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.

Acknowledgements

The work was supported by the National Natural Science Foundation of China (No. 32102317 and No. 31972368), the China Agriculture Research System (No. CARS-29-yc-6), the China Postdoctoral Science Foundation (No. 2021 M693866), the Department of Science and Technology of Liaoning Province (No. 2022030723-JH5/104), the Shenyang Science and Technology Bureau Funds (No. 21-116-3-27), and the Liaoning key R&D Program (No. 2020JH2/10200032).

Author contributions

H.L. performed the experiments, analysed data, and wrote the paper; L.M. and Q.G. performed the experiments. Y.H. and C.L. cultivated grapes and collected samples; Z.L. and Y.Z. performed the grape berry texture and analysed data; C.J. analysed data; X.G. and Y.G. contributed to the experimental design and critically reviewed the paper. All authors approved the final manuscript.

Data availability

The data that support the results are included in this article and supplementary materials. The whole-genome resequencing data reported in this paper have been deposited in the NCBI BioProject under accession number PRJNA1018136.

Conflict of interest

The authors have no conflict of interest to declare.

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