Euroopasse visiidile sõitev USA välisminister Condoleezza Rice külastab Saksamaad, Rumeeniat, Ukrainat ja Belgiat. Süüdistusi CIA lennukite maandumiste ja salavanglate kohta ei olevat tal kavas kommenteerida

  18. Rice vaikib salavanglaist / Tõnis Erilaid

    Index Scriptorium Estoniae

    Erilaid, Tõnis, 1943-

    2005-01-01

    Euroopasse visiidile sõitev USA välisminister Condoleezza Rice külastab Saksamaad, Rumeeniat, Ukrainat ja Belgiat. Süüdistusi CIA lennukite maandumiste ja salavanglate kohta ei olevat tal kavas kommenteerida

  19. Gibberellin Signal Transduction in Rice

    Institute of Scientific and Technical Information of China (English)

    Liu-Min Fan; Xiaoyan Feng; Yu Wang; Xing Wang Deng

    2007-01-01

    In the past decade, significant knowledge has accumulated regarding gibberellin (GA) signal transduction in rice as a result of studies using multiple approaches, particularly molecular genetics. The present review highlights the recent developments in the identification of GA signaling pathway components, the discovery of GA-induced destruction of GA signaling represser (DELLA protein), and the possible mechanism underlying the regulation of GA-responsive gene expression in rice.

  20. Physical maps and recombination frequency of six rice chromosomes.

    Science.gov (United States)

    Wu, Jianzhong; Mizuno, Hiroshi; Hayashi-Tsugane, Mika; Ito, Yukiyo; Chiden, Yoshino; Fujisawa, Masaki; Katagiri, Satoshi; Saji, Shoko; Yoshiki, Shoji; Karasawa, Wataru; Yoshihara, Rie; Hayashi, Akiko; Kobayashi, Harumi; Ito, Kazue; Hamada, Masao; Okamoto, Masako; Ikeno, Maiko; Ichikawa, Yoko; Katayose, Yuichi; Yano, Masahiro; Matsumoto, Takashi; Sasaki, Takuji

    2003-12-01

    We constructed physical maps of rice chromosomes 1, 2, and 6-9 with P1-derived artificial chromosome (PAC) and bacterial artificial chromosome (BAC) clones. These maps, with only 20 gaps, cover more than 97% of the predicted length of the six chromosomes. We submitted a total of 193 Mbp of non-overlapping sequences to public databases. We analyzed the DNA sequences of 1316 genetic markers and six centromere-specific repeats to facilitate characterization of chromosomal recombination frequency and of the genomic composition and structure of the centromeric regions. We found marked changes in the relative recombination rate along the length of each chromosome. Chromosomal recombination at the centromere core and surrounding regions on the six chromosomes was completely suppressed. These regions have a total physical length of about 23 Mbp, corresponding to 11.4% of the entire size of the six chromosomes. Chromosome 6 has the longest quiescent region, with about 5.6 Mbp, followed by chromosome 8, with quiescent region about half this size. Repetitive sequences accounted for at least 40% of the total genomic sequence on the partly sequenced centromeric region of chromosome 1. Rice CentO satellite DNA is arrayed in clusters and is closely associated with the presence of Centromeric Retrotransposon of Rice (CRR)- and RIce RetroElement 7 (RIRE7)-like retroelement sequences. We also detected relatively small coldspot regions outside the centromeric region; their repetitive content and gene density were similar to those of regions with normal recombination rates. Sequence analysis of these regions suggests that either the amount or the organization patterns of repetitive sequences may play a role in the inactivation of recombination.

  1. Increasing rice plant growth by Trichoderma sp.

    Science.gov (United States)

    Doni, Febri; Isahak, Anizan; Zain, Che Radziah Che Mohd; Sulaiman, Norela; Fathurahman, F.; Zain, Wan Nur Syazana Wan Mohd.; Kadhimi, Ahsan A.; Alhasnawi, Arshad Naji; Anhar, Azwir; Yusoff, Wan Mohtar Wan

    2016-11-01

    Trichoderma sp. is a plant growth promoting fungi in many crops. Initial observation on the ability to enhance rice germination and vigor have been reported. In this study, the effectiveness of a local isolate Trichoderma asprellum SL2 to enhance rice seedling growth was assessed experimentally under greenhouse condition using a completely randomized design. Results showed that inoculation of rice plants with Trichoderma asprellum SL2 significantly increase rice plants height, root length, wet weight, leaf number and biomass compared to untreated rice plants (control). The result of this study can serve as a reference for further work on the application of beneficial microorganisms to enhance rice production.

