Abstract
Adventitious rooting (AR) is critical to the propagation, breeding, and genetic engineering of trees. The capacity for plants to undergo this process is highly heritable and of a polygenic nature; however, the basis of its genetic variation is largely uncharacterized. To identify genetic regulators of AR, we performed a genome-wide association study (GWAS) using 1148 genotypes of Populus trichocarpa. GWASs are often limited by the abilities of researchers to collect precise phenotype data on a high-Throughput scale; to help overcome this limitation, we developed a computer vision system to measure an array of traits related to adventitious root development in poplar, including temporal measures of lateral and basal root length and area. GWAS was performed using multiple methods and significance thresholds to handle non-normal phenotype statistics and to gain statistical power. These analyses yielded a total of 277 unique associations, suggesting that genes that control rooting include regulators of hormone signaling, cell division and structure, reactive oxygen species signaling, and other processes with known roles in root development. Numerous genes with uncharacterized functions and/or cryptic roles were also identified. These candidates provide targets for functional analysis, including physiological and epistatic analyses, to better characterize the complex polygenic regulation of AR.
Original language | English |
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Article number | uhad125 |
Journal | Horticulture Research |
Volume | 10 |
Issue number | 8 |
DOIs | |
State | Published - Aug 2023 |
Funding
We thank the National Science Foundation Plant Genome Research Program for support (IOS #1546900, Analysis of genes affecting plant regeneration and transformation in poplar), and members of GREAT TREES Research Cooperative at OSU for its support of the Strauss laboratory. Support for the Poplar GWAS dataset is provided by the U.S. Department of Energy, Office of Science Biological and Environmental Research via the Center for Bioenergy Innovation (CBI) under Contract No. DE-PS02-06ER64304. The Poplar GWAS Project used resources of the Oak Ridge Leadership Computing Facility and the Compute and Data Environment for Science at Oak Ridge National Laboratory, which is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC05-00OR22725. We would like to thank the efforts of the personnel from the CBI in establishing the GWAS resource used for this study. This work used the COMET high-performance cluster at the San Diego Supercomputing Center (University of California, San Diego) made available through the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562.