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. 2018 Dec 1;25(6):587-596.
doi: 10.1093/dnares/dsy027.

Transcriptome-referenced Association Study of Clove Shape Traits in Garlic

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Free PMC article

Transcriptome-referenced Association Study of Clove Shape Traits in Garlic

Xiaojun Chen et al. DNA Res. .
Free PMC article

Abstract

Genome-wide association studies are a powerful approach for identifying genes related to complex traits in organisms, but are limited by the requirement for a reference genome sequence of the species under study. To circumvent this problem, we propose a transcriptome-referenced association study (TRAS) that utilizes a transcriptome generated by single-molecule long-read sequencing as a reference sequence to score population variation at both transcript sequence and expression levels. Candidate transcripts are identified when both scores are associated with a trait and their potential interactions are ascertained by expression quantitative trait loci analysis. Applying this method to characterize garlic clove shape traits in 102 landraces, we identified 22 candidate transcripts, most of which showed extensive interactions. Eight transcripts were long non-coding RNAs (lncRNAs), and the others were proteins involved mainly in carbohydrate metabolism, protein degradation, etc. TRAS, as an efficient tool for association study independent of a reference genome, extends the applicability of association studies to a broad range of species.

Figures

Figure 1
Figure 1
Length distribution of garlic transcripts generated by single-molecule long-read sequencing. A logarithmic scale with a base of three was used in the Y-axis.
Figure 2
Figure 2
Characterization of the garlic population. (a) Tridimensional presentation of garlic clove illustrating CL, CW, and CT. The direction from the bottom to the top represents the direction of the bulb axis. (b) Phenotype variation of CL, CW, and CT in the population. The unit of scale in X-, Y-, and Z-axes is millimeter (mm). (c) Distribution of SNPs identified in the population. CDS: coding sequence; UTR: untranslated region. (d) Phylogenetic tree of the 102 landraces based on the 19,912 SNPs identified from the population. The unrooted tree was generated using the TreeBest program with the neighbour-joining method. The 102 landraces were clustered into three distinct groups, and cyan, green, and purple clusters represent groups I, II, and III, respectively.
Figure 3
Figure 3
Identification of candidate transcripts involved in clove thickness (CT), weight (CW), and length (CL). (a–c) Manhattan and quantile-quantile plots result from the transcriptome-based association study (TRAS) data for CT, CW, and CL, respectively. The dashed horizontal line indicates the significance threshold (P <5 × 10−5). (d) Overlap of the transcripts associated with CT, CW, and CL. (e) The distribution of correlation coefficient between the expression of associated transcripts and the traits. (f) Venn diagram of the candidate transcripts related to CT, CW, and CL.
Figure 4
Figure 4
Visualization of a network consisting of eight lncRNAs related to CSTs and their co-expressed transcripts. Green and red dots represent lncRNAs identified as candidate transcripts and their co-expressed transcripts, respectively. Transcripts co-expressed with ASTG1548 were significantly enriched in the GO term ‘proteasome-mediated ubiquitin-dependent protein catabolic process.’.
Figure 5
Figure 5
Visualization of the interaction network of 13 candidate transcripts for CL and CW.

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