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. 2023 Jan 3:11:e14617.
doi: 10.7717/peerj.14617. eCollection 2023.

Integrative genomic and transcriptomic analyses of a bud sport mutant 'Jinzao Wuhe' with the phenotype of large berries in grapevines

Jianquan Huang #  1 , Guan Zhang #  2   3 , Yanhao Li  1   4 , Mingjie Lyu  2 , He Zhang  1 , Na Zhang  1 , Rui Chen  2
Affiliations

Integrative genomic and transcriptomic analyses of a bud sport mutant 'Jinzao Wuhe' with the phenotype of large berries in grapevines

Jianquan Huang et al. PeerJ. .

Abstract

Background: Bud sport mutation occurs frequently in fruit plants and acts as an important approach for grapevine improvement and breeding. 'Jinzao Wuhe' is a bud sport of the elite cultivar 'Himord Seedless' with obviously enlarged organs and berries. To date, the molecular mechanisms underlying berry enlargement caused by bud sport in grapevines remain unclear.

Methods: Whole genome resequencing (WGRS) was performed for two pairs of bud sports and their maternal plants with similar phenotype to identify SNPs, InDels and structural variations (SVs) as well as related genes. Furthermore, transcriptomic sequencing at different developmental stages and weighted gene co-expression network analysis (WGCNA) for 'Jinzao Wuhe' and its maternal plant 'Himord Seedless' were carried out to identify the differentially expressed genes (DEGs), which were subsequently analyzed for Gene Ontology (GO) and function annotation.

Results: In two pairs of enlarged berry bud sports, a total of 1,334 SNPs, 272 InDels and 74 SVs, corresponding to 1,022 target genes related to symbiotic microorganisms, cell death and other processes were identified. Meanwhile, 1,149 DEGs associated with cell wall modification, stress-response and cell killing might be responsible for the phenotypic variation were also determined. As a result, 42 DEGs between 'Himord Seedless' and 'Jinzao Wuhe' harboring genetic variations were further investigated, including pectin esterase, cellulase A, cytochromes P450 (CYP), UDP-glycosyltransferase (UGT), zinc finger protein, auxin response factor (ARF), NAC transcription factor (TF), protein kinase, etc. These candidate genes offer important clues for a better understanding of developmental regulations of berry enlargement in grapevine.

Conclusion: Our results provide candidate genes and valuable information for dissecting the underlying mechanisms of berry development and contribute to future improvement of grapevine cultivars.

Keywords: Berry enlargement; Bud sport; Genetic variation; Grapevine; RNA-seq; WGRS.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1. The comparison of ‘Himord Seedless’ and its bud sport ‘Jinzao Wuhe’.
Comparison of longitudinal diameter (B), transverse diameter (C), volume (D) and weight (E) of ‘Himord Seedless’ (black line) and ‘Jinzao Wuhe’ (red line) at different developmental stages. Standard deviations (SDs) were calculated with 30 biological replicates for each timepoint. The error bars represented 1 SD.
Figure 2
Figure 2. Annotation and distribution of (A) SNPs, (B) InDels and (C) SVs of ‘Thompson Seedless’ and its bud sports ‘Dawuhebai’, ‘Himord Seedless’ and its bud sports ‘Jinzao Wuhe’.
Figure 3
Figure 3. The statistics of SNPs, InDels and SVs and corresponding genes.
(A–C) Venn diagrams represent the numbers of unique and shared SNPs, InDels and SVs, respectively. (a) ‘Thompson Seedless’; (b) ‘Dawuhebai’; (c) ‘Himord Seedless’; (d) ‘Jinzao Wuhe’. (D) The circos plots of SNPs, InDels and SVs distribution on the nineteen V.vivfera chromosomes (a) Chromosome; (b) GC content; (c) Gene density; (d) SNP density; (e) InDel density; (f) SV density. (E) The GO annotation of potential causal genes harbored with determining SNPs, InDels and SVs.
Figure 4
Figure 4. Analyses and statistics of DEGs and GO enrichment.
Analyses and statistics of DEGs and GO enrichment. (A) Principal component analysis (PCA) of transcriptome data. (B, C, E, and F) Volcano plots for expressed genes at different developmental stages. Red dots represented the upregulated genes while blue dots represented the down-regulated genes. (D) Venn diagram of DEGs at four different stages. (G–J) GO enrichment results of DEGs at four development stages. WT: ‘Himord Seedless’; MUT: ‘Jinzao Wuhe’. Stage 1–4: full-flowering stage, fruit enlargement stage (14 days post-anthesis), véraison stage (35 days post-anthesis) and maturity stage (56 days post-anthesis). The ‘Himord Seedless’ in the stage 1–4 were the control group and ‘Jinzao Wuhe’ in the stage 1–4 were the experiment group.
Figure 5
Figure 5. Weighted gene co-expression network analysis of berry development transcriptomes.
(A) Dendrogram plot of co-expression modules. This plot shows 18 modules and different colors represent different modules. (B) Module-trait relationship and corresponding p values. LD: longitudinal diameter; TD: transverse diameter.
Figure 6
Figure 6. Analyses and statistics of DEGs carrying specified SNPs, InDels and SVs.
(A) The intersection between DEGs and genes containing SNPs, InDels and SVs. (B) Expression profiles of DEGs harboring specified SNPs, InDels and SV.
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