High-resolution expression profiling of selected gene sets during plant immune activation.

Abstract:

:The plant immune system involves detection of pathogens via both cell-surface and intracellular receptors. Both receptor classes can induce transcriptional reprogramming that elevates disease resistance. To assess differential gene expression during plant immunity, we developed and deployed quantitative sequence capture (CAP-I). We designed and synthesized biotinylated single-strand RNA bait libraries targeted to a subset of defense genes, and generated sequence capture data from 99 RNA-seq libraries. We built a data processing pipeline to quantify the RNA-CAP-I-seq data, and visualize differential gene expression. Sequence capture in combination with quantitative RNA-seq enabled cost-effective assessment of the expression profile of a specified subset of genes. Quantitative sequence capture is not limited to RNA-seq or any specific organism and can potentially be incorporated into automated platforms for high-throughput sequencing.

journal_name

Plant Biotechnol J

authors

Ding P,Ngou BPM,Furzer OJ,Sakai T,Shrestha RK,MacLean D,Jones JDG

doi

10.1111/pbi.13327

subject

Has Abstract

pub_date

2020-07-01 00:00:00

pages

1610-1619

issue

7

eissn

1467-7644

issn

1467-7652

journal_volume

18

pub_type

杂志文章
  • High-Spatiotemporal-Resolution Transcriptomes Provide Insights into Fruit Development and Ripening in Citrus sinensis.

    abstract::Citrus fruit has a unique structure with soft leathery peel and pulp containing vascular bundles and several segments with many juice sacs. The function and morphology of each fruit tissue are different. Therefore, analysis at the organ-wide or mixed-tissue level inevitably obscures many tissue-specific phenomena. Hig...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13549

    authors: Feng G,Wu J,Xu Y,Lu L,Yi H

    更新日期:2021-01-20 00:00:00

  • Screening for resistance against Pseudomonas syringae in rice-FOX Arabidopsis lines identified a putative receptor-like cytoplasmic kinase gene that confers resistance to major bacterial and fungal pathogens in Arabidopsis and rice.

    abstract::Approximately 20,000 of the rice-FOX Arabidopsis transgenic lines, which overexpress 13,000 rice full-length cDNAs at random in Arabidopsis, were screened for bacterial disease resistance by dip inoculation with Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). The identities of the overexpressed genes were determi...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2010.00568.x

    authors: Dubouzet JG,Maeda S,Sugano S,Ohtake M,Hayashi N,Ichikawa T,Kondou Y,Kuroda H,Horii Y,Matsui M,Oda K,Hirochika H,Takatsuji H,Mori M

    更新日期:2011-05-01 00:00:00

  • Immunomodulation confers herbicide resistance in plants.

    abstract::In order to create a novel mechanism for herbicide resistance in plants, we expressed a single-chain antibody fragment (scFv) in tobacco with specific affinity to the auxinic herbicide picloram. Transgenic tobacco plants and seedlings expressing this scFv against picloram were protected from its effect in a dose-depen...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2004.00060.x

    authors: Almquist KC,Niu Y,McLean MD,Mena FL,Yau KY,Brown K,Brandle JE,Hall JC

    更新日期:2004-05-01 00:00:00

  • CRISPR/Cas9-mediated knockout of Ms1 enables the rapid generation of male-sterile hexaploid wheat lines for use in hybrid seed production.

    abstract::The development and adoption of hybrid seed technology have led to dramatic increases in agricultural productivity. However, it has been a challenge to develop a commercially viable platform for the production of hybrid wheat (Triticum aestivum) seed due to wheat's strong inbreeding habit. Recently, a novel platform f...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13106

    authors: Okada A,Arndell T,Borisjuk N,Sharma N,Watson-Haigh NS,Tucker EJ,Baumann U,Langridge P,Whitford R

    更新日期:2019-10-01 00:00:00

  • Developing xylem-preferential expression of PdGA20ox1, a gibberellin 20-oxidase 1 from Pinus densiflora, improves woody biomass production in a hybrid poplar.

