Quantitative Genetics Intern

Trans Ova Genetics•Madison, WI

4d•Remote

About The Position

The Quantitative Genetics Intern supports the development of new genetic evaluations for economically and biologically relevant traits in internal beef and dairy breeding programs. Working with the Product Development and Innovation quantitative genetics team, the intern will apply contemporary single-step genomic evaluation methods and the BLUPF90 family of programs to phenotypic, pedigree, and genomic data. The internship is designed to produce a defined technical deliverable while providing practical experience with the development, validation, documentation, and application of genetic evaluations in commercial livestock breeding programs. Based in Madison, Wisconsin, the intern will work with R&D scientists and laboratory staff on basic and/or applied research related to reproductive biology, cell biology, embryology, or vitro fertilization.

Requirements

Currently enrolled in a PhD program in quantitative genetics, animal breeding, animal science, genetics, genomics, or a closely related discipline.
Practical experience conducting genetic evaluations in livestock, preferably cattle.
Hands-on experience implementing single-step BLUP or single-step genomic BLUP evaluations using the BLUPF90 family of programs.
Sound understanding of mixed models, breeding value estimation, genomic relationship matrices, genetic parameter estimation, prediction accuracy, and evaluation validation.
Experience working with phenotypic, pedigree, and genomic data, including data editing, quality control, and construction of analysis-ready files.
Proficiency in Python for data manipulation, workflow development, quality control, or result processing.
Experience working in Linux or Unix environments and using shell scripting, job scheduling, or high-performance computing resources is preferred.
Ability to write clear, well-documented, reproducible code and maintain organized analytical records.
Strong analytical judgment, attention to detail, problem-solving skills, and ability to work independently while seeking input when needed.
Effective written and verbal communication skills, including the ability to explain technical methods and findings to scientific and cross-functional audiences.
Ability to work remotely and participate reliably in meetings and collaborative work during regular Central Time business hours.

Nice To Haves

Experience with Fortran is strongly preferred.

Responsibilities

Contribute to the development of one or more genetic evaluations for traits relevant to internal beef and dairy breeding programs.
Define analysis populations, contemporary groups, fixed and random effects, and other model specifications in collaboration with team geneticists.
Estimate or evaluate genetic parameters and implement single-step genomic evaluations using appropriate programs within the BLUPF90 family.
Compare alternative data edits, model specifications, or evaluation scenarios and summarize implications for prediction quality and operational use.
Prepare, integrate, and quality-control phenotypic, pedigree, and genomic datasets used in assigned evaluations.
Assess evaluation outputs for convergence, data integrity, predictive performance, bias, stability, biological plausibility, and suitability for use in breeding decisions.
Develop reproducible scripts and workflows for data preparation, program execution, results processing, validation, and reporting.
Document datasets, code, parameter files, methods, assumptions, quality-control rules, analytical decisions, limitations, and results to support reproducibility and future implementation.
Participate in regular project meetings, communicate progress and technical risks, and incorporate feedback from quantitative genetics and business stakeholders.
Prepare and deliver a final technical report and presentation summarizing methods, results, limitations, and recommended next steps.