Cereal Genomics: Methods and Protocols

  title={Cereal Genomics: Methods and Protocols},
  author={Robert James Henry and Agnelo Furtado},
  journal={Cereal Genomics},
1. Dna Extraction from Vegetative Tissue for Next Generation Sequencing Agnelo Furtado 2. DNA Extraction from Rice Endosperm (Including a Protocol for Extraction of DNA from Ancient Seed Samples) Chiaki Mutou, Katsunori Tanaka, Ryuji Ishikawa 3. RNA Extraction from Cereal Vegetative Tissue Julie A. Pattemore 4. RNA Extraction from Developing or Mature Wheat Seeds Agnelo Furtado 5. cDNA Library Preparation Maarten Kooiker and Gang-Ping Xue 6. Preparation of High Molecular Weight gDNA and… Expand
10 Citations
Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species
This protocol describes simple modifications to the established CTAB- based extraction method that allows for reliable isolation of high molecular weight genomic DNA from difficult to isolate plant species Corymbia and Coffea. Expand
A modular cloning toolkit for genome editing in plants
An expanded cloning toolkit that contains modules encoding a variety of CRISPR/Cas-based nucleases and their corresponding guide RNA backbones and a set of modules that enable quick and facile assembly of tRNA-sgRNA polycistronic units without a PCR step involved is presented. Expand
Acceleration of the Breeding Program for Winter Wheat
Two approaches that can help plant breeders hasten cultivar development for winter wheat are described, which show the potential to reduce the development of cultivars using six generations of backcrossing with gene introgression by 2 years. Expand
Characterisation of an antimicrobial and phytotoxic ribonuclease secreted by the fungal wheat pathogen Zymoseptoria tritici
The expression pattern of Zt6 and potent toxicity towards microorganisms suggests that whilst it may contribute to the execution of wheat cell death, it is also likely to have an important secondary function in antimicrobial competition and niche protection. Expand
Gene transfer to plants by electroporation: methods and applications
In modern biotechnology, numerical methods have been used in electrotransformation, electroporation-based inactivation, electroextraction, and electroporative biomass drying, where numerical models to iteratively optimize the field homogeneity considering the cell size, shape, number, and electrode positions supplemented by real-time measurements. Expand
The wheat Sr22, Sr33, Sr35 and Sr45 genes confer resistance against stem rust in barley
Assessment of the functionality, in barley, of cloned wheat Sr genes effective against Ug99 found all four genes were found to confer effective stem rust resistance and are therefore a potential source of resistance against wheat stem rust in barley. Expand
Calmodulin HvCaM1 Negatively Regulates Salt Tolerance via Modulation of HvHKT1s and HvCAMTA41[OPEN]
It is proposed that HvCaM1 is involved in regulating Na+ transport, probably via certain class I high-affinity potassium transporter (HvHKT1;5 and HvHK T1;1)-mediated Na+ translocation in roots, which may be a critical factor in the regulation of HKT1s in barley. Expand
Influence of Gene Expression on Hardness in Wheat
The identification of wheat genotypes with hard grain texture and wild-type/soft Pin alleles indicating that hardness in wheat may be controlled by factors other than mutations in the coding region of the Pin genes is reported. Expand
Genomics of Food Grains
Functional genomics and association genetics link genome sequence data to grain-quality attributes to study the study and utilization of grain foods. Expand
Transgene expression and plant regeneration in the Brassicaceae Aethionema arabicum
Transformation, der Einbau zusatzlicher DNA Abschnitte, ist eines der wichtigsten Werkzeuge in der modernen Molekularbiologie and Genetik, um Pflanzengenome modifizieren und folglich die Funktion undExpand


Transcription Activator-Like Effector Nucleases Enable Efficient Plant Genome Engineering1[W][OA]
The optimized reagents implemented in plant protoplasts should be useful for targeted modification of cells from diverse plant species and using a variety of means for reagent delivery. Expand
DNA-Free Genetically Edited Grapevine and Apple Protoplast Using CRISPR/Cas9 Ribonucleoproteins
It is demonstrated that direct delivery of purified CRISPR/Cas9 RNPs to the protoplast system enables targeted gene editing and paves the way to the generation of DNA-free genome edited grapevine and apple plants. Expand
Genetic transformation of wheat: current status and future prospects
The objective of this review is to summarize current successful techniques for wheat transformation and stimulate further research into long-term wheat improvement by genetic engineering approaches. Expand
Analysis of the bread wheat genome using whole genome shotgun sequencing
It is shown that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Expand
A highly efficient rice green tissue protoplast system for transient gene expression and studying light/chloroplast-related processes
A simplified and highly efficient transient gene expression system using photosynthetically active rice green tissue protoplasts and its broad applications in protein immunoblot, localization and protein-protein interaction assays are shown. Expand
The Palomero Genome Suggests Metal Effects on Domestication
The results indicate that environmental changes were important selective forces acting on maize domestication and the availability of the maize genome will help to guide future agricultural and biofuel applications. Expand
The Sorghum bicolor genome and the diversification of grasses
An initial analysis of the ∼730-megabase Sorghum bicolor (L.) Moench genome is presented, placing ∼98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Expand
Co-transformed, diploid Lolium perenne (perennial ryegrass), Lolium multiflorum (Italian ryegrass) and Lolium temulentum (darnel) plants produced by microprojectile bombardment
The transgenic nature of the plants was demonstrated by Southern hybridisation analysis, which showed that the non-selected (GUS) gene was generally present at a higher copy number than the selected (HYG) gene. Expand
Analysis of gene expression in transgenic plants.
This chapter focuses on RNA-based techniques for the analysis of transgene expression, beginning with the extraction of RNA and its evaluation in terms of purity and integrity by spectrophotometry and gel electrophoresis, respectively. Expand
The B73 Maize Genome: Complexity, Diversity, and Dynamics
The sequence of the maize genome reveals it to be the most complex genome known to date and the correlation of methylation-poor regions with Mu transposon insertions and recombination and how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state is reported. Expand