EU-OSTID: A Collection of Transposon Insertional Mutants for Functional Genomics in Rice

Enckevort, L.J.G. van; Droc, Gaëtan; Piffanelli, Pietro; Greco, Raffaella; Gagneur, C.; Weber, Christele; González, Víctor; Cabot, Pere; Fornara, Fabio; Berri, Stefano; Miró, Berta; Lan, Ping; Rafel, Marta; Capell, Teresa; Puigdomènech, Pere; Ouwerkerk, Pieter B.F.; Meijer, Annemarie H.; Pè, Enrico; Colombo, Lucia; Christou, Paul; Guiderdoni, Emmanuel; Pereira, Andy

doi:10.1007/s11103-005-8532-6

Cited by 68 publications

(44 citation statements)

References 32 publications

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“…For the other 26.9% (125/463) FSTs that showed no homology to rice cDNA sequences, we were not able to make a consistently clear distinction between the FSTs from 5# or 3# regulatory sequences of rice genes and the FSTs from Ds insertions in the intergenic regions. These results confirmed the previous reports that the Ac-Ds elements preferentially transpose to genic regions (Enoki et al, 1999;Kolesnik et al, 2004;van Enckevort et al, 2005). For the strategy of activation tagging, Ds insertions in the intergenic regions are desirable as compared to the insertions in genic regions.…”

Section: Rfpsupporting

confidence: 90%

A Versatile Transposon-Based Activation Tag Vector System for Functional Genomics in Cereals and Other Monocot Plants

Desai

Wing

et al. 2007

Plant Physiology

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Transposon insertional mutagenesis is an effective alternative to T-DNA mutagenesis when transformation through tissue culture is inefficient as is the case for many crop species. When used as activation tags, transposons can be exploited to generate novel gain-of-function phenotypes without transformation and are of particular value in the study of polyploid plants where gene knockouts will not have phenotypes. We have developed an in cis-activation-tagging Ac-Ds transposon system in which a T-DNA vector carries a Dissociation (Ds) element containing 43 cauliflower mosaic virus enhancers along with the Activator (Ac) transposase gene. Stable Ds insertions were selected using green fluorescent protein and red fluorescent protein genes driven by promoters that are functional in maize (Zea mays) and rice (Oryza sativa). The system has been tested in rice, where 638 stable Ds insertions were selected from an initial set of 26 primary transformants. By analysis of 311 flanking sequences mapped to the rice genome, we could demonstrate the wide distribution of the elements over the rice chromosomes. Enhanced expression of rice genes adjacent to Ds insertions was detected in the insertion lines using semiquantitative reverse transcription-PCR method. The in cis-two-element vector system requires minimal number of primary transformants and eliminates the need for crossing, while the use of fluorescent markers instead of antibiotic or herbicide resistance increases the applicability to other plants and eliminates problems with escapes. Because Ac-Ds has been shown to transpose widely in the plant kingdom, the activation vector system developed in this study should be of utility more generally to other monocots.

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Section: Rfpsupporting

confidence: 90%

A Versatile Transposon-Based Activation Tag Vector System for Functional Genomics in Cereals and Other Monocot Plants

Desai

Wing

et al. 2007

Plant Physiology

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“…The insertion of transferred DNA (T-DNA) , Chen et al 2003, Ryu et al 2004, Sallaud et al 2004, the transposition of the endogenous retrotransposon Tos17 (Miyao et al 2003, and the insertion and transposition of maize Ac/Ds transposable elements (Kolesnik et al 2004, Park et al 2007, Upadhyaya et al 2002, van Enckevort et al 2005 have been applied to generate large populations of loss-offunction mutant lines. Such DNA insertion lines have been used as rice mutant resources for the identification of various genes and their functions , Hirochika et al 2004, Krishnan et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Production and characterization of a large population of cDNA-overexpressing transgenic rice plants using Gateway-based full-length cDNA expression libraries

