Transcriptome analysis of table grapes (Vitis vinifera L.) identified a gene network module associated with berry firmness.

Li Ma,Xiuwu Guo,Hong Lin,Kun Li,Lingjun Sun,Yinshan Guo,Zhendong Liu,Panagiotis Kalaitzis

doi:10.1371/journal.pone.0237526

Abstract

Berry firmness is one of the main selection criteria for table grape breeding. However, the underlying genetic determinants and mechanisms involved in gene expression during berry development are still poorly understood. In this study, eighteen libraries sampled from Vitis vinifera L. cv. ‘Red Globe’ and ‘Muscat Hamburg’ at three developmental stages (preveraison, veraison and maturation) were analyzed by RNA sequencing (RNA-Seq). The firmness of ‘Red Globe’ was significantly higher than that of ‘Muscat Hamburg’ at the three developmental stages. In total, a set of 4,559 differentially expressed genes (DEGs) was identified between ‘Red Globe’ and ‘Muscat Hamburg’ in the preveraison (2,259), veraison (2030) and maturation stages (2682), including 302 transcription factors (TFs). Weighted gene coexpression network analysis (WGCNA) showed that 23 TFs were predicted to be highly correlated with fruit firmness and propectin content. In addition, the differential expression of the PE, PL, PG, β-GAL, GATL, WAK, XTH and EXP genes might be the reason for the differences in firmness between ‘Red Globe’ and ‘Muscat Hamburg’. The results will provide new information for analysis of grape berry firmness and softening.

Highlights

Grape is a globally cultivated fruit, with 7.15 million hectares of area harvested and 79.18 million tons of production in 2018
The total soluble solid (TSS) content increased and total acid (TA) content decreased in both ‘Muscat Hamburg’ and ‘Red Globe’ from preveraison (56 days after full bloom (DAFB)) to maturation (98 DAFB)
The TA content in ‘Red Globe’ was lower than that in ‘Muscat Hamburg’ from 56 DAFB to 84 DAFB, but there was no significant difference between these two cultivars at pre-veraison and maturation

Summary

Introduction

Grape is a globally cultivated fruit, with 7.15 million hectares of area harvested and 79.18 million tons of production in 2018 (http://www.fao.org/faostat/en/#data/QC/visualize). Berry firmness is considered one of the most important traits for grape breeding. Grape firmness has been considered a measure of freshness [1], and the high berry firmness of table grape contributes to its desirable crunchy texture, which is an important factor that affects eating quality and prolongs postharvest shelf life with decreased loss during storage. Berry firmness is a typical quantitative trait attributed to polygenes. The berry flesh texture can be roughly divided into soft, medium, slightly firm and very firm based on firmness [2]. A few studies on the identification of quantitative trait loci (QTLs) associated with firmness have been performed based on linkage maps and genome-wide association analyses, and the QTLs for firmness are located in different linkage groups (LGs), including 1, 3, 4, 5, 8, 9, 10, 13, 16

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Discussion

Conclusion