Description
This is a USDA ARS position and is offered through the ORISE educational opportunity system of the Oak Ridge National Laboratories and is based in Pullman, Washington. Please note, ORISE will pay a stipend that will include funding for all health and associated insurance; benefits are not offered in addition to the annual stipend.
Research Project: Temperate pulses (i.e. peas, chickpeas and lentils) are important plant-based protein sources and rotational crops, and their plant genetic resource (PGR) collections contain important genetic diversity for crop improvement. Improved methodology for regenerations would increase efficiency of the genebanks. Systematic and thorough genotypic and phenotyped characterization would improve collection utility and aid in Genomewide Association Studies (GWAS).
Objective: Apply high-throughput genomics and phenomics tools to characterize the USDA ARS National Plant Germplasm System (NPGS) pea, lentil and chickpea collections, (up to ~9,000 accessions). Research seed viability testing, regeneration protocols including breaking dormancy of crop wild relative species, and more efficient long-term seed storage conditions. Data analyses including data handling, filtering, and calculations of genetic diversity, relationships, and GWAS. Upload data into public databases to ensure all data becoming publicly available.
Approach: During the educational appointment, you will collaborate closely with Washington State University pulse breeders and geneticists, PGITRU unit members and established USDA ARS/academic collaborators while conducting research. The pulse collections will be characterized during regeneration activities in the field in Pullman and Central Ferry, Washington. Genotyping activities will be outsourced, and data receipt and initial quality assessment will be coordinated with the genotyping service institution. You will receive sequence/genotype data, conduct analyses to survey variation, calculate relationships, and other relevant analyses of genebank accessions. High-throughput analyses of agronomic traits and seed nutritional traits can be complimented with measurements of biotic and/or abiotic resistance following standard phenotyping protocols. You will interact with collaborators to upload genotypic and phenotypic data directly into the GRIN-Global database or to link all data via an external public platform for access. The program has office, laboratory, greenhouse, field space, equipment, and supplies for planned experiments. Staff, collaborators, and lead scientists will support you in technical aspects of project.
Expected Results: New genetic and phenotypic characterization of the temperate pulse PGR would improve collection management and promote its efficient use. Results include:
Estimating genetic diversity and population structure among and between all accessions in the collection,
Correct accession taxonomic assignments,
Redundancy identification leading to increased efficiency,
Gaps in coverage revealed leading to targets for acquisition, and;
Aptly characterized PGR accessions in collections that can be used to identify subsets of variation for in-house and stakeholder mining of beneficial alleles in pre-breeding.
This last result will allow US breeders to create new varieties that are more nutritious, require fewer chemical or irrigation inputs, and be more resistant to new insect, disease, or environmental threats, thus increasing farmer profits. With fully characterized collections, breeders and geneticists can request the best accessions for their research programs, including expanded marker trait associations via GWAS and breeding of new cultivars for all traits of interest. Characterization of the pulse collection can aid in effective management of this important resource while improving and promoting its use by stakeholders.
Learning Objectives: As a result of this experience, you will:
Learn how to measure, analyze, and use the genetic diversity in the USDA National Plant Germplasm System pulse collection,
Learn phenomics and phenotyping approaches in greenhouse and field experiments,
Learn approaches used for marker traits associations in crop plants, and;
Develop skills in communication (writing, presenting, etc.), collaboration and in conducting scientific research.
Requirements
The qualified candidate must be a U.S. citizen and should have received a doctoral degree in plant breeding, agricultural research, agronomy and crop science, botany, genetics including genome science, horticulture, plant science, or closely related field.
Preferred skills:
Experience with agricultural plant sciences, plant genetic resources, forage legumes, plant genetics, plant breeding, molecular biology, bioinformatics, and data management.
Organizational capacity for curating, cataloging, and storing large amounts of data, samples, such as seeds, plants or DNA.
Experience caring for plants in the field, greenhouse, and growth chamber.
Attention to detail in data collection and record keeping.
Team player and comfortable with communication through phone, email, and in person to coordinate with collaborators locally and in other offices and states.
Consistency, timeliness, and independence.