  2. Introduction of a rice blight resistance gene, Xa21, into five Chinese rice varieties through an Agrobacterium -mediated system

    Institute of Scientific and Technical Information of China (English)

    翟文学; 李晓兵; 田文忠; 周永力; 潘学彪; 曹守云; 赵显峰; 赵彬; 章琦; 朱立煌

    2000-01-01

    A cloned gene, Xa21 was transferred into five widely-used Chinese rice varieties through an Agrobacterium-mediated system, and over 110 independent transgenic lines were obtained. PCR and Southern analysis of transgenic plants revealed the integration of the whole Xa21 gene into the host genomes. The integrated Xa21 gene was stably inherited, and segregated in a 3 : 1 ratio in the selfed T1 generation when one copy of the gene was integrated in the transfor-mants. Inoculation tests displayed that transgenic T0 plants and Xa21 PCR-positive T1 plants were highly resistant to bacterial blight disease. The selected Xa21 homozygous resistant transgenic lines with desirable qualities may be propagated as new varieties or utilized in hybrid rice breeding.

  3. Introduction of a rice blight resistance gene, Xa21, into five Chinese rice varieties through an Agrobacterium-mediated system

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A cloned gene, Xa21 was transferred into five widely-used Chinese rice varieties through an Agrobacterium-mediated system, and over 110 independent transgenic lines were obtained. PCR and Southern analysis of transgenic plants revealed the integration of the whole Xa21 gene into the host genomes. The integrated Xa21 gene was stably inherited, and segregated in a 3∶1 ratio in the selfed T1 generation when one copy of the gene was integrated in the transformants. Inoculation tests displayed that transgenic T0 plants and Xa21 PCR-positive T1 plants were highly resistant to bacterial blight disease. The selected Xa21 homozygous resistant transgenic lines with desirable qualities may be propagated as new varieties or utilized in hybrid rice breeding.

  4. Independent domestication of Asian rice followed by gene flow from japonica to indica.

    Science.gov (United States)

    Yang, Ching-chia; Kawahara, Yoshihiro; Mizuno, Hiroshi; Wu, Jianzhong; Matsumoto, Takashi; Itoh, Takeshi

    2012-05-01

    Results from studies on the domestication process of Asian rice Oryza sativa have been controversial because of its complicated evolutionary history. Previous studies have yielded two alternative hypotheses about the origin(s) of the two major groups of O. sativa: japonica and indica. One study proposes a single common wild ancestor, whereas the other suggests that there were multiple domestication events of different types of wild rice. Here, we provide clear evidence of the independent domestication of japonica and indica obtained via high-throughput sequencing and a large-scale comparative analysis of two wild rice accessions (W1943 and W0106) and two cultivars (a japonica cultivar called "Nipponbare" and an indica cultivar called "Guangluai-4"). The different domestication processes of the two cultivar groups appear to have led to distinct patterns of molecular evolution in protein-coding regions. The intensity of purifying selection was relaxed only in the japonica group, possibly because of a bottleneck effect. Moreover, a genome-wide comparison between Nipponbare, Guangluai-4, and another indica cultivar (93-11) suggests multiple hybridization events between japonica and indica, both before and after the divergence of the indica cultivars. We found that a large amount of genomic DNA, including domestication-related genes, was transferred from japonica to indica, which might have been important in the development of modern rice. Our study provides an overview of the dynamic process of Asian rice domestication, including independent domestication events and subsequent gene flow.

  5. [Chromosomal localization of the hormone-sensitive lipase gene (Hsl) in rice field eel].

