GWAS supported by computer vision identifies large numbers of candidate regulators of in planta regeneration in Populus trichocarpa.

Autor: Nagle MF; Department of Forest Ecosystems and Society, Oregon State University, 321 Richardson Hall, Corvallis, OR 97311, USA., Yuan J; Department of Electrical Engineering and Computer Science, Oregon State University, 1148 Kelley Engineering Center, Corvallis, OR 97331, USA., Kaur D; Department of Electrical Engineering and Computer Science, Oregon State University, 1148 Kelley Engineering Center, Corvallis, OR 97331, USA., Ma C; Department of Forest Ecosystems and Society, Oregon State University, 321 Richardson Hall, Corvallis, OR 97311, USA., Peremyslova E; Department of Forest Ecosystems and Society, Oregon State University, 321 Richardson Hall, Corvallis, OR 97311, USA., Jiang Y; Statistics Department, Oregon State University, 239 Weniger Hall, Corvallis, OR 97331, USA., Niño de Rivera A; Department of Forest Ecosystems and Society, Oregon State University, 321 Richardson Hall, Corvallis, OR 97311, USA., Jawdy S; Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.; Center for Bioenergy Innovation, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA., Chen JG; Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.; Center for Bioenergy Innovation, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.; Bredesen Center for Interdisciplinary Research, University of Tennessee-Knoxville, 310 Ferris Hall 1508 Middle Dr, Knoxville, TN 37996, USA., Feng K; Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.; Center for Bioenergy Innovation, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA., Yates TB; Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.; Center for Bioenergy Innovation, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.; Bredesen Center for Interdisciplinary Research, University of Tennessee-Knoxville, 310 Ferris Hall 1508 Middle Dr, Knoxville, TN 37996, USA., Tuskan GA; Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.; Center for Bioenergy Innovation, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA., Muchero W; Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.; Center for Bioenergy Innovation, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA.; Bredesen Center for Interdisciplinary Research, University of Tennessee-Knoxville, 310 Ferris Hall 1508 Middle Dr, Knoxville, TN 37996, USA., Fuxin L; Department of Electrical Engineering and Computer Science, Oregon State University, 1148 Kelley Engineering Center, Corvallis, OR 97331, USA., Strauss SH; Department of Forest Ecosystems and Society, Oregon State University, 321 Richardson Hall, Corvallis, OR 97311, USA.
Jazyk: angličtina
Zdroj: G3 (Bethesda, Md.) [G3 (Bethesda)] 2024 Apr 03; Vol. 14 (4).
DOI: 10.1093/g3journal/jkae026
Abstrakt: Plant regeneration is an important dimension of plant propagation and a key step in the production of transgenic plants. However, regeneration capacity varies widely among genotypes and species, the molecular basis of which is largely unknown. Association mapping methods such as genome-wide association studies (GWAS) have long demonstrated abilities to help uncover the genetic basis of trait variation in plants; however, the performance of these methods depends on the accuracy and scale of phenotyping. To enable a large-scale GWAS of in planta callus and shoot regeneration in the model tree Populus, we developed a phenomics workflow involving semantic segmentation to quantify regenerating plant tissues over time. We found that the resulting statistics were of highly non-normal distributions, and thus employed transformations or permutations to avoid violating assumptions of linear models used in GWAS. We report over 200 statistically supported quantitative trait loci (QTLs), with genes encompassing or near to top QTLs including regulators of cell adhesion, stress signaling, and hormone signaling pathways, as well as other diverse functions. Our results encourage models of hormonal signaling during plant regeneration to consider keystone roles of stress-related signaling (e.g. involving jasmonates and salicylic acid), in addition to the auxin and cytokinin pathways commonly considered. The putative regulatory genes and biological processes we identified provide new insights into the biological complexity of plant regeneration, and may serve as new reagents for improving regeneration and transformation of recalcitrant genotypes and species.
Competing Interests: Conflicts of interest. The author(s) declare no conflict of interest.
(© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)
Databáze: MEDLINE
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