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

Jianquan Huang; Guan Zhang; Yanhao Li; Mingjie Lyu; He Zhang; Na Zhang; Rui Chen

doi:10.7717/peerj.14617

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

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

Authors

Jianquan Huang^#¹, Guan Zhang^#^{2

3}, Yanhao Li^{1

4}, Mingjie Lyu², He Zhang¹, Na Zhang¹, Rui Chen²

Affiliations

¹ The Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, China.
² Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China.
³ College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.
⁴ College of Horticulture and Gardening, Tianjin Agricultural University, Tianjin, China.

^# Contributed equally.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Fruit* / genetics
Genomics
Phenotype
Plant Breeding
Transcriptome / genetics
Vitis* / genetics

Grants and funding

This research was funded by the China Agriculture Research System of MOF and MARA, grant number CARS-29, and the Innovative Research and experimental Projects for young researchers of Tianjin Academy of Agricultural Science, grant number 20211002. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.