    Science.gov (United States)

    Ji, Fu-Yun; Yu, Qi-Xing; Pan, Pei-Wen

    2003-03-01

    Adipose tissue triacylglycerols are the quantitatively most important source of stored energy in animals. Hormone-sensitive lipase encoded by hormone-sensitive lipase gene (Hsl) is a multifunctional enzyme that catalyzes the hydrolysis of triacylglycerol stored in adipose tissue and cholesterol esters in the adrenals, ovaries, testes and macrophages. Using pig Hsl gene inserted into pBS labeled by the radioactive isotope and the digoxigenin as the probes respectively one band, 11.5kb, has been shown to hybridized with total DNA of rice field eel digested with Pst I by Southern blotting and Hsl gene has been assigned to metaphase chromosome 5, at the position of 78.35+/-1.26 from the centromere in rice field eel by fluorescent in situ hybridization (FISH). The mapping results are corresponding to that of "specific-chromosomal DNA pool" obtained by chromosome microisolation used to map gene and the mapping result is more accurate. The results of the study further illustrate the importance of the presence of Hsl gene in rice field eel genome and provide the first FISH mapping data for rice field eel chromosome 5. The current studies would advance the addition of known genetic markers and the construction of high resolution genetic map in rice field eel genome.

  6. Genomewide survey and characterization of metacaspase gene family in rice (Oryza sativa)

    Indian Academy of Sciences (India)

    Likai Wang; Hua Zhang

    2014-04-01

    Metacaspases (MCs), which are cysteine-dependent proteases found in plants, fungi, and protozoa, may be involved in programmed cell death processes, being distant relatives of metazoan caspases. In this study, we analysed the structures, phylogenetic relationship, genome localizations, expression patterns and domestic selections of eight MC genes identified in rice (OsMC). Alignment analysis of the corresponding protein sequences suggested OsMC proteins can be classified into two sub-types. The expression profiles of eight OsMC genes were analysed in 27 tissues covering the whole life cycle of rice. There are four OsMC genes uniquely expressed in mature tissues, indicating that these genes might play certain roles in senescence. Under abiotic and biotic stresses, four OsMC genes were expressed with treatments of one or more of Magnaporthe oryzae (M. oryzae) infected, pest damaged, cold stress and drought stress, indicating they might be involved in plant defense. In addition, gene trees and genetic diversity $(\\pi)$ were performed to measure whether candidate genes were selected during rice domestication. The results suggested that all the type I genes could not be domestication genes. However, two of five type II OsMC genes showed strong evidence for selective sweep, suggesting that these genes might be involved in cultivated rice domestication. These results provide a foundation for future functional genomic studies of this family in rice.

  7. Study on the Morphological Characteristics of the Allotetraploid of Red Crucian Carp(♀) × Common Carp(♂)%异源四倍体鲫鲤的形态特征研究

    Institute of Scientific and Technical Information of China (English)

    李建中; 张轩杰; 刘少军; 周工健; 刘筠

    2001-01-01

    The morphological characteristics of the allotetraploid fi sh were studied by ordinary regulations and were compared with those of Red crucia n Carp (Carassius auratus red var.) and Common Carp (Cyprinus carpio L.). The results were as follows: D.3,16~19; A.3,5~7; scalles in lateral line 30 ~34,scalles above lateral line 5~7,scalles below lateral line 5~8; gill raker 32 ~35; pharyngeal tooth 2, 1.4~4.1; vertebrae, 31~33; body length/body height = 2.33~3.33, body length/head length =2.73~4.60; head length / Lip length =2.67 ~4.01, head length /eye diameter =3.33~5.13; caudal peduncel length/caudal ped uncel height =0.83~1.32. The results indicated that the morphological character istics of the allotetraploid fish were steady.%按常规标准测定了异源四倍体鲫鲤的形态特征,并与二倍体的红鲫和湘江野鲤进行了比较.主要结果如下:异源四倍体鲫鲤的背鳍条Ⅲ,16~19;臀鳍条Ⅲ,5~7;侧线鳞30~34,侧线上鳞为5~7,侧线下鳞为5~8;鳃耙数32~35;下咽齿2行,1.4~4.1;脊椎骨31~33;口须2对;体长为体高的2.23~3.33倍,为头长的2.73~4.60倍;头长为吻长的2.67~4.01倍,为眼径的3.33~5.13倍;尾柄长为尾柄高的0.83~1.32倍.研究表明,异源四倍体鲫鲤形态性状稳定,已形成了一个新的四倍体鱼种群.