    abstract::Woody biomass has gained popularity as an environmentally friendly, renewable and sustainable resource for liquid fuel production. Here, we demonstrate biotechnological improvement of the quantity and quality of woody biomass by employing developing xylem (DX)-preferential production of gibberellin (GA), a phytohormon...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12484

    authors: Jeon HW,Cho JS,Park EJ,Han KH,Choi YI,Ko JH

    更新日期:2016-04-01 00:00:00

  • Commercialization of new biotechnology: a systematic review of 16 commercial case studies in a novel manufacturing sector.

    abstract::The 1980s and 1990s saw a major expansion of biotechnology into new areas of science including genomics and recombinant technologies. This was coupled to the widespread emergence of academics into the commercial sector as they were encouraged to spin out companies or commercialize their intellectual property. There we...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1111/pbi.12426

    authors: Paul MJ,Thangaraj H,Ma JK

    更新日期:2015-10-01 00:00:00

  • The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants.

    abstract::Reverse transcription-polymerase chain reaction (RT-PCR) approaches have been used in a large proportion of transcriptome analyses published to date. The accuracy of the results obtained by this method strongly depends on accurate transcript normalization using stably expressed genes, known as references. Statistical ...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2008.00346.x

    authors: Gutierrez L,Mauriat M,Guénin S,Pelloux J,Lefebvre JF,Louvet R,Rusterucci C,Moritz T,Guerineau F,Bellini C,Van Wuytswinkel O

    更新日期:2008-08-01 00:00:00

  • Improvement of stress tolerance of wheat and barley by modulation of expression of DREB/CBF factors.

    abstract::Transcription factors have been shown to control the activity of multiple stress response genes in a coordinated manner and therefore represent attractive targets for application in molecular plant breeding. We investigated the possibility of modulating the transcriptional regulation of drought and cold responses in t...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2010.00547.x

    authors: Morran S,Eini O,Pyvovarenko T,Parent B,Singh R,Ismagul A,Eliby S,Shirley N,Langridge P,Lopato S

    更新日期:2011-02-01 00:00:00

  • Synthesis of bacteriophage lytic proteins against Streptococcus pneumoniae in the chloroplast of Chlamydomonas reinhardtii.

    abstract::There is a pressing need to develop novel antibacterial agents given the widespread antibiotic resistance among pathogenic bacteria and the low specificity of the drugs available. Endolysins are antibacterial proteins that are produced by bacteriophage-infected cells to digest the bacterial cell wall for phage progeny...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12703

    authors: Stoffels L,Taunt HN,Charalambous B,Purton S

    更新日期:2017-09-01 00:00:00

  • Overexpression of Hevea brasiliensis ethylene response factor HbERF-IXc5 enhances growth and tolerance to abiotic stress and affects laticifer differentiation.

    abstract::Ethylene response factor 1 (ERF1) is an essential integrator of the jasmonate and ethylene signalling pathways coordinating a large number of genes involved in plant defences. Its orthologue in Hevea brasiliensis, HbERF-IXc5, has been assumed to play a major role in laticifer metabolism and tolerance to harvesting str...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12774

    authors: Lestari R,Rio M,Martin F,Leclercq J,Woraathasin N,Roques S,Dessailly F,Clément-Vidal A,Sanier C,Fabre D,Melliti S,Suharsono S,Montoro P

    更新日期:2018-01-01 00:00:00

  • OsNAC2 integrates auxin and cytokinin pathways to modulate rice root development.

    abstract::The rice root system is important for growth. The crosstalk between auxin and cytokinin mediates root initiation and elongation. However, it remains unclear how the transcriptional network upstream of the auxin and cytokinin signalling pathways determines root development. Here, we observed that the knockdown of OsNAC...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.13209

    authors: Mao C,He J,Liu L,Deng Q,Yao X,Liu C,Qiao Y,Li P,Ming F

    更新日期:2020-02-01 00:00:00

  • Genetic spell-checking: gene editing using single-stranded DNA oligonucleotides.

