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    Protocols in Current Issue
    Construction of a Single Transcriptional Unit for Expression of Cas9 and Single-guide RNAs for Genome Editing in Plants
    Authors:  Xu Tang, Zhaohui Zhong, Xuelian Zheng and Yong Zhang, date: 09/05/2017, view: 5626, Q&A: 0
    [Abstract] The CRISPR (clustered regularly interspaced short palindromic repeats)-associated protein9 (Cas9) is a simple and efficient tool for genome editing in many organisms including plant and crop species. The sgRNAs of the CRISPR/Cas9 system are typically expressed from RNA polymerase III promoters, such as U6 and U3. In many transformation events, ...
    Experimental Pipeline for SNP and SSR Discovery and Genotyping Analysis of Mango (Mangifera indica L.)
    [Abstract] Establishing a reservoir of polymorphic markers is an important key for marker-assisted breeding. Many crops are still lack of such genomic infrastructure. Single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) are useful as markers because they are widespread over the genome and many technologies were developed for high ...
    EST-SSR Analysis and Cross-species Transferability Study in Lavandula
    Authors:  Ayelign M. Adal, Zerihun A. Demissie and Soheil S. Mahmoud, date: 08/05/2016, view: 4961, Q&A: 0
    [Abstract] The genus Lavandula comprises of several economically important lavender species that are mainly cultivated worldwide for essential oil production. Identification of lavender species and their cultivars has been a huge bottleneck in lavender industries due to lack of appropriate identification mechanisms. Recent advances in ...
    Chromosome Dosage Analysis in Plants Using Whole Genome Sequencing
    Authors:  Ek Han Tan, Luca Comai and Isabelle M. Henry, date: 07/05/2016, view: 5947, Q&A: 0
    [Abstract] Relative chromosome dosage, i.e., increases or decreases in the number of copies of specific chromosome regions in one sample versus another, can be determined using aligned read-counts from Illumina sequencing (Henry et al., 2010). The following protocol was used to identify the different classes of aneuploids that ...
    Identification of Natural Hybrids by SSR Markers in Mussaenda
    Authors:  Zhonglai Luo, Tingting Duan, Shuai Yuan, Shi Chen, Xiufeng Bai and Dianxiang Zhang, date: 07/05/2016, view: 4861, Q&A: 0
    [Abstract] Detection of natural hybrids is of great significance for plant taxonomy, reproductive biology, and population genetic studies. Compared with methods depending on morphological characters, molecular markers provide reliable and much more accurate results. This protocol describes approaches employing microsatellite (SSR) markers to identify ...
    Telomere-mediated Chromosomal Truncation via Agrobacterium tumefaciens or Particle Bombardment to Produce Engineered Minichromosomes in Plants
    [Abstract] Minichromosomes are small, autonomously functioning chromosomes that exist separately from the normal chromosomal set. Creation of minichromosomes in plants relies on telomere truncation to remove the chromosome arms and the native telomere sequence and replace them with a transgene together with a new telomere sequence to generate a modifiable ...
    Whole Genome Bisulfite Sequencing and DNA Methylation Analysis from Plant Tissue
    Authors:  Daniela Pignatta, George W. Bell and Mary Gehring, date: 02/20/2015, view: 12410, Q&A: 0
    [Abstract] This protocol describes whole genome bisulfite-sequencing library preparation from plant tissue and subsequent data analysis. Allele-specific methylation analysis and genome-wide identification of differentially methylated regions are additional features of the analysis procedure.
    DNA Fragmentation Analysis
    Authors:  Kei-ichiro Mishiba, Yukihiro Nagashima, Noriko Hayashi and Nozomu Koizumi, date: 08/05/2014, view: 10482, Q&A: 0
    [Abstract] DNA fragmentation with length corresponding to multiple integer of approximately 180 base pairs is a distinct feature of apoptosis in animals and programmed cell death in plants. This feature can simply be detected by DNA gel electrophoresis followed by ethidium bromide staining, although in some cases it is difficult to distinguish the DNA ...
    Plant Sequence Capture Optimised for Illumina Sequencing
    Authors:  Axel Himmelbach, Manuela Knauft and Nils Stein, date: 07/05/2014, view: 9791, Q&A: 0
    [Abstract] Plant Sequence Capture is used for targeted resequencing of whole exomes (all exons of a genome) of complex genomes e.g. barley and its relatives (Mascher et al., 2013). Sequencing and computing costs are significantly reduced since only the greatly enriched and gene-coding part of the barley genome is targeted, that corresponds ...



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