  8. 75 FR 56911 - Request for Public Comment on the United States Standards for Rough Rice, Brown Rice for...

    Science.gov (United States)

    2010-09-17

    ..., Brown Rice for Processing, and Milled Rice standards were last revised in 1993 (58 FR 68015) and appear... Comment on the United States Standards for Rough Rice, Brown Rice for Processing, and Milled Rice AGENCY... Administration (GIPSA) is reviewing the United States Standards and grading procedures for Rough Rice, Brown...

  9. 7 CFR 319.55a - Administrative instructions relating to entry of rice straw and rice hulls into Guam.

    Science.gov (United States)

    2010-01-01

    ... straw and rice hulls into Guam. 319.55a Section 319.55a Agriculture Regulations of the Department of... QUARANTINE NOTICES Rice Quarantine § 319.55a Administrative instructions relating to entry of rice straw and rice hulls into Guam. Rice straw and rice hulls may be imported into Guam without further permit,...

  10. Rice blast fungus (Magnaporthe oryzae) infects Arabidopsis via a mechanism distinct from that required for the infection of rice.

    Science.gov (United States)

    Park, Ju-Young; Jin, Jianming; Lee, Yin-Won; Kang, Seogchan; Lee, Yong-Hwan

    2009-01-01

    Magnaporthe oryzae is a hemibiotrophic fungal pathogen that causes rice (Oryza sativa) blast. Although M. oryzae as a whole infects a wide variety of monocotyledonous hosts, no dicotyledonous plant has been reported as a host. We found that two rice pathogenic strains of M. oryzae, KJ201 and 70-15, interacted differentially with 16 ecotypes of Arabidopsis (Arabidopsis thaliana). Strain KJ201 infected all ecotypes with varying degrees of virulence, whereas strain 70-15 caused no symptoms in certain ecotypes. In highly susceptible ecotypes, small chlorotic lesions appeared on infected leaves within 3 d after inoculation and subsequently expanded across the affected leaves. The fungus produced spores in susceptible ecotypes but not in resistant ecotypes. Fungal cultures recovered from necrotic lesions caused the same symptoms in healthy plants, satisfying Koch's postulates. Histochemical analyses showed that infection by the fungus caused an accumulation of reactive oxygen species and eventual cell death. Similar to the infection process in rice, the fungus differentiated to form appressorium and directly penetrated the leaf surface in Arabidopsis. However, the pathogenic mechanism in Arabidopsis appears distinct from that in rice; three fungal genes essential for pathogenicity in rice played only limited roles in causing disease symptoms in Arabidopsis, and the fungus seems to colonize Arabidopsis as a necrotroph through the secretion of phytotoxic compounds, including 9,12-octadecadienoic acid. Expression of PR-1 and PDF1.2 was induced in response to infection by the fungus, suggesting the activation of salicylic acid- and jasmonic acid/ethylene-dependent signaling pathways. However, the roles of these signaling pathways in defense against M. oryzae remain unclear. In combination with the wealth of genetic and genomic resources available for M. oryzae, this newly established pathosystem allows comparison of the molecular and cellular mechanisms underlying

  11. Genetic analysis and gene mapping of a rice few-tillering mutant in early backcross populations (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    TANG; Jiabin; (

    2001-01-01

    [1]Xu, Y. B., Shen, Z. T., Diallel analysis of tiller number at different growth stages in rice (Oryza sativa L.), Theoretical and Applied Genetics, 1991, 83(2): 243-249.[2]Wu, W. R., Li, W. M., Tang, D. Z. et al., Time-related mapping of quantitative trait loci underlying tiller number in rice, Genetics, 1999, (151): 297-303.[3]Wu, P., Zhang, G ., Huang, N., Identification of QTLs controlling quantitative characters in rice using RFLP markers, Euphytica, 1996, 89(3): 349-354.[4]Khush, G . S., Breaking the yield frontier of rice, GeoJournal, 1995, 35(3): 329-332.[5]Chen, X., Themnykh, S., Xu, Y. et al., Development of microsatellite framework providing genome-wide coverage in rice (Oryzae sativa L.), Theoretical and Applied Genetics, 1997, 95(4): 553-567.[6]Panaud, O., Chen, X., McCouch, S. R. et al., Development of microsatellite markers