et al. 2010

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We applied the full-length cDNA overexpressor (FOX) gene-hunting system for systematic and genome-wide functional analysis of rice genes. In this study, we constructed a novel binary vector carrying the Gateway site-specific recombination cassette and then constructed rice FOX libraries containing a maximum of 13,823 independent, full-length cDNAs (fl-cDNAs) that correspond to approximately half the total number of rice fl-cDNA clones. By introducing the FOX libraries via Agrobacterium, we generated 2,586 FOX-rice lines exhibiting various visible alterations (e.g., plant height, tillers, leaves, and heading dates). The introduced flcDNAs, integrated into individual transgenic rice genomes, were amplified by genomic PCR and identified using sequencing analysis. The fl-cDNAs were PCR-amplified in 2,251 (94.2%) of the 2,389 FOX-rice lines that were examined, identifying 1,920 independent fl-cDNAs in the FOX lines. In addition to the previously generated FOX-rice plants, our new collection of FOX-rice lines produced through the Gateway system should be a useful tool for the efficient identification of gene functions in rice. Moreover, this Gateway-based technology should be applicable to other species in which a collection of fl-cDNA clones is available.

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“…For rice, several resources with large collections of insertion mutants were also generated, including those in Australia (http://www. pi.csiro.au/fgrttpub/) [29], China (http://rmd.ncpgr.cn/; http://trim.sinica.edu.tw/) [30][31][32], Europe (http://orygenesdb.cirad.fr/) [33], France (http://urgi.versailles.inra. fr/OryzaTagLine/) [34], Japan (http://pfg101.nias.affrc.…”

Section: Fang-fang Fu Et Al 381mentioning

confidence: 99%

Studies on rice seed quality through analysis of a large-scale T-DNA insertion population

et al. 2009

Cell Res

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A rice (Oryza sativa) T-DNA insertion population, which included more than 63 000 independent transgenic lines and 8 840 identified flanking sequence tags (FSTs) that were mapped onto the rice genome, was developed to systemically study the rice seed quality control. Genome-wide analysis of the FST distribution showed that T-DNA insertions were positively correlated with expressed genes, but negatively with transposable elements and small RNAs. In addition, the recovered T-DNAs were preferentially located at the untranslated region of the expressed genes. More than 11 000 putative homozygous lines were obtained through multi-generations of planting and resistance screening, and measurement of seed quality of around half of them, including the contents of starch, amylose, protein and fat, with a nondestructive near-infrared spectroscopy method, identified 551 mutants with unique or multiple altered parameters of seed quality. Analysis of the corresponding FSTs showed that genes participating in diverse functions, including metabolic processes and transcriptional regulation, were involved, indicating that seed quality is regulated by a complex network. IntroductionRice (Oryza sativa), as a wholesome and nutritious cereal grain, provides the staple food for more than half of the world's population [1]. Along with the growth of economies and population throughout the world, there is an increasing demand for high-yield and high-quality rice. The grain quality of rice, including that of milling, appearance, cooking and eating, and nutrition, is determined by multiple physicochemical properties [2], and studies on the involved key genes and relevant regulatory mechanisms will help to illustrate the regulatory networks of rice quality control and benefit for the breeding efforts.Starch, which is composed of amylose and amylopectin, comprises ∼90% of dry endosperm of rice seed.The apparent amylose content (AAC) is recognized as an important determinant of the appearance and texture of grain [3]. Thai jasmine rice (KDML 105), one of the best-quality rice with good cooking and eating qualities, has low amylose content (AC) and medium gel consistency (GC) [4].The nutritional quality includes the proportions of protein, fat, mineral and other substances [5]. The rice protein is rich in methionine and cysteine, and compares favorably with proteins of other cereals, but is poor in lysine and threonine, making it an incomplete protein source for human infants [6]. Storage triacylglycerols are stored in oil bodies containing phospholipids and oleosins at the surface [7], and oil bodies are abundant in embryo and aleurone layer of rice seed. However, the aleurone layer is usually removed by milling because it turns rancid upon storage [8]. In addition, oil also influences other aspects of seed quality, and a recent report showed that the quality and viability of Arabidopsis seeds can be enhanced by suppressing phospholipase D [9].The near-infrared spectroscopy (NIRS) technology, which is based on the fact that several natural pr...

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EU-OSTID: A Collection of Transposon Insertional Mutants for Functional Genomics in Rice

Cited by 68 publications

References 32 publications

A Versatile Transposon-Based Activation Tag Vector System for Functional Genomics in Cereals and Other Monocot Plants

A Versatile Transposon-Based Activation Tag Vector System for Functional Genomics in Cereals and Other Monocot Plants

Production and characterization of a large population of cDNA-overexpressing transgenic rice plants using Gateway-based full-length cDNA expression libraries

Studies on rice seed quality through analysis of a large-scale T-DNA insertion population

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