Generation and flanking sequence analysis of a rice T-DNA tagged population

Sha, Yingying; Li, S.; Pei, Zhibin; Luo, Le; Tian, Yingchuan; He, Chaozu

doi:10.1007/s00122-003-1423-9

Cited by 72 publications

(60 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…For this reason, transgenes may be inserted in functional genomic regions, disrupting the structure and/or altering the regulation patterns of genes from the plant host genome. Results obtained from largescale T-DNA tagging experiments in Arabidopsis thaliana (Szabados et al 2002;Alonso et al 2003;Forsbach et al 2003;Qin et al 2003) and Oryza sativa (Jeong et al 2002(Jeong et al , 2006Chen et al 2003;Sha et al 2004;Zhang et al 2007) showed a non-random distribution of T-DNA insertion sites, more frequent in genic sequences endowed with different functions such as metabolism, signal transduction and transcription, disease processes and defence mechanisms, intracellular traffic. Experiments in other organisms, namely the legume Medicago truncatula (Scholte et al 2002), barley (Salvo-Garrido et al 2004, potato and tobacco (Koncz et al 1989;Lindsey et al 1993) also suggested that T-DNA insertion occurred generally into coding sequences.…”

Section: Introductionmentioning

confidence: 99%

Characterisation of 3′ transgene insertion site and derived mRNAs in MON810 YieldGard® maize

et al. 2008

View full text Add to dashboard Cite

The construct inserted in YieldGard Ò MON810 maize, produced by Monsanto, contains the CaMV 35S promoter, the hsp70 intron of maize, the cryI(A)b gene for resistance to lepidopterans and the NOS terminator. In a previous work a truncation event at the 3 0 end of the cryI(A)b gene leading to the complete loss of the NOS terminator was demonstrated. The 3 0 maize genome junction region was isolated in the same experiment not showing any homology with known sequences. The aim of the experiments here reported was therefore to isolate and characterize a larger portion of the 3 0 integration junction from genomic DNA of two commercial MON810 maize lines. Specific primers were designed on the 3 0 integration junction sequence for the amplification of a 476 bp fragment downstream of the sequence previously detected. In silico analysis identified the whole isolated 3 0 genomic region as a gene putatively coding for the HECT E3 ubiquitin ligase. RT-PCR performed in this region produced cDNA variants of different length. In silico translation of these transcripts identified 2 and 18 putative additional aminoacids in different variants, all derived from the adjacent host genomic sequences, added to the truncated CRY1A protein. These putative recombinant proteins did not show homology with any known protein domains. Our data gave new insights on the genomic organization of MON810 in the YieldGard Ò maize and confirmed the previous suggestion that the integration in the genome of maize caused a complex recombination event without, apparently, interfering with the activity of the partial CRY1A endotoxin and both the vigor and yield of the YieldGard Ò maize.Keywords Cry-hect recombinant mRNAs Á 3 0 insertion site Á HECT protein ligase Á YieldGard Ò MON810 maize

show abstract

Section: Introductionmentioning

confidence: 99%

Characterisation of 3′ transgene insertion site and derived mRNAs in MON810 YieldGard® maize

et al. 2008

View full text Add to dashboard Cite

show abstract

“…The promise of this technology as illustrated by the cloning and characterization of several genes in Arabidopsis and the world wide efforts in progress should enable coverage of this model genome in a few years to come. Interestingly, T-DNA mutational approach is now being successfully modified to tag genes in a number of economically important plant species, rice (430 Mbp) (Hiroyuki et al 1999;Kolesnik et al 2004;Sha et al 2004), tomato (953 Mb) (Meissner et al 2000), Brassica napus (1182 Mbp) (Bade et al 2003), Medicago truncatula (~454 to 526 Mbp) (Trieu et al 2000) and poplar (550 Mbp America, March 2000, vol. 97, no.…”

Section: Discussionmentioning

confidence: 99%

“…T-DNA tagging has been used successfully for gene discovery in rice. An initial database has also been constructed using T-DNA flanking sequences (Sha et al 2004). T-DNA tags have also been observed to insert preferentially into gene rich regions Sha et al 2004).…”

Section: Insertional Mutagenesis In Other Angiospermsmentioning

confidence: 99%

See 1 more Smart Citation

T-DNA insertional mutagenesis in Arabidopsis: a tool for functional genomics

Srinivasan¹,

Radhamony²

2005

Electro Journal of Biotech

View full text Add to dashboard Cite

show abstract

“…In addition, the T-DNA distribution was positively correlated with expressed genes but negatively with transposable elements and small RNAs. Indeed, it has been suggested that the positive correlation between expressed genes and T-DNA insertions may be due to the "open" state of actively transcribed regions, rendering the DNA in these regions more accessible [58,60,61]. The negative correlation with small RNAs suggests that small RNAs also play roles in influencing T-DNA integration by maintaining the DNA in a condensed state.…”

Section: Distribution Of T-dna Insertions On Chromosomesmentioning

confidence: 99%

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

et al. 2009

Cell Res

View full text Add to dashboard Cite

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...

show abstract

Generation and flanking sequence analysis of a rice T-DNA tagged population

Cited by 72 publications

References 49 publications

Characterisation of 3′ transgene insertion site and derived mRNAs in MON810 YieldGard® maize

Characterisation of 3′ transgene insertion site and derived mRNAs in MON810 YieldGard® maize

T-DNA insertional mutagenesis in Arabidopsis: a tool for functional genomics

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

Contact Info

Product

Resources

About