JSM 2015 Preliminary Program

Online Program Home
My Program

Abstract Details

Activity Number: 194
Type: Contributed
Date/Time: Monday, August 10, 2015 : 10:30 AM to 12:20 PM
Sponsor: ENAR
Abstract #316028
Title: Hierarchical Modeling and Differential Expression Analysis for RNA-Seq Experiments with Inbred and Hybrid Genotypes
Author(s): Andrew Lithio* and Dan Nettleton
Companies: Iowa State University and Iowa State University
Keywords: empirical Bayes ; split-plot ; genetics ; Integrated Nested Laplace Approximation ; ShrinkBayes ; INLA
Abstract:

The performance of inbred and hybrid plant genotypes is of interest in plant breeding and genetics. High-throughput sequencing of RNA (RNA-seq) has proven to be a useful tool in the study of the molecular genetic responses of inbreds and hybrids to environmental stresses. Commonly used experimental designs and sequencing methods lead to complex data structures that require careful attention in data analysis. We demonstrate an analysis of RNA-seq data from a split-plot design involving drought stress applied to two inbred genotypes and two hybrids formed by crosses between the inbreds. Our modeling strategy incorporates random effects for whole-plot and split-plot experimental units and uses sample-specific normalization to account for variation in gene length and base content, as well as differences in sequencing intensity across experimental units. Thoughtful parameterization that accounts for the natural relationships among genotypes and hierarchical modeling allow for borrowing of information across genes to improve estimation of dispersion parameters, genotype effects, treatment effects, and interaction effects of primary interest.


Authors who are presenting talks have a * after their name.

Back to the full JSM 2015 program





For program information, contact the JSM Registration Department or phone (888) 231-3473.

For Professional Development information, contact the Education Department.

The views expressed here are those of the individual authors and not necessarily those of the JSM sponsors, their officers, or their staff.

2015 JSM Online Program Home