Berry texture QTL and candidate gene analysis in grape (Vitis vinifera L.)

Abstract

Berry texture is a noteworthy economic trait for grape; however, the genetic bases and the complex gene expression and regulatory mechanism for the diverse changes in berry texture are still poorly understood. In this study, the results suggest that it is difficult to obtain high-mesocarp firmness (MesF) and high-pericarp puncture hardness (PPH) grape cultivars with high pericarp brittleness (PerB). The high-density linkage map was constructed using whole-genome resequencing based on 151 F₁ individuals originating from intraspecific hybridization between the firm-flesh cultivar 'Red Globe' and soft-flesh cultivar 'Muscat Hamburg'. The total length of the consensus map was 1613.17 cM, with a mean genetic distance between adjacent bin markers of 0.59 cM. Twenty-seven quantitative trait loci (QTLs) for berry MesF, PPH, and PerB were identified in linkage groups (LGs) 1, 3, 4, 6, 8, 9, 10, 11, 14, 16, and 17, including twelve QTLs that were firstly detected in LGs 6, 11, and 14. Fourteen promising candidate genes were identified from the stable QTL regions in LGs 10, 11, 14, and 17. In particular, VvWARK2 and VvWARK8 refer to chromosome 17 and are two promising candidate genes for MesF and PPH, as the VvWARK8 gene may increase pectin residue binding with WARK for high berry firmness maintenance and the allele for VvWARK2 carrying the 'CC' and 'GA' genotypes at Chr17:1836764 and Chr17:1836770 may be associated with non-hard texture grape cultivars. In addition, real-time quantitative polymerase chain reaction (RT-qPCR) verification revealed that the promising candidate transcription factor genes VvMYB4-like, VvERF113, VvWRKY31, VvWRKY1, and VvNAC83 may regulate cell wall metabolism candidate gene expression for grape berry texture changes.

Figure 1

Distribution of MesF, PPH, and PerB in the ‘Red Globe’ × ‘Muscat Hamburg’ population. Histograms show data variations from 2017 to 2019. RG and MH indicate female parent ‘Red Globe’ and male parent ‘Muscat Hamburg’ mean values, respectively.

Figure 2

Phenotypic correlations between MesF, PPH, and PerB from 2017 to 2019. Numbers in the upper right corner represent strong or weak correlations, and the red asterisks indicate a significant difference.

Figure 3

The genetic diversity of 25 grape cultivars (lines) with different berry textures. Purple, yellow, and green stars represent hard-, medium-, and soft-textured grape cultivars (lines), respectively.

Figure 4

Stable QTLs for MesF, PPH, and PerB on the consensus map. Linkage group distances are in Kosambi cM. QTLs are shown on the right side and are named starting with the abbreviation of the trait (MesF for mesocarp firmness, PPH for pericarp puncture hardness, PerB for pericarp brittleness), followed by the linkage group number and the position of the identified QTL per trait. The QTLs with red, green, and blue colors are associated with MesF, PPH, and PerB, respectively. The QTLs with different solid lines, cross-hatching and vertical lines are QTLs identified in 2017, 2018, and 2019, respectively. Height of the QTL boxes indicates the confidence interval of QTLs.

Figure 5

Expression of ten candidate genes in ‘Red Globe’ and ‘Muscat Hamburg’ at preveraison and maturation. Asterisks indicate significant differences detected by one-way ANOVA with Tukey’s test at P ≤ 0.05. Data are means ± SEs of three replications.

Figure 6

Schematic graph of VvWARK2 and VvWARK8 in the grape 12X.v2 genome and SNP effect analysis. (a) VvWARK2 and VvWARK8 refer to chromosome 17. (b) The ‘T/C’ (Chr17:1836764) and ‘G/A’ (Chr17:1836770) SNPs identified in 27 cultivars (lines). Purple, yellow, and green stars represent hard-, medium-, and soft-textured grape cultivars (lines), respectively. 1 to 27 represent the grape cultivars (lines) ‘Changezhi’, ‘Red Globe’, ‘Christmas Rose’, ‘Sweet Sapphire’, ‘Crimson Seedless’, ‘Thompson Seedless’, ‘Shennong Cuifeng’, ‘Tiangong Cuixiangmi’, ‘9–22’, ‘Blackcrunchy Seedless’, ‘Queen Nina’, ‘Cuiguang’, ‘Moldova’, ‘Zaoxia Meigui’, ‘Hongyanxiang’, ‘Muscat Hamburg’, ‘9–1-358’, ‘15–71’, ‘9–1-254’, ‘Zhuosexiang’, ‘Beibinghong’, ‘Takatsuma’, ‘Venus Seedless’, ‘Beta’, ‘Kyoho’, ‘Shennong Jinhuanghou’, and ‘Zui Jinxiang’, respectively.