WheatCRISPR: a web-based guide RNA design tool for CRISPR/Cas9-mediated genome editing in wheat.

Abstract:

BACKGROUND:CRISPR/Cas9 gene editing has become a revolutionary technique for crop improvement as it can facilitate fast and efficient genetic changes without the retention of transgene components in the final plant line. Lack of robust bioinformatics tools to facilitate the design of highly specific functional guide RNAs (gRNAs) and prediction of off-target sites in wheat is currently an obstacle to effective application of CRISPR technology to wheat improvement. DESCRIPTION:We have developed a web-based bioinformatics tool to design specific gRNAs for genome editing and transcriptional regulation of gene expression in wheat. A collaborative study between the Broad Institute and Microsoft Research used large-scale empirical evidence to devise algorithms (Doech et al., 2016, Nature Biotechnology 34, 184-191) for predicting the on-target activity and off-target potential of CRISPR/SpCas9 (Streptococcus pyogenes Cas9). We applied these prediction models to determine on-target specificity and potential off-target activity for individual gRNAs targeting specific loci in the wheat genome. The genome-wide gRNA mappings and the corresponding Doench scores predictive of the on-target and off-target activities were used to create a gRNA database which was used as a data source for the web application termed WheatCRISPR. CONCLUSION:The WheatCRISPR tool allows researchers to browse all possible gRNAs targeting a gene or sequence of interest and select effective gRNAs based on their predicted high on-target and low off-target activity scores, as well as other characteristics such as position within the targeted gene. It is publicly available at https://crispr.bioinfo.nrc.ca/WheatCrispr/ .

journal_name

BMC Plant Biol

journal_title

BMC plant biology

authors

Cram D,Kulkarni M,Buchwaldt M,Rajagopalan N,Bhowmik P,Rozwadowski K,Parkin IAP,Sharpe AG,Kagale S

doi

10.1186/s12870-019-2097-z

subject

Has Abstract

pub_date

2019-11-06 00:00:00

pages

474

issue

1

issn

1471-2229

pii

10.1186/s12870-019-2097-z

journal_volume

19

pub_type

杂志文章
  • Identification of salt gland-associated genes and characterization of a dehydrin from the salt secretor mangrove Avicennia officinalis.

    abstract:BACKGROUND:Salt stress is a major challenge for growth and development of plants. The mangrove tree Avicennia officinalis has evolved salt tolerance mechanisms such as salt secretion through specialized glands on its leaves. Although a number of structural studies on salt glands have been done, the molecular mechanism ...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-014-0291-6

    authors: Jyothi-Prakash PA,Mohanty B,Wijaya E,Lim TM,Lin Q,Loh CS,Kumar PP

    更新日期:2014-11-18 00:00:00

  • Rapid identification and characterization of genetic loci for defective kernel in bread wheat.

    abstract:BACKGROUND:Wheat is a momentous crop and feeds billions of people in the world. The improvement of wheat yield is very important to ensure world food security. Normal development of grain is the essential guarantee for wheat yield formation. The genetic study of grain phenotype and identification of key genes for grain...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-019-2102-6

    authors: Fu C,Du J,Tian X,He Z,Fu L,Wang Y,Xu D,Xu X,Xia X,Zhang Y,Cao S

    更新日期:2019-11-08 00:00:00

  • Comparative transcriptome analyses of fruit development among pears, peaches, and strawberries provide new insights into single sigmoid patterns.

    abstract:BACKGROUND:Pear fruit exhibit a single sigmoid pattern during development, while peach and strawberry fruits exhibit a double sigmoid pattern. However, little is known about the differences between these two patterns. RESULTS:In this study, fruit weights were measured and paraffin sections were made from fruitlet to m...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-020-2317-6

    authors: Pei MS,Cao SH,Wu L,Wang GM,Xie ZH,Gu C,Zhang SL

    更新日期:2020-03-06 00:00:00

  • GmFLD, a soybean homolog of the autonomous pathway gene FLOWERING LOCUS D, promotes flowering in Arabidopsis thaliana.

    abstract:BACKGROUND:Flowering at an appropriate time is crucial for seed maturity and reproductive success in all flowering plants. Soybean (Glycine max) is a typical short day plant, and both photoperiod and autonomous pathway genes exist in soybean genome. However, little is known about the functions of soybean autonomous pat...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-014-0263-x

    authors: Hu Q,Jin Y,Shi H,Yang W

    更新日期:2014-10-07 00:00:00

  • High-throughput genotyping of wheat-barley amphiploids utilising diversity array technology (DArT).