    abstract::Single-stranded oligonucleotides (ssODNs) can be used to direct the exchange of a single nucleotide or the repair of a single base within the coding region of a gene in a process that is known, generically, as gene editing. These molecules are composed of either all DNA residues or a mixture of RNA and DNA bases and u...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1111/pbi.12473

    authors: Rivera-Torres N,Kmiec EB

    更新日期:2016-02-01 00:00:00

  • Identification of bottlenecks in the accumulation of cyclic fatty acids in camelina seed oil.

    abstract::Modified fatty acids (mFA) have diverse uses; for example, cyclopropane fatty acids (CPA) are feedstocks for producing coatings, lubricants, plastics and cosmetics. The expression of mFA-producing enzymes in crop and model plants generally results in lower levels of mFA accumulation than in their natural-occurring sou...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12839

    authors: Yu XH,Cahoon RE,Horn PJ,Shi H,Prakash RR,Cai Y,Hearney M,Chapman KD,Cahoon EB,Schwender J,Shanklin J

    更新日期:2018-04-01 00:00:00

  • Expression of the P(₁B) -type ATPase AtHMA4 in tobacco modifies Zn and Cd root to shoot partitioning and metal tolerance.

    abstract::Genetic modification of Zn/Cd accumulation in roots and shoots for biofortification or phytoremediation is a focus of this manuscript. We expressed AtHMA4 (a P(₁B) ATPase involved in Zn and Cd transport), AtHMA4-trunc (lacking the C-terminal region) and AtHMA4-C terminus (the C-terminal region alone) in tobacco under ...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2010.00531.x

    authors: Siemianowski O,Mills RF,Williams LE,Antosiewicz DM

    更新日期:2011-01-01 00:00:00

  • The in silico identification and characterization of a bread wheat/Triticum militinae introgression line.

    abstract::The capacity of the bread wheat (Triticum aestivum) genome to tolerate introgression from related genomes can be exploited for wheat improvement. A resistance to powdery mildew expressed by a derivative of the cross-bread wheat cv. Tähti × T. militinae (Tm) is known to be due to the incorporation of a Tm segment into ...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12610

    authors: Abrouk M,Balcárková B,Šimková H,Komínkova E,Martis MM,Jakobson I,Timofejeva L,Rey E,Vrána J,Kilian A,Järve K,Doležel J,Valárik M

    更新日期:2017-02-01 00:00:00

  • GbSOBIR1 confers Verticillium wilt resistance by phosphorylating the transcriptional factor GbbHLH171 in Gossypium barbadense.

    abstract::Receptor-like kinases (RLKs) are important components of plant innate immunity. Although recent studies have revealed that the RLK suppressor of BIR1-1 (SOBIR1) can interact with multiple receptor-like proteins and is required for resistance against fungal pathogens, how the signal is transduced and triggers immune re...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12954

    authors: Zhou Y,Sun L,Wassan GM,He X,Shaban M,Zhang L,Zhu L,Zhang X

    更新日期:2019-01-01 00:00:00

  • A maize phytochrome-interacting factors protein ZmPIF1 enhances drought tolerance by inducing stomatal closure and improves grain yield in Oryza sativa.

    abstract::Phytochrome-interacting factors (PIFs) play major roles in regulating plant growth and development, but their roles in drought stress remain elusive. Here, we cloned and characterized a maize (Zea mays) PIF transcription factor, ZmPIF1. The expression level of ZmPIF1 was significantly induced by independent drought an...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12878

    authors: Gao Y,Wu M,Zhang M,Jiang W,Ren X,Liang E,Zhang D,Zhang C,Xiao N,Li Y,Dai Y,Chen J

