School of Integrative Plant Science – Section of Plant Breeding and Genetics, Cornell University

Position ID:Cornell-School of Integrative Plant Science – Section of Plant Breeding and Genetics-POSTDOC [#11282]
Position Title: Multiomic Prediction of Oat Seed Composition
Position Location:Ithaca, New York 14853, United States [map]
Subject Area: Plant Science
Appl Deadline:2018/07/31 (posted 2018/06/11, updated 2018/06/08)
Position Description:    

The position is in the Plant Breeding and Genetics Section at Cornell University, and is part of a USDA Agriculture and Food Research Initiative grant to breed more nutritious oat. Oat is uniquely valued among grain crops for the health-promoting composition of its seeds. The project will leverage extensive genomic, transcriptomic, and metabolomic datasets collected in oat to develop and evaluate methods to improve the health-promoting composition of oat seed effectively. We will identify important causal loci and characterize new mutations affecting seed composition. The Plant Breeding & Genetics Section, within the School of Integrative Plant Science, trains interdisciplinary scientists in the elaboration of new breeding methods, the discovery of genetic mechanisms important for economically important traits, and the development of genetic stocks, germplasm, and varieties. Cornell University plant breeders are world leaders in innovative plant breeding research, teaching, and extension, and we collaborate globally.

This lab works with several crop species (wheat, oat, barley, cassava, and the brown algae sugar kelp) to develop genomic prediction methods and integrate them optimally within breeding schemes. We source tools from genomics, quantitative, statistical, and population genetics, and from machine learning and operations research. With the Jannink lab, Dr. Michael Gore and Dr. Mark Sorrells provide leadership on the multiomic oat selection project.

In research for this project, the postdoc will collaborate with oat breeders at the Universities in Minnesota, Wisconsin and South Dakota, as well as a postdoctoral associate currently working on the project. We have characterized an oat diversity panel of 384 genotypes with high-density DNA marker data, RNA-seq gene expression data, and non-targeted LC-MS, GC-MS, and targeted fatty acid methyl ester data of mature oat seed. We will analyze these data to identify important genomic drivers of the mature oat seed metabolome. Results from this analysis will guide the sequencing of 80 target genomic segments in a population of 1,920 oat TILLING (Targeted Induced Local Lesions In Genomes) lines. TILLING lines mutated for putative metabolomic regulators will be evaluated to validate their function. We have also used these data to select 15 crosses among elite oat cultivars and will characterize 50 inbred progeny from each cross. We will assess whether results from the multiomic analysis of the diversity panel enables improved prediction among full-sib progeny for seed composition traits.

Term is one year renewable to three years contingent on performance and continued funding.

The candidate would be expected to contribute needed metabolomics expertise to the project. The postdoc responsibilities will therefore involve work on experiments with new oat lines and interpreting the output of metabolomic assays and connecting metabolite levels to gene expression and genotype through knowledge of biochemistry. In collaboration with other project personnel, the postdoc will conduct and interpret genome- and transcriptome-wide association studies. These studies should result in the identification of genomic regions targeted for sequencing in the TILLING population. Identified regions will also be used to inform genomic prediction models aimed at improving breeder selection of oat seed composition traits.

Position Requirements Ph.D. in plant biochemistry or metabolomics with experience or interest in breeding applications, or Ph.D. in plant or animal breeding with emphasis on biochemistry, metabolomics, nutritional science. Proven scientific writing ability and communication skills.

Preferred Specific Skills Genome-wide association studies and genomic prediction methods. High-dimensional data analysis. Programming skills in R or other quantitative / statistical scripting. Basic bioinformatics skills (sequence alignment, use of gene annotations). Basic notions of mating designs in breeding.

Candidates are encouraged to send a statement of interest, curriculum vitae, and contact information for three references. Submit all application materials to Academic Jobs Online at Questions about the position can be addressed to Dr. Michael Gore at: . Review of applications will begin immediately and continue until the position is filled.

Diversity and Inclusion are a part of Cornell University’s heritage. We are a recognized employer and educator valuing AA/EEO, Protected Veterans, and Individuals with Disabilities.

Application Materials Required:
Submit the following items online at this website to complete your application:
And anything else requested in the position description.

Further Info:
(607) 255-5492
School of Integrative Plant Science
College of Agriculture and Life Sciences
358 Plant Science Building
Cornell University
Ithaca, NY 14853

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