Genome-wide association studies of bark texture in Populus trichocarpa

Roba Bdeir, Wellington Muchero, Yordan Yordanov, Gerald A. Tuskan, Victor Busov, Oliver Gailing

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12 Scopus citations

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 significant trait-associated region. 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.

Original languageEnglish
Article number14
JournalTree Genetics and Genomes
Volume15
Issue number1
DOIs
StatePublished - Feb 1 2019

Funding

Whole-genome resequencing, SNP/indel calling, and SnpEff analysis for the 544 individuals of this Populus GWAS population was previously described by Evans et al. (2014). In this study, we used the same sequencing and analytical pipelines to incorporate an additional 373 accessions (altogether 917 accessions). Briefly, reads were aligned to the P. trichocarpa reference genome version 3 using BWA 0.5.9-r16 with default parameters and SNPs and indels were called using SAMtools mpileup (-E –C 50 –DS –m 2 –F 0.000911 –d 50000) and bcftools (-bcgv –p 0.999089). The resulting SNP and indel dataset is available at http://bioenergycenter.org/besc/gwas/. The resulting SNP and indel dataset is available at http://bioenergycenter.org/besc/gwas /. To assess genetic control, we used the EMMA algorithm in the EMMAX software with kinship as the correction factor for genetic background effects (Zhou and Stephens 2012) to compute genotype to phenotype associations using 8.253,066 SNP variants with minor allele frequencies > 0.05 identified from whole-genome resequencing. Linkage disequilibrium (LD) was determined using HAPLOVIEW v.4.2 (Barrett et al. 2005). To account for multiple testing, we used the Bonferroni correction and considered as significant only those SNPs for which P < 0.05/8253066 = 6.06910−9. This correction is known to be conservative and thus “overcorrected” the raw P values (McIntyre et al. 2000). Funding information Support for the phenotyping and graduate support for Roba Bdeir was provided by the USDA-NIFA grant (# 2012-67013-19389) to VB, YY, and OG. Additional partial support for Roba Bdeir was provided by the National Science Foundation grant to OG (# 1230803) as part of the BSustainable Forest-Based Biofuel Pathways to Hydrocarbon Transportation Fuels^ project at Michigan Tech. The Center for Bioenergy Innovation is a U.S. Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. This work was supported by the U.S. Department of Energy under Contract to Oak Ridge National Laboratory. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the US Department of Energy under contract number DE-AC05-00OR22725. We also acknowledge support from the German Research Foundation (DFG) and the Open Access Publication Funds of Göttingen University.

Keywords

  • Association mapping
  • Bark texture
  • Genome-wide association studies (GWAS)
  • Populus trichocarpa

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