    更新日期:2018-07-01 00:00:00

  • Targeted molecular trait stacking in cotton through targeted double-strand break induction.

    abstract::Recent developments of tools for targeted genome modification have led to new concepts in how multiple traits can be combined. Targeted genome modification is based on the use of nucleases with tailor-made specificities to introduce a DNA double-strand break (DSB) at specific target loci. A re-engineered meganuclease ...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12085

    authors: D'Halluin K,Vanderstraeten C,Van Hulle J,Rosolowska J,Van Den Brande I,Pennewaert A,D'Hont K,Bossut M,Jantz D,Ruiter R,Broadhvest J

    更新日期:2013-10-01 00:00:00

  • Trans-species synthetic gene design allows resistance pyramiding and broad-spectrum engineering of virus resistance in plants.

    abstract::To infect plants, viruses rely heavily on their host's machinery. Plant genetic resistances based on host factor modifications can be found among existing natural variability and are widely used for some but not all crops. While biotechnology can supply for the lack of natural resistance alleles, new strategies need t...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12896

    authors: Bastet A,Lederer B,Giovinazzo N,Arnoux X,German-Retana S,Reinbold C,Brault V,Garcia D,Djennane S,Gersch S,Lemaire O,Robaglia C,Gallois JL

    更新日期:2018-03-05 00:00:00

  • Characterization of scientific studies usually cited as evidence of adverse effects of GM food/feed.

    abstract::GM crops are the most studied crops in history. Approximately 5% of the safety studies on them show adverse effects that are a cause for concern and tend to be featured in media reports. Although these reports are based on just a handful of GM events, they are used to cast doubt on all GM crops. Furthermore, they tend...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1111/pbi.12798

    authors: Sánchez MA,Parrott WA

    更新日期:2017-10-01 00:00:00

  • Comparison of pathogen-induced expression and efficacy of two amphibian antimicrobial peptides, MsrA2 and temporin A, for engineering wide-spectrum disease resistance in tobacco.

    abstract::The rapid accumulation of defensive transgene products in plants only on pathogen invasion has clear advantages over their constitutive synthesis. In this study, two antimicrobial peptides from the skin secretions of frogs, MsrA2 (N-methionine-dermaseptin B1) and temporin A, were evaluated for engineering pathogen-ind...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2007.00277.x

    authors: Yevtushenko DP,Misra S

    更新日期:2007-11-01 00:00:00

  • RNAi trigger fragment truncation attenuates soybean FAD2-1 transcript suppression and yields intermediate oil phenotypes.

    abstract::Suppression of the microsomal ω6 oleate desaturase during the seed development of soybean (Glycine max) with the 420-bp soybean FAD2-1A intron as RNAi trigger shifts the conventional fatty acid composition of soybean oil from 20% oleic and 60% polyunsaturates to one containing greater than 80% oleic acid and less than...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2010.00573.x

    authors: Wagner N,Mroczka A,Roberts PD,Schreckengost W,Voelker T

    更新日期:2011-09-01 00:00:00

  • High level protein expression in plants through the use of a novel autonomously replicating geminivirus shuttle vector.

    abstract::We constructed a novel autonomously replicating gene expression shuttle vector, with the aim of developing a system for transiently expressing proteins at levels useful for commercial production of vaccines and other proteins in plants. The vector, pRIC, is based on the mild strain of the geminivirus Bean yellow dwarf...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2009.00462.x

    authors: Regnard GL,Halley-Stott RP,Tanzer FL,Hitzeroth II,Rybicki EP

    更新日期:2010-01-01 00:00:00

  • Constitutive expression of cell wall invertase genes increases grain yield and starch content in maize.

    abstract::Grain size, number and starch content are important determinants of grain yield and quality. One of the most important biological processes that determine these components is the carbon partitioning during the early grain filling, which requires the function of cell wall invertase. Here, we showed the constitutive exp...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12102

    authors: Li B,Liu H,Zhang Y,Kang T,Zhang L,Tong J,Xiao L,Zhang H

    更新日期:2013-12-01 00:00:00

  • ZmSTK1 and ZmSTK2, encoding receptor-like cytoplasmic kinase, are involved in maize pollen development with additive effect.