    abstract:BACKGROUND:Hordeum chilense, a native South American diploid wild barley, is one of the species of the genus Hordeum with a high potential for cereal breeding purposes, given its high crossability with other members of the Triticeae tribe. Hexaploid tritordeum (×Tritordeum Ascherson et Graebner, 2n=6×=42, AABBH(ch)H(ch...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-13-87

    authors: Castillo A,Ramírez MC,Martín AC,Kilian A,Martín A,Atienza SG

    更新日期:2013-06-03 00:00:00

  • Validation of reference genes for quantitative real-time PCR during leaf and flower development in Petunia hybrida.

    abstract:BACKGROUND:Identification of genes with invariant levels of gene expression is a prerequisite for validating transcriptomic changes accompanying development. Ideally expression of these genes should be independent of the morphogenetic process or environmental condition tested as well as the methods used for RNA purific...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-10-4

    authors: Mallona I,Lischewski S,Weiss J,Hause B,Egea-Cortines M

    更新日期:2010-01-07 00:00:00

  • Transcript profiling for early stages during embryo development in Scots pine.

    abstract:BACKGROUND:Characterization of the expression and function of genes regulating embryo development in conifers is interesting from an evolutionary point of view. However, our knowledge about the regulation of embryo development in conifers is limited. During early embryo development in Pinus species the proembyo goes th...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-016-0939-5

    authors: Merino I,Abrahamsson M,Sterck L,Craven-Bartle B,Canovas F,von Arnold S

    更新日期:2016-11-18 00:00:00

  • Characterization of a putative grapevine Zn transporter, VvZIP3, suggests its involvement in early reproductive development in Vitis vinifera L.

    abstract:BACKGROUND:Zinc (Zn) deficiency is one of the most widespread mineral nutritional problems that affect normal development in plants. Because Zn cannot passively diffuse across cell membranes, it must be transported into intracellular compartments for all biological processes where Zn is required. Several members of the...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-12-111

    authors: Gainza-Cortés F,Pérez-Dïaz R,Pérez-Castro R,Tapia J,Casaretto JA,González S,Peña-Cortés H,Ruiz-Lara S,González E

    更新日期:2012-07-23 00:00:00

  • Conservation of ciliary proteins in plants with no cilia.

    abstract:BACKGROUND:Eukaryotic cilia are complex, highly conserved microtubule-based organelles with a broad phylogenetic distribution. Cilia were present in the last eukaryotic common ancestor and many proteins involved in cilia function have been conserved through eukaryotic diversification. However, cilia have also been lost...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-11-185

    authors: Hodges ME,Wickstead B,Gull K,Langdale JA

    更新日期:2011-12-30 00:00:00

  • Cytological evidence of BSD2 functioning in both chloroplast division and dimorphic chloroplast formation in maize leaves.

    abstract:BACKGROUND:Maize bsd2 (bundle sheath defective2) is a classical C4 mutant with defective C4 photosynthesis, accompanied with reduced accumulation of Rubisco (ribulose bisphosphate carboxylase oxygenase) and aberrant mature chloroplast morphology in the bundle sheath (BS) cells. However, as a hypothetical chloroplast ch...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-019-2219-7

    authors: Li H,Bai M,Jiang X,Shen R,Wang H,Wang H,Wu H

    更新日期:2020-01-09 00:00:00

  • Genome-wide exploration and characterization of miR172/euAP2 genes in Brassica napus L. for likely role in flower organ development.

    abstract:BACKGROUND:APETALA2-like genes encode plant-specific transcription factors, some of which possess one microRNA172 (miR172) binding site. The miR172 and its target euAP2 genes are involved in the process of phase transformation and flower organ development in many plants. However, the roles of miR172 and its target AP2 ...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-019-1936-2

    authors: Wang T,Ping X,Cao Y,Jian H,Gao Y,Wang J,Tan Y,Xu X,Lu K,Li J,Liu L

    更新日期:2019-08-01 00:00:00

  • MicroRNA profiling analysis of developing berries for 'Kyoho' and its early-ripening mutant during berry ripening.

    abstract:BACKGROUND:'Fengzao' is an early-ripening bud mutant of 'Kyoho', which matures nearly 30 days earlier than 'Kyoho'. To gain a better understanding of the regulatory role of miRNAs in early-ripening of grape berry, high-throughput sequencing approach and quantitative RT-PCR validation were employed to identify miRNAs at...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-018-1516-x

    authors: Guo DL,Li Q,Lv WQ,Zhang GH,Yu YH

    更新日期:2018-11-16 00:00:00

  • Drought stress in maize causes differential acclimation responses of glutathione and sulfur metabolism in leaves and roots.

    abstract:BACKGROUND:Drought is the most important environmental stress that limits crop yield in a global warming world. Despite the compelling evidence of an important role of oxidized and reduced sulfur-containing compounds during the response of plants to drought stress (e.g. sulfate for stomata closure or glutathione for sc...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-016-0940-z

    authors: Ahmad N,Malagoli M,Wirtz M,Hell R

    更新日期:2016-11-09 00:00:00

  • Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.).

