WSU CAHNRS

College of Agricultural, Human, and Natural Resource Sciences

Department of Plant Pathology

Deven See Lab

Lab Email: wrsggl@wsu.edu


Graduate Students                    Staff                             Computational Capacity

Technologies & Capabilities     Undergraduates           Former Members


Lab Forms:

GBS job request forms can be downloaded here: GBS Job Request Form.

GBS plate layout submission can be downloaded here: GBS Plate Layout Submission Document.

GBS Computational Pipeline documentation can be downloaded here: GBS Pipeline Documentation.

Job request forms for ABI/KASP/SEQUENOM can be downloaded here: Non-GBS Job Request Form.

Procedure on how to prepare and ship DNA for the Genotyping Lab: DNA Shipping Procedure.

Updates on job status can be found here: Genotyping Job Status.

Sign Up remotely for the Zeto/ABI machine (needs generic google account): Zeto Scheduler.

To access the lab’s generic google account, contact us at wrsggl@wsu.edu


Graduate Students

 

Taras Nazarov

Ph.D. Student, Plant Pathology

TarasPic

Interests: Molecular and omics biology, genetics, epigenetics, plant-pathogen interaction. Main project is focused on the analysis of wheat and stripe rust interaction at the transcriptome level.

 

 

 

Esraa Alwan

Ph.D. Student, Crop and Soil Sciences

EsraaPic

Interests: Spring Wheat breeding, genetics, tissue culture/doubled haploids production, identifying new sources of resistance to wheat pathogens and insects. Main project is focused on identifying new sources of resistance to stripe rust and Hessian fly in the Pacific Northwest Spring Wheat germplasm.

Publications: Alwan, E., Ogbonnaya, F.C., Nazari, K., Hakim. Identification and characterization of wild tetraploids wheat for durable stem rust resistance. 2010.

 

 

 

Jonathan EagleJonathan pic

Ph.D. Student, Plant Pathology

Interests: Plant-pathogen interactions, genetics, and plant breeding. My project pertains to a seedling stripe rust resistance in wheat which will involve gene mapping with SSR in hopes of finding new genes responsible for stripe rust resistance.

 

Sajal Sthapit

Ph.D. Student, Plant Pathology

SajalPic

Interests: Plant breeding and genetics, evolution, population genetics, bioinformatics, pre-breeding in neglected and underutilized species. My main project is to discover the genes that are associated with adaptation of wheat genotypes to the Washington state growing conditions.

Professional Experience: Senior Program Officer, LI-BIRD, Nepal, 2010-2015, now on study leave. URL: www.libird.org

Program Associate, EcoAgriculture Partners, Washington DC, 2007-2010. URL: www.ecoagriculture.org

Publications:
Palikhey, E., L. Sherpa, and S. Sthapit. 2015. From rarity to ubiquity: entrepreneurship revives rare rice variety. LEISA India June: 22-5
Shrestha, P. and S. Sthapit. 2015. Nepal: LI-BIRD’s approach to supporting community seed banks. In: Vernooy et al. eds. Community Seed Banks: Origins, Evolution and Prospects. Earthscan by Routledge, p. 187-93
Sthapit, S., G. Meldrum, S. Padulosi and N. Bergamini. 2015. Strengthening the role of custodian farmers in the national conservation programme of Nepal. Bioversity International and LI-BIRD
Mijatovic, D. and S. Sthapit. 2014. Conservation of agrobiodiversity in landscape mosaics, Nepal. ETFRN News 56, p. 88-93
Shrestha, P. and S. Sthapit. 2014. Conservation by communities: the CBM approach. LEISA India March: 11-3
Sthapit, S. and D. Mijatovic. 2014. The evolving landscape of agrobiodiversity conservation. LI-BIRD and Bioversity International
Happychuk, N., E. Palikhey, L. Lama, S. Sthapit and S. Shukla. 2014. Reacquiring a taste for diversity: changing food habits, their causal factors, and the value of dietary diversity in Jumla, Nepal. Biodiversity Watch 4: 167-97
Neupane, S., S. Sthapit and B. Sthapit. 2014. Following walnut footprints in Nepal. Scripta Horticulturae 17: 275-81
Paudel, B. and S. Sthapit. 2013. Empowering rights-holders and facilitating duty-bearers to secure farmers’ rights in Nepal. In: Jonas, H. and H. Jonas eds. The Right to Responsibility: Resisting and Engaging Development, Conservation, and the Law in Asia. p. 120-34
Shrestha, P., S. Sthapit, A. Subedi and B. Sthapit. 2013. Community biodiversity management fund: promoting conservation through livelihood development in Nepal. In: de Boef et al. eds. Community Biodiversity Management: Promoting Resilience and the Conservation of Plant Genetic Resources. Earthscan from Routledge, p. 118-22
Pudasaini, R., S. Sthapit, R. Suwal and B. Sthapit. 2013. Case study 2 – The role of integrated home gardens and local, neglected and underutilized plant species in food security in Nepal and meeting the Millennium Development Goal 1 (MDG). In: Fanzo et al. eds. Diversifying Food and Diets: Using Agricultural Biodiversity to Improve Nutrition and Health. Earthscan from Routledge, p. 242-56
Sthapit, B., V. Ramanatha Rao and S. Sthapit, eds. 2012. Tropical Fruit Tree Species and Climate Change. Bioversity International
Scherr, S.J. and S. Sthapi­t. 2009. Putting food on the table, crops and livestock. In: McNeely et al. eds. The Wealth of Nature: Ecosystem Services, Biodiversity, and Human Well-Being. Intl. League of Conservation Photographers, p. 219-26
Scherr, S.J. and S. Sthapit. 2009. Mitigating climate change through food and land use. Worldwatch Report 179
Scherr, S.J. and S. Sthapit. 2009. Farming and land use to cool the planet. In: Starke, L. ed. State of the World, p. 30-49