    abstract::Pollen germination and pollen tube growth are important physiological processes of sexual reproduction of plants and also are involved in signal transduction. Our previous study reveals that ZmSTK1 and ZmSTK2 are two receptor-like cytoplasmic kinases (RLCK) homologs in Zea mays as members of receptor-like protein kina...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12880

    authors: Fan M,Zhang C,Shi L,Liu C,Ma W,Chen M,Liu K,Cai F,Wang G,Wei Z,Jiang M,Liu Z,Javeed A,Lin F

    更新日期:2018-08-01 00:00:00

  • Expression of pigeonpea hybrid-proline-rich protein encoding gene (CcHyPRP) in yeast and Arabidopsis affords multiple abiotic stress tolerance.

    abstract::A hybrid-proline-rich protein encoding gene (CcHyPRP) has been isolated and characterized, for the first time, from the subtracted cDNA library of pigeonpea (Cajanus cajan L.) plants subjected to drought stress. Functionality of CcHyPRP has been validated for abiotic stress tolerance using the heterologous yeast and A...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2009.00467.x

    authors: Priyanka B,Sekhar K,Reddy VD,Rao KV

    更新日期:2010-01-01 00:00:00

  • Suspension-cultured BY-2 tobacco cells produce and mature immunologically active house dust mite allergens.

    abstract::The replacement of crude allergen extracts by selected allergens currently represents a major goal for the improvement of allergy diagnosis and immunotherapy. Indeed, the development of molecularly defined vaccines would facilitate both standardization and enhance batch-to-batch reproducibility as well as treatment sp...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/j.1467-7652.2006.00221.x

    authors: Lienard D,Tran Dinh O,van Oort E,Van Overtvelt L,Bonneau C,Wambre E,Bardor M,Cosette P,Didier-Laurent A,de Borne FD,Delon R,van Ree R,Moingeon P,Faye L,Gomord V

    更新日期:2007-01-01 00:00:00

  • QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea.

    abstract::Whole-genome sequencing-based bulked segregant analysis (BSA) for mapping quantitative trait loci (QTL) provides an efficient alternative approach to conventional QTL analysis as it significantly reduces the scale and cost of analysis with comparable power to QTL detection using full mapping population. We tested the ...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12964

    authors: Deokar A,Sagi M,Daba K,Tar'an B

    更新日期:2019-01-01 00:00:00

  • Improving nutritional quality and fungal tolerance in soya bean and grass pea by expressing an oxalate decarboxylase.

    abstract::Soya bean (Glycine max) and grass pea (Lathyrus sativus) seeds are important sources of dietary proteins; however, they also contain antinutritional metabolite oxalic acid (OA). Excess dietary intake of OA leads to nephrolithiasis due to the formation of calcium oxalate crystals in kidneys. Besides, OA is also a known...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12503

    authors: Kumar V,Chattopadhyay A,Ghosh S,Irfan M,Chakraborty N,Chakraborty S,Datta A

    更新日期:2016-06-01 00:00:00

  • RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat.

    abstract::The identification of genetic markers linked to genes of agronomic importance is a major aim of crop research and breeding programmes. Here, we identify markers for Yr15, a major disease resistance gene for wheat yellow rust, using a segregating F2 population. After phenotyping, we implemented RNA sequencing (RNA-Seq)...

    journal_title:Plant biotechnology journal

    pub_type: 杂志文章

    doi:10.1111/pbi.12281

    authors: Ramirez-Gonzalez RH,Segovia V,Bird N,Fenwick P,Holdgate S,Berry S,Jack P,Caccamo M,Uauy C

    更新日期:2015-06-01 00:00:00