Genome-wide association studies of bark texture in Populus trichocarpa
Abstract
Plants have developed bark as a defense barrier to deal with environmental stresses, such as pathogen invasion, drought, and UV radiation. Bark is composed of dead differentiated cells and is formed when radial expansion pushes the cortex and epidermis outward creating secondary meristem. However, the genetic control of this complex phenotype is generally unknown. Here, we use association mapping to define the genomic regions associated with natural variation in bark texture (BT) in Populus trichocarpa. Clonally replicated provenance trials of P. trichocarpa were studied for BT collected across three sites, multiple years, and (2–3) biological replicates per site. Forty-one genomic intervals containing SNPs significantly associated with BT were detected that were highly reproducible across sites, years, and replicates. A list of candidate genes within these regions with related putative function was identified. A total of 98 genes were considered candidate genes due to significance and putative function with connection to the phenotype. Association mapping using low coverage sequencing allowed us to detect narrow genomic intervals (1–20 kb) with high reproducibility and shared candidate genes. For example, a membrane-associated apoptosis protein and a wall-associated receptor kinase (PR5K-like) protein, which both are involved in radial growth and tissue differentiation, lie within significantmore »
- Authors:
-
[2];
[2];
- Michigan Technological Univ., Houghton, MI (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Eastern Illinois Univ., Charleston, IL (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1823377
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Tree Genetics & Genomes
- Additional Journal Information:
- Journal Volume: 15; Journal Issue: 1; Journal ID: ISSN 1614-2942
- Publisher:
- Springer Nature
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Bark texture; Genome-wide association studies (GWAS); Association mapping; Populus trichocarpa
Citation Formats
Bdeir, Roba, Muchero, Wellington, Yordanov, Yordan, Tuskan, Gerald A., Busov, Victor, and Gailing, Oliver. Genome-wide association studies of bark texture in Populus trichocarpa. United States: N. p., 2019.
Web. doi:10.1007/s11295-019-1320-2.
Bdeir, Roba, Muchero, Wellington, Yordanov, Yordan, Tuskan, Gerald A., Busov, Victor, & Gailing, Oliver. Genome-wide association studies of bark texture in Populus trichocarpa. United States. https://doi.org/10.1007/s11295-019-1320-2
Bdeir, Roba, Muchero, Wellington, Yordanov, Yordan, Tuskan, Gerald A., Busov, Victor, and Gailing, Oliver. Sat .
"Genome-wide association studies of bark texture in Populus trichocarpa". United States. https://doi.org/10.1007/s11295-019-1320-2. https://www.osti.gov/servlets/purl/1823377.
@article{osti_1823377,
title = {Genome-wide association studies of bark texture in Populus trichocarpa},
author = {Bdeir, Roba and Muchero, Wellington and Yordanov, Yordan and Tuskan, Gerald A. and Busov, Victor and Gailing, Oliver},
abstractNote = {Plants have developed bark as a defense barrier to deal with environmental stresses, such as pathogen invasion, drought, and UV radiation. Bark is composed of dead differentiated cells and is formed when radial expansion pushes the cortex and epidermis outward creating secondary meristem. However, the genetic control of this complex phenotype is generally unknown. Here, we use association mapping to define the genomic regions associated with natural variation in bark texture (BT) in Populus trichocarpa. Clonally replicated provenance trials of P. trichocarpa were studied for BT collected across three sites, multiple years, and (2–3) biological replicates per site. Forty-one genomic intervals containing SNPs significantly associated with BT were detected that were highly reproducible across sites, years, and replicates. A list of candidate genes within these regions with related putative function was identified. A total of 98 genes were considered candidate genes due to significance and putative function with connection to the phenotype. Association mapping using low coverage sequencing allowed us to detect narrow genomic intervals (1–20 kb) with high reproducibility and shared candidate genes. For example, a membrane-associated apoptosis protein and a wall-associated receptor kinase (PR5K-like) protein, which both are involved in radial growth and tissue differentiation, lie within significant trait-associated region. Here, two copies of root hair defective3 genes, transmembrane protein in Populus differentiating xylem and phloem, were also significantly associated with BT and co-located with major quantitative trait locus (QTL) for BT, bark thickness, and diameter from our previous study suggesting an important role in radial growth.},
doi = {10.1007/s11295-019-1320-2},
journal = {Tree Genetics & Genomes},
number = 1,
volume = 15,
place = {United States},
year = {Sat Feb 02 00:00:00 EST 2019},
month = {Sat Feb 02 00:00:00 EST 2019}
}
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