Association Mapping and Expression Analysis of the Genes Involved in the Wood Formation of Poplar

Abstract

Xylogenesis is a complex and sequential biosynthetic process controlled by polygenes. Deciphering the genetic architecture of this complex quantitative trait could provide valuable information for increasing wood biomass and improving its properties. Here, we performed genomic resequencing of 64 24-year-old trees (64 hybrids of section Aigeiros and their parents) grown in the same field and conducted full-sib family-based association analyses of two growth and six woody traits using GEMMA as a choice of association model selection. We identified 1342 significantly associated single nucleotide polymorphisms (SNPs), 673 located in the region upstream and downstream of 565 protein-encoding genes. The transcriptional regulation network of secondary cell wall (SCW) biosynthesis was further constructed based on the published data of poplar miRNA, transcriptome, and degradome. These provided a certain scientific basis for the in-depth understanding of the mechanism of poplar timber formation and the molecular-assisted breeding in the future.

Keywords: Populus; association analysis; large-diameter timber; transcriptional regulation; wood property.

Figure 1

Scatterplot matrix for eight traits (fiber length (FL), fiber width (FW), double wall thickness (DWT), cell lumen diameter (CLD), air-dry density (AD), basic density (BD), diameter at breast height (DBH), and height (H)). Lower triangle: Scatter plots of units between pairs of eight poplar traits. Diagonal: density plot of eight traits. Upper triangle: correlation coefficient (Pearson’s r) between the eight traits within the full-sib poplar family. *, 0.01 < p < 0.05; **, 0.001 < p < 0.01; ***, p < 0.001.

Figure 2

(a) SNP (single-nucleotide polymorphism) density plot across all 19 poplar chromosomes. The horizontal axis at the top represents the physical location (Mbp) on the chromosome. The color bar indicates the number of SNPs within the size of the 0.5 Mbp window. (b) Plot of the LD (linkage disequilibrium) rate (r²) against the physical distance in Kbp. The red line indicates the pattern of LD decay for the entire genome, and the gray line represents the LD decay for each of 10 randomly selected chromosomes.

Figure 3

Upset plot of the top 500 SNPs (single-nucleotide polymorphisms) of four methods GWAS (genome-wide association studies) results for eight poplar traits. Subplot (a): fiber length (FL). Subplot (b): fiber width (FW). Subplot (c): double wall thickness (DWT). Subplot (d): cell lumen diameter (CLD). Subplot (e): air-dry density (AD). Subplot (f): basic density (BD). Subplot (g): diameter at breast height (DBH). Subplot (h): height (H). Each row in the lower panel represents a method, and the corresponding colored bars on the lower left represent the number of each method, whereas the main bar plot (top) is the number of SNPs in different sets.

Figure 4

Quantile–quantile plot (QQ plot) of fiber length (FL), fiber width (FW), double wall thickness (DWT), cell lumen diameter (CLD), air-dry density (AD), basic density (BD), diameter at breast height (DBH), and height (H) for four GWAS (genome-wide association studies) methods (GAPIT.GLM, GCTA, GEMMA, and PLINK).

Figure 5

Manhattan plots of the GWAS (genome-wide association studies) results for eight poplar characters. SNPs (single-nucleotide polymorphisms) were removed when p > 0.005 in all traits from inside to outside. Fiber length (FL), fiber width (FW), double wall thickness (DWT), cell lumen diameter (CLD), air-dry density (AD), basic density (BD), diameter at breast height (DBH), and height (H). Notes: when p > 0.0005.

Figure 6

Typical pathways of the NAC-containing gene. The “T” arrows indicate interacting miRNAs, and the shades of color represent different category values.