PAG XXV - San Diego, CA

14 - 18 January 2017

Thank you for visiting us at PAG. If you missed our workshop, view the recordings of our PAG workshop in our Scientific Community section!

Trait to Table: NGS Solutions for Agrigenomics

Come learn about recent advances in genotyping and RNA-Seq enabling agricultural research. 

  • Targeted genotyping
  • Species specific RNA-Seq 
  • Highly sensitive Methyl-Seq

Location: Royal Palm Salon 5-6
When: 17 January 2017

Flexible and Cost-Effective Genotyping By Targeted Sequencing

Joe Don Heath

NuGEN Technologies, San Diego, CA

Next-generation sequencing (NGS) technology is increasingly being adopted as an essential research and development tool in plant and animal genomics. As accessibility and affordability continue to improve, NGS is being used for marker-assisted selection (MAS) to accelerate plant breeding and selection, as well as in transcriptomics, plant or animal-pathogen interactions and epigenetics. We will present a highly multiplexed novel targeted sequencing genotyping solution that is cost-effective, flexible and features a simple workflow.

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Joe Don Heath

NuGEN Technologies, San Diego, CA

Joe Don has been a scientific leader and customer advocate at NuGEN since 2003, in which time he has worn a number of hats, including leadership roles in technical service, training, collaborations, and marketing, to name a few. He presently is responsible for market development in diagnostics and emerging markets and still enjoys a hands-on role in developing and deploying assays on customer robotics systems.  Prior to joining NuGEN, JD worked at Incyte Genomics in Palo Alto where he was scientific lead for the PathoSeq microbial database and LifeTools analysis platforms as well as head of the Field Application Science team. JD earned his PhD in biochemistry and molecular biology from the University of Texas Health Science Center in Houston and completed a postdoctoral fellowship in plant-microbe interactions at the University of Washington in Seattle.  JD’s calling outside of work is to bring joy to the lives of his friends, family, church community and friends he has yet to meet through the creation of good music and the brewing of good beer.

Targeted Genotyping-By-Sequencing with Single Primer Enrichment Technology (SPET): A Case Study in Black Poplar

Davide Scaglione

IGA Technology Services, Udine, Italy

David Scaglione1, Mike Allwright2, Simone Scalabrin1, Hazel Katherine Smith2, Giovanni Emiliani3, Cyril Douthe4, Jaime Puertolas5, Elisabeth Larsen5, Billy Valdes-Fragoso2, Giorgio Alberti6, Alessandro Zaldei7, Michele Morgante8, and Gail Taylor2

(1)IGA Technology Services, Udine, Italy, (2)University of Southampton, Southampton, United Kingdom, (3)CNR-IVALSA, Sesto Fiorentino, Italy, (4)Universitat de les Illes Belears, Palma, Spain, (5)University of Lancaster, Lancaster, United Kingdom, (6)Università Di Udine, Udine, Italy, (7)CNR - Institute for Biometeorology, Florence, Italy, (8)IGA Istituto di Genomica Applicata, Udine, Italy

Genotyping-by-sequencing has now become a widely adopted strategy to generate massive genotypic information to a fraction of the cost used in array technologies. Sequencing-based genotyping carries several advantages such as greater scalability, given the current sequencing platforms, and being an “open system”, allowing for the scoring of polymorphisms that were not necessarily a prior knowledge. However, one major limitation of widely adopted genotyping-by-sequencing methods, driven by restriction enzymes or oligomers, is its random access to the genome. On the other side, enrichment methodologies based on hybridization come with some limitation in cost, hand-on time, enrichment efficiency and dilution of the sequencing coverage on valuable sites. Here we propose the NuGEN Ovation Target Enrichment - a method originally developed for exon-centric enrichment - as a unique tool for large-scale targeted genotyping. Slight modification to the original sequencing protocol allowed to generate RAD-like stacks of reads on 90,000 pre-selected SNPs over 540 black poplar genotypes, maximizing efficiency. Moreover, the sequencing of extra bases, from both paired reads, allowed the discovery of hundreds of thousands novel SNPs, sampling rarer variants not originally included in the panel. The system showed its powerful combination of array-like target SNP paradigm along with the random sampling of variants of traditional genotyping-by-sequencing solutions, circumventing ascertainment bias. Data showed complete usability for the discovery of trait-associated polymorphisms within the 7th Framework Programme EU-funded project WATBIO.

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Davide Scaglione

IGA Technology Services, Udine, Italy

RNA-Seq Simplified. Solutions for Every Sample.

Denise Stephens

NuGEN Technologies, San Diego, CA

RNA-Seq solutions for Agrigenomics presented by Denise Stephens, Field Application Scientist at NuGEN Technologies. In this presentation, we discuss NuGEN’s RNA-Seq solutions for a broad range of sample inputs and quality. In addition, an overview of our technology (AnyDeplete and SPIA) used in the RNA-Seq portfolio is described.

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Denise Stephens

NuGEN Technologies, San Diego, CA

Initiation of Zygotic Genome Activation in the Unicellular Rice Zygote

Sarah N. Anderson

Universtiy of Minnesota

Sarah N Anderson1, Cameron Johnson2, Joshua Chesnut3, Daniel Jones3, Maggie Woodhouse4, Imtiyaz Khanday2, Chenxin Li2, Liza Conrad5, Scott Russell3 and Venkatesan Sundaresan2

(1)University of Minnesota, Twin Cities, St. Paul, MN, (2)University of California-Davis, Davis, CA, (3)University of Oklahoma, Norman, OK, (4)University of California - Davis, Davis, CA, (5)Eckerd College, St. Petersburg, FL

The fusion of the two terminally differentiated gametes, the egg and sperm cells, to form the totipotent zygote is critical to successful reproduction. Following fertilization, embryos must transition from reliance on maternal transcripts deposited in the mature egg cell before fertilization to transcriptional activation of its own genome. The timing and regulation of this process, called zygotic genome activation, has been difficult to decipher in plants. By transcriptome profiling of isolated time-staged zygotes in rice, we demonstrate large-scale expression changes before the first cell division, including a burst of expression of S phase genes. Hybrid zygote transcriptomes display a strong maternal allele bias, though a small set of genes with paternal or biparental expression unexpectedly includes key embryogenic factors, contrasting with maternal sequestration of animal pluripotency factors. We conclude that in plants, unlike animals, zygotic genome activation initiates within the unicellular zygote, with differential but functionally significant contributions from both parental genomes.

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Sarah N. Anderson

Universtiy of Minnesota

Sarah Anderson is a postdoctoral researcher at the University of Minnesota, Twin Cities where she studies the regulation of gene expression by transposable elements across development and following abiotic stress in maize. Previously, she completed her PhD in Integrative Genetics and Genomics at the University of California, Davis, studying the timing and parental regulation of zygotic genome activation in rice. Outside of research, Sarah enjoys making homemade candy, designing crochet patterns, and walking her dog.