Staff

 

JenniferPic

Jennifer Logan

Research Technician

Education: B.A., Psychology, University of Montana
Expertise: GBS sequencing, DNA extraction, PCR

Email: jennifer.logan@wsu.edu

TravisPicTravis Ruff

USDA Research Technician

Education: B.S., Biotechnology and Microbiology, Washington State University
Expertise: GBS sequencing, PCR, Sanger sequencing

Email:truff@wsu.edu

 

DoloresPicDolores Covarrubias

Research Technician

Education: B.S., Field Crops Management, Washington State University
Expertise: Greenhouse Maintenance, DNA Extraction,PCR, and SEQUENOM.

Email:dolores.covarrubias@wsu.edu

 

 


Computational Capacity

 

The See Lab as its computational capabilities required to handle large data sets generated by the in-house NGS platforms. We have a 32 core, 512GB RAM system for running the various computational jobs in the lab. In addition, there is a 96 core, 1TB RAM high performance computing cluster for massive parallel computation.

 

Servers

  • Supercomputer: WRSGGL01

32 cores, 512GB RAM total memory

  • High Performance Computing Cluster: WRSGGLcluster

4 compute nodes, 24 cores per node, 1TB RAM memory

Storage

  • Supercomputer
  • HPC
  • RAID storage connected to HPC
  • Independent RAID storage


Technologies, Equipment & Capabilities

Next-Gen Sequencing

  • Ion Proton (90 Billion Reads/2.5 hours)

-SNP variant calling (Genotyping by Sequencing or GBS)

-RNA Sequencing

-Whole genome sequencing

  • Ion Torrent (3 billion reads)

-RNA seq(Transcriptome sequencing)

Sanger Sequencing

  • ABI 3730

Fragment Analysis

  • SSR
  • STS
  • CAP

DNA Extraction

  • Bead Shaker
  • Oktopure
  • Synergy Microplate Reader (Quantification)
  • QiAgility

SNP Analysis

  • Sequenom
  • KASP
  • Synergy Microplate Reader

Software

  • GeneMarker (v1.5,v1.9) [Soft Genetics]
  • MassArray/Typer4.0.20 [Sequenom]
  • Gen5 2.0 [BioTek/Synergy Plate reader]
  • [QiAgility]
  • JMP Genomics
  • Multipoint
  • MultiQTL

Computational Resources

  •   Supercomputer

32 cores, 512GB RAM total

  • High Performance Computing Cluster: WRSGGLcluster

4 compute nodes, 24 cores per node, 256 GB RAM per node

  • Storage devices


Undergraduates

 


Former Members


Department of Plant Pathology, PO Box 646430, Washington State University, Pullman WA 99164-6430, 509-335-9541, Contact Us
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