Steve Strauss, Oregon State University
January 27 @ 1:30 pm - 2:30 pm
A phenomic and GWAS adventure studying the causes of genetic variation in amenability to regeneration and transformation in black cottonwood (Populus trichocarpa)
Steve Strauss, University Distinguished Professor of Forest Biotechnology at Oregon State University
Abstract
Recalcitrance to transformation and associated regeneration of transgenic or gene-edited plants continue to present major obstacles to the use of transformation in research and biotechnology. Recalcitrance generally varies widely among species and genotypes, however, the biological mechanisms for this variation are very poorly understood. To shed light on the underlying mechanisms, we performed GWAS using up to 1,219 genotypes from the resequenced association population of wild Populus trichocarpa developed by the US Department of Energy. Its extensive diversity, high density of SNPs (over 30 million including rare variants), and low linkage disequilibrium (R2 < 0.2 within 2kb) facilitates association of informative SNPs with causative genes. To improve GWAS sensitivity, we first developed new machine vision-aided phenomic systems for quantifying variation in callus, shoot, and root regeneration in planta, and then developed the “GMOdetector” system available in GitHub to cross-reference fluorescent hyperspectral and RGB images to enable quantitation of transgenic tissue regeneration during the course of in vitro development. We also adapted new pipelines for statistical analysis of multi-SNP genotype:phenotype relationships that greatly improved sensitivity for detection of associations. We conducted four GWAS experiments resulting in the identification of over 500 candidate genes implicated by SNPs in intragenic regions or within 5kb, and analyzed their likely biological roles in relation to physiological and developmental pathways. For example, amenability to transformation appears to be a result of complex cross-talk between wound response, hormonal signaling, and meristem developmental pathways. Some of the nodal genes in these interacting pathways are logical candidates for new morphogenic regulator genes to help overcome recalcitrance.
Join us on Monday, January 27 at 1:30 PM in Stephens Room (3503 Thomas Hall) and ZOOM for the Genetics and Genomics Seminar Series.
This event will be held in person in Stephens Room (3503 Thomas Hall) and on Zoom. REGISTER to attend Zoom: https://ncsu.zoom.us/meeting/register/tJUufu2rrDwuGtMzQ2ivMoBl4_LJ-eSGAZ4q
If you are a student or postdoc who would like to meet with Dr. Strauss please sign up here: https://docs.google.com/spreadsheets/d/1_5-iHgJi8ei3uFBg1d5k1md8yX-PTzIJy7hEg7RwKa0/edit?gid=1057466659#gid=1057466659
