Location: Palm 1-2

Date: Monday, January 10, 12:50 p.m.

Speakers:

Jacob Enk, PhD (Daicel Arbor Biosciences) – 12:55 p.m. PT – Introduction to Renseq from Daicel Arbor Biosciences
Sanu Arora, PhD (John Innes Centre) – 1:15 p.m. PT – Understanding the Genetic Basis of Disease Resistance in Peas
Ingo Hein, PhD (James Hutton Institute) – 1:35 p.m. PT
Tim Hewitt, PhD (CSIRO) – 1:55 p.m. PT – Target Acquired: Using Renseq on Knockout Mutants to Rapidly Clone R Genes in Wheat

The resistance gene enrichment sequencing (RenSeq) workflow supports the comprehensive study of highly complex disease resistance gene (R-gene) families within crop plant genomes. Over the last few years, RenSeq and related NGS approaches have been utilized in or contributed to hundreds of studies across a wide range of plant species. In this workshop, we will highlight the major principles, benefits, and recent advances of RenSeq, and hear from several leading researchers who are actively utilizing it and related NGS techniques in their crop research programs, facilitated by myBaits® Custom hybridization capture kits. 

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Number PE0340

Authors: Junli Zhang, German Burguener, Juan Debernardi, Frederic Choulet, Etienne Paux, Jacob Enk, Jorge Dubcovsky

As genome resources for wheat expand at a rapid pace, it is important to update targeted sequencing tools to incorporate improved sequence assemblies and regions of previously unknown significance. Here we present a regulatory region NGS hybridization capture panel developed for hexaploid and tetraploid wheat. We used the upstream ~2 kbp of each annotated gene in the most up-to-date Chinese Spring wheat genome assembly as the primary target source, supplemented with homologous sequences from a draft assembly of tetraploid Kronos wheat as well as regions of observed open chromatin state identified with ATACseq. To improve specificity compared to similar legacy designs, candidate repetitive sequences were aggressively filtered using a combination of cross-alignment clustering, TREP19 affinity filtration, and kmer frequency capping. Once converted to candidate probes, these were once again filtered for specificity using a standard design pipeline, resulting in a final target space of ~175 Mbp relative to the IWGSC RefSeq v1.0 genome. Test captures using the probe set on both hexaploid and tetraploid wheat exhibit excellent coverage of the target with significantly improved specificity compared to captures performed using legacy probe designs. Captures of 24 lines from the Kronos TILLING population (EMS-induced mutations) detected an average of ~3300 mutations per line (~5 million predicted mutations in the complete TILLING population of 1500 lines). This probe set is available through Daicel Arbor Biosciences as either a stand-alone capture kit or a full service option from library prep through secondary bioinformatics analysis.​

[ab_icon icon=”file-pdf-o”] Poster – PAG XXIX – Genomic Regulatory Element Sequencing in Wheat

Number PO0409

Authors: Brian Brunelle, Alison Devault, Jacob Enk and Tina Lan, Daicel Arbor Biosciences, Ann Arbor, MI 

The detection of pathogenic variants and pathobiome profiling in plant and animal samples using next-generation sequencing (NGS) is often impeded by the dominant host/background DNA and/or RNA, necessitating extremely deep total NGS in order to accurately resolve genomes/genes of interest or to fully characterize community members. Targeted NGS methods can dramatically reduce the overall costs of sequencing and data analysis per sample. Of the available targeted NGS methods, hybridization capture is the best technique for comprehensive, low-bias, and cost-effective genome or community sequencing of viruses and bacteria from complex samples. Here we review the principles of hybridization capture for microbial sequencing applications, and highlight several peer-reviewed studies relevant to the plant and animal research community, powered by efficient myBaits® target capture kits. ​​

[ab_icon icon=”file-pdf-o”] Poster – PAG XXIX – Simplified Pathogen and Commensal Sequencing

Location: Pacific C

Date: Sunday, January 9, 8:00 a.m.

Duration: 2 hours, 10 minutes

The Feline & Canine Workshop includes presentations of recent genetic studies involving cats, dogs, and their wild relatives. Topics include the basis of morphology, behavior, and inherited disease, conservation, evolution, paleogenomics, genetic testing, and genomic resource development. This session is generously sponsored by Daicel Arbor Biosciences, ThermoFisher, Embark, Hills, Nippon Genetics, and Retsch.

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Location: Town and Country C

Date: Sunday, January 9, 10:30 a.m.

Duration: 2 hours, 10 minutes

Though the first DNA sequences from an extinct organism were first extracted 30 years ago, the revolution in sequencing technology has recently allowed for the retrieval and characterization of ancient organisms dating back more than 50,000 years. This new capability has been used to address questions related to admixture, phylogenetic inference, and evolution writ large. This session will attract leading experts in the use of ancient DNA to discuss their recent findings related to both the optimization of methodology, and specific case studies pertaining to humans, plants, and animals.

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Location: Pacific D

Date: Sunday, January 9, 4:00 p.m.

Duration: 2 hours, 10 minutes

Plant and animal domestication genomics, with a focus on evolutionary history, the impacts of domestication on genome-wide variation, and the genomic basis of domestication traits.

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Click on the product below to view PDF.

• myTags

[ab_icon icon=”file-pdf-o”] myTags Chromosome Indexing by FISH App Note

[ab_icon icon=”file-pdf-o”] myTags Custom Product Sheet

• myReads

[ab_icon icon=”file-pdf-o”] myReads NGS Services Product Sheet

• myBaits

[ab_icon icon=”file-pdf-o”] myBaits Hybridization Capture Kits Product Sheet

[ab_icon icon=”file-pdf-o”] myBaits Custom DNA Seq Product Sheet

[ab_icon icon=”file-pdf-o”] myBaits Custom RNA Seq Product Sheet

[ab_icon icon=”file-pdf-o”] myBaits Custom Methyl Seq Product Sheet

[ab_icon icon=”file-pdf-o”] myBaits Microbial Targeted Genomics App Note

[ab_icon icon=”file-pdf-o”] myBaits NLR_Gene_Resequencing Expression using cDNA RenSeq App Note

• myTXTL

[ab_icon icon=”file-pdf-o”] myTXTL Product Sheet

• myCurio

[ab_icon icon=”file-pdf-o”] Curio

Since we cannot personally hand you our great booth gift, you can claim it using promotion code DAB PAG 2022 at Daicel Arbor PAG gift.