Industry Workshop #6905
Date: Tuesday, January 14, 2020
Time: 1:30 PM - 3:40 PM
Location: Town & Country, Pacific Salon 1
Registration: see form below
New England Biolabs: Enabling transformative crop science through innovative molecular biology
During this workshop, we will discuss the application of cutting-edge molecular biology solutions to address real-world issues that scientists worldwide are tackling. As an innovative supplier of premier quality enzymes and molecular biology reagents, New England Biolabs has developed products that present tractable solutions towards the understanding of molecular mechanisms that drive improved crop production efficiency and elucidation of pathogen resistance.
A highly multiplexed, targeted NGS approach for high-throughput and cost-effective genotyping
Sarah Bowman, Ph.D., Head of Research, Directed Genomics
Targeted DNA sequencing is rapidly being adopted for the molecular screening of markers during selective crop breeding. For these applications, there exists a need for a cost-effective and high-throughput technology to process large numbers of samples. Here we describe a novel capture-by-hybridization method for targeted genotyping of crops. Pre-capture multiplexing of up to 96 samples combined with dual indexed sequencing allows over 3.8 million genotypes in a single Illumina sequencing run.
Automation of NEBNext Direct Genotyping Solution on the Biomek® i7 automated workstation
Bjoern Textor, Ph.D. Sr. Application Specialist, NEB GmbH
Genotyping for molecular breeding applications requires solutions that can support robust processes in order to implement at scale. The NEBNext Direct Genotyping Solution has intrinsic features facilitating high-throughput sample processing including pre-capture barcoding, pooling of up to 96 samples per capture, and dual barcoding, which allows up to 9,216 samples to be run in parallel on Illumina sequencers. In order to address the need for robust, automated processing, we have collaborated with Beckman Coulter and The European Molecular Biology Laboratory (EMBL) to develop an automated protocol for the NEBNext Direct Genotyping Solution. The utilization of the Biomek i7 instrument’s two pipetting heads and accessories for on-deck incubation and PCR, facilitates high-throughput parallel processing. The protocol can process 384 samples per run without the need for user intervention. Here we will present details and results of implementation of the technology on the Biomek i7 Automated Workstation in order to address the throughput demands of marker-assisted breeding applications.
Evaluation of the NEBNext Direct Genotyping Solution for molecular breeding of ornamentals
Bart Brugmans, Ph.D., R&D Program Manager, GenNovation B.V.
Ornamental plants present unique challenges in genomics due to the variability that is inherent across species. Genome sizes ranging between 1-40Gb can result in high costs associated with performing whole genome sequencing across many samples. Secondly the ploidy level that ranges from 2n to 8n requires obtaining reliable doses of the different alleles necessary for genetic analysis. Finally, the high level of heterogeneity in variants, including large indels, challenges the ability to target all alleles at a given locus. Elucidation of the genetics of a given species requires a technology that can provide the dose information of selected SNP, while also providing additional information about alternative haplotypes flanking the selected SNPs. In this pilot, we tested 100 SNPs in two different crops, providing the information necessary to assess applicability of NEBNext Direct Genotyping Solution technology as a solution for these challenges.
Enhancing transcript detection across species: Removing abundant RNAs from plants and other species of interest.
Deyra Rodriguez, Ph.D. Development Scientist, New England Biolabs
The large dynamic range of transcript expression within total RNA presents a challenge to whole-transcriptome sequencing. Highly expressed transcripts with minimal biological interest can dominate readouts, masking detection of more informative lower abundance transcripts. NEBNext offers a suite of solutions to remove abundant transcripts and enhance transcript detection in RNA-seq experiments. We will introduce our new solution for the removal of rRNA from flowering plants, as well as a customizable approach for depleting selective RNAs from total RNA of any species of interest.
NEBNext® Ultra™ II FS DNA: a robust, DNA library preparation method compatible with plant samples
Karen McKay, Development Associate, New England Biolabs
The NEBNext Ultra II FS DNA Library Preparation Kit is a fast and reliable solution for DNA fragmentation and library construction. This method integrates a unique enzymatic fragmentation reagent and optimized library conversion method to streamline library construction by reducing the sample preparation bottleneck associated with mechanical shearing and sample transfer. We have applied this robust workflow to generate high quality sequencing data from a wide range of input amounts and sample types, including a variety of plant sources.
Please fill out the form below to register for the workshop. Refreshments and snacks will be provided.
Please also visit us at Booth #330.