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Genome-wide association studies of bark texture in Populus trichocarpa

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A Correction to this article was published on 29 November 2019

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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.

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Change history

  • 29 November 2019

    The co-author Jin Zhang was unintentionally forgotten on the original author list. The correct Author list is presented in this paper.

Abbreviations

GWAS:

genome-wide association study

BT:

bark texture

QTL:

quantitative trait loci

LG:

linkage group

CLA:

Clatskanie site

COR:

Corvallis site

PLC:

Placerville sites

FDR:

false discovery rate

EMMA:

efficient mixed model association

LD:

linkage disequilibrium

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Data archiving statement

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

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 “Sustainable 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.

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  1. Oliver Gailing

    Present address: Forest Genetics and Forest Tree Breeding, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany

Authors and Affiliations

  1. School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA

    Roba Bdeir, Victor Busov & Oliver Gailing

  2. Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA

    Wellington Muchero & Gerald A. Tuskan

  3. Departement of Biology, Eastern Illinois University, 600 Lincoln Ave, Charleston, IL, 61920, USA

    Yordan Yordanov

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  1. Roba Bdeir
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Correspondence to Oliver Gailing.

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Electronic supplementary material

Online Resource 1

Bark texture scale from smooth (1), medium flaky (2) to rough flaky (3) for the P. trichocarpa populations. (DOCX 395 kb)

Online Resource 2

Spearman’s rank correlation coefficients for bark texture phenotypes across five datasets (DOCX 18 kb)

Online Resource 3

Frequency distribution for bark texture across Clatskanie (CLA), Corvallis (COR) and Placerville (PLC) sites and various years (a, b, c, respectively). (DOCX 228 kb)

Online Resource 4

All 1825 SNPs associated with bark texture and the underlying genes within a 6 kb interval. The population in which these SNP were detected in, their position, linkage group and significance score along with the physical localization, annotation and expression profiles of the underlying genes are summarized. (XLSX 87 kb)

Online Resource 5

The 50 genomic regions most strongly associated with bark texture and the underlying genes. The population in which these 129 individual SNPs were detected, position, linkage group and significance score as well as the physical localization and annotation of the underlying genes are summarized. SNPs are categorized into three groups: reproducible across sites, reproducible within a site and reproducible but no putative gene detected within 50 kb interval. Scores of -log10 P > 6 are in bold, genes with SNPs within its genomic sequence are highlighted in yellow. (XLSX 47 kb)

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Bdeir, R., Muchero, W., Yordanov, Y. et al. Genome-wide association studies of bark texture in Populus trichocarpa. Tree Genetics & Genomes 15, 14 (2019). https://doi.org/10.1007/s11295-019-1320-2

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