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Article|14 Jun 2023|OPEN
GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa
Michael F. Nagle1 , , Jialin Yuan2 , Damanpreet Kaur2 , Cathleen Ma1 , Ekaterina Peremyslova1 , Yuan Jiang3 , Bahiya Zahl1 , Alexa Niño de Rivera1 , Wellington Muchero4,5,6 , Li Fuxin2 , Steven H. Strauss,1 ,
1Department of Forest Ecosystems and Society, Oregon State University, 3180 SW Jefferson Way, Corvallis, OR, 97331, United States
2Department of Electrical Engineering and Computer Science, Oregon State University, 110 SW Park Terrace, Corvallis, OR, 97331, United States
3Statistics Department, Oregon State University, 103 SW Memorial Place, Corvallis, OR, 97331, United States
4Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, United States
5Center for Bioenergy Innovation, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, United States
6Bredesen Center for Interdisciplinary Research, University of Tennessee, 821 Volunteer Blvd., Knoxville, TN, 37996, United States
*Corresponding author. E-mail:,

Horticulture Research 10,
Article number: uhad125 (2023)
Views: 99

Received: 29 Dec 2022
Accepted: 05 Jun 2023
Published online: 14 Jun 2023


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.