    abstract:BACKGROUND:Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in South Asia and Sub-Saharan Africa. In order to harness the untapped genetic potential available for chickpea improvement, we re-sequenced 35 chickpea genotypes representing parental lines of 16 mapp...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-015-0690-3

    authors: Thudi M,Khan AW,Kumar V,Gaur PM,Katta K,Garg V,Roorkiwal M,Samineni S,Varshney RK

    更新日期:2016-01-27 00:00:00

  • The study of a barley epigenetic regulator, HvDME, in seed development and under drought.

    abstract:BACKGROUND:Epigenetic factors such as DNA methylation and histone modifications regulate a wide range of processes in plant development. Cytosine methylation and demethylation exist in a dynamic balance and have been associated with gene silencing or activation, respectively. In Arabidopsis, cytosine demethylation is a...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-13-172

    authors: Kapazoglou A,Drosou V,Argiriou A,Tsaftaris AS

    更新日期:2013-10-31 00:00:00

  • Disruption of actin filaments induces mitochondrial Ca2+ release to the cytoplasm and [Ca2+]c changes in Arabidopsis root hairs.

    abstract:BACKGROUND:Mitochondria are dynamic organelles that move along actin filaments, and serve as calcium stores in plant cells. The positioning and dynamics of mitochondria depend on membrane-cytoskeleton interactions, but it is not clear whether microfilament cytoskeleton has a direct effect on mitochondrial function and ...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-10-53

    authors: Wang Y,Zhu Y,Ling Y,Zhang H,Liu P,Baluska F,Samaj J,Lin J,Wang Q

    更新日期:2010-03-24 00:00:00

  • Constraints to virus infection in Nicotiana benthamiana plants transformed with a potyvirus amplicon.

    abstract:BACKGROUND:Plant genomes have been transformed with full-length cDNA copies of viral genomes, giving rise to what has been called 'amplicon' systems, trying to combine the genetic stability of transgenic plants with the elevated replication rate of plant viruses. However, amplicons' performance has been very variable r...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-10-139

    authors: Calvo M,Dujovny G,Lucini C,Ortuño J,Alamillo JM,Simón-Mateo C,López-Moya JJ,García JA

    更新日期:2010-07-06 00:00:00

  • Molecular distinction amongst varieties of mulberry using RAPD and DAMD profiles.

    abstract:BACKGROUND:Mulberry trees are the most important host for rearing mulberry silkworms in sericulture. Improved varieties of mulberry tree have been developed through traditional breeding procedures. Not much work, however, has been carried out on the molecular characterization of these varieties. Random Amplified Polymo...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-1-3

    authors: Bhattacharya E,Ranade SA

    更新日期:2001-01-01 00:00:00

  • Meiotic abnormalities affect genetic constitution and pollen viability in dicots from Indian cold deserts.

    abstract:BACKGROUND:Meiotic abnormalities lead to morphological and genetic variations which caused not only to evolution but also intraspecific reproductive barriers. During present study of detailed meiotic course in dicotyledonous plants sampled from Indian cold deserts, various meiotic abnormalities have been detected. For ...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-018-1596-7

    authors: Kaur D,Singhal VK

    更新日期:2019-01-07 00:00:00

  • Comparative phosphoproteomic analysis of blast resistant and susceptible rice cultivars in response to salicylic acid.

    abstract:BACKGROUND:Salicylic acid (SA) is a significant signaling molecule that induces rice resistance against pathogen invasion. Protein phosphorylation carries out an important regulatory function in plant defense responses, while the global phosphoproteome changes in rice response to SA-mediated defense response has not be...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-019-2075-5

    authors: Sun R,Qin S,Zhang T,Wang Z,Li H,Li Y,Nie Y

    更新日期:2019-10-28 00:00:00

  • Identification and comprehensive analyses of the CBL and CIPK gene families in wheat (Triticum aestivum L.).

    abstract:BACKGROUND:Calcineurin B-like (CBL) proteins belong to a unique group of calcium sensors in plant that decode the Ca(2+) signature by interacting with CBL-interacting protein kinases (CIPKs). Although CBL-CIPK complexes have been shown to play important roles in the responses to various stresses in plants, little is kn...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-015-0657-4

    authors: Sun T,Wang Y,Wang M,Li T,Zhou Y,Wang X,Wei S,He G,Yang G

    更新日期:2015-11-04 00:00:00

  • Flowering in Persian walnut: patterns of gene expression during flower development.

