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 Bioljournal_title
BMC plant biologyauthors
Cram D,Kulkarni M,Buchwaldt M,Rajagopalan N,Bhowmik P,Rozwadowski K,Parkin IAP,Sharpe AG,Kagale Sdoi
10.1186/s12870-019-2097-zsubject
Has Abstractpub_date
2019-11-06 00:00:00pages
474issue
1issn
1471-2229pii
10.1186/s12870-019-2097-zjournal_volume
19pub_type
杂志文章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
更新日期:2014-11-18 00:00:00
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
更新日期:2019-11-08 00:00:00
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
更新日期:2020-03-06 00:00:00
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
更新日期:2014-10-07 00:00:00
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
更新日期:2013-06-03 00:00:00
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
更新日期:2010-01-07 00:00:00
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
更新日期:2016-11-18 00:00:00
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
更新日期:2012-07-23 00:00:00
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
更新日期:2011-12-30 00:00:00
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
更新日期:2020-01-09 00:00:00
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
更新日期:2019-08-01 00:00:00
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
更新日期:2018-11-16 00:00:00
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
更新日期:2016-11-09 00:00:00
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
更新日期:2016-01-27 00:00:00
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journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-13-172
更新日期:2013-10-31 00:00:00
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
更新日期:2010-03-24 00:00:00
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
更新日期:2010-07-06 00:00:00
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
更新日期:2001-01-01 00:00:00
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
更新日期:2019-01-07 00:00:00
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journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-019-2075-5
更新日期:2019-10-28 00:00:00
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
更新日期:2015-11-04 00:00:00
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journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-020-02372-w
更新日期:2020-04-03 00:00:00
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journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-020-02606-x
更新日期:2020-08-25 00:00:00
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journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-020-02588-w
更新日期:2020-08-15 00:00:00
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
更新日期:2015-09-17 00:00:00
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
更新日期:2021-01-07 00:00:00
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
更新日期:2020-09-16 00:00:00
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journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-017-1002-x
更新日期:2017-02-21 00:00:00
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journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-10-177
更新日期:2010-08-16 00:00:00
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
更新日期:2009-06-19 00:00:00