    abstract:BACKGROUND:Flower development and sufficient fruit set are important parameters with respect to walnut yield. Knowledge about flowering genes of fruit trees can help to conduct better molecular breeding programs. Therefore, this study was carried out to investigate the expression pattern of some flowering genes (FT, SO...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-020-02372-w

    authors: Hassankhah A,Rahemi M,Ramshini H,Sarikhani S,Vahdati K

    更新日期:2020-04-03 00:00:00

  • Transcriptome analysis provides new insights into the transcriptional regulation of methyl jasmonate-induced flavonoid biosynthesis in pear calli.

    abstract:BACKGROUND:Flavonoid biosynthesis is strongly influenced by phytohormones. For example, methyl jasmonate (MeJA) enhances the flavonoid accumulation in pear. However, the molecular mechanism underlying the MeJA-induced flavonoid biosynthesis in pear is largely uncharacterized. Therefore, the transcriptome of pear calli ...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-020-02606-x

    authors: Premathilake AT,Ni J,Shen J,Bai S,Teng Y

    更新日期:2020-08-25 00:00:00

  • Functional analysis of the SlERF01 gene in disease resistance to S. lycopersici.

    abstract:BACKGROUND:Tomato gray leaf spot caused by Stemphylium lycopersici (S. lycopersici) is a serious disease that can severely hinder tomato production. To date, only Sm has been reported to provide resistance against this disease, and the molecular mechanism underlying resistance to this disease in tomato remains unclear....

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-020-02588-w

    authors: Yang H,Shen F,Wang H,Zhao T,Zhang H,Jiang J,Xu X,Li J

    更新日期:2020-08-15 00:00:00

  • Timing of shoot development transitions affects degree of perenniality in Arabidopsis lyrata (Brassicaceae).

    abstract:BACKGROUND:Perenniality is best understood in quantitative terms, involving the relationship between production vs. turnover of meristems, biomass, or energy reserves. Previous quantitative trait locus (QTL) studies using divergent populations of the perennial rock cress Arabidopsis lyrata have shown that trade-offs in...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-015-0606-2

    authors: Remington DL,Figueroa J,Rane M

    更新日期:2015-09-17 00:00:00

  • Identification of plant leaf phosphorus content at different growth stages based on hyperspectral reflectance.

    abstract:BACKGROUND:Modern agriculture strives to sustainably manage fertilizer for both economic and environmental reasons. The monitoring of any nutritional (phosphorus, nitrogen, potassium) deficiency in growing plants is a challenge for precision farming technology. A study was carried out on three species of popular crops,...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-020-02807-4

    authors: Siedliska A,Baranowski P,Pastuszka-Woźniak J,Zubik M,Krzyszczak J

    更新日期:2021-01-07 00:00:00

  • Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes.

    abstract:BACKGROUND:Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies h...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-020-02616-9

    authors: Duarte-Delgado D,Dadshani S,Schoof H,Oyiga BC,Schneider M,Mathew B,Léon J,Ballvora A

    更新日期:2020-09-16 00:00:00

  • Quantitative evaluation of protocorm growth and fungal colonization in Bletilla striata (Orchidaceae) reveals less-productive symbiosis with a non-native symbiotic fungus.

    abstract:BACKGROUND:In nature, orchid plants depend completely on symbiotic fungi for their nutrition at the germination and the subsequent seedling (protocorm) stages. However, only limited quantitative methods for evaluating the orchid-fungus interactions at the protocorm stage are currently available, which greatly constrain...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/s12870-017-1002-x

    authors: Yamamoto T,Miura C,Fuji M,Nagata S,Otani Y,Yagame T,Yamato M,Kaminaka H

    更新日期:2017-02-21 00:00:00

  • EST-derived SSR markers used as anchor loci for the construction of a consensus linkage map in ryegrass (Lolium spp.).

    abstract:BACKGROUND:Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-10-177

    authors: Studer B,Kölliker R,Muylle H,Asp T,Frei U,Roldán-Ruiz I,Barre P,Tomaszewski C,Meally H,Barth S,Skøt L,Armstead IP,Dolstra O,Lübberstedt T

    更新日期:2010-08-16 00:00:00

  • The HaDREB2 transcription factor enhances basal thermotolerance and longevity of seeds through functional interaction with HaHSFA9.

    abstract:BACKGROUND:Transcription factor HaDREB2 was identified in sunflower (Helianthus annuus L.) as a drought-responsive element-binding factor 2 (DREB2) with unique properties. HaDREB2 and the sunflower Heat Shock Factor A9 (HaHSFA9) co-activated the Hahsp17.6G1 promoter in sunflower embryos. Both factors could be involved ...

    journal_title:BMC plant biology

    pub_type: 杂志文章

    doi:10.1186/1471-2229-9-75

    authors: Almoguera C,Prieto-Dapena P,Díaz-Martín J,Espinosa JM,Carranco R,Jordano J

    更新日期:2009-06-19 00:00:00