葡萄芽变品种‘津早无核’大果型浆果表型的整合基因组和转录组分析。

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

机构信息

The Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, China.

Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China.

出版信息

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

DOI:10.7717/peerj.14617

PMID:36620751

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9817954/

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, . 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.

摘要

背景

芽变在水果植物中经常发生，是葡萄改良和育种的重要途径。“津早乌核”是优质品种“贺莫尔无核”的芽变品种，其器官和浆果明显增大。迄今为止，葡萄芽变导致浆果增大的分子机制尚不清楚。

方法

对两对芽变及其表型相似的母本进行全基因组重测序（WGRS），以鉴定 SNP、InDels 和结构变异（SV）以及相关基因。此外，对“津早乌核”及其母本“贺莫尔无核”在不同发育阶段进行转录组测序，并进行加权基因共表达网络分析（WGCNA），以鉴定差异表达基因（DEGs），并对其进行基因本体论（GO）和功能注释分析。

结果

在两对增大浆果的芽变中，共鉴定出 1334 个 SNP、272 个 InDels 和 74 个 SV，对应 1022 个与共生微生物、细胞死亡等过程相关的靶基因。同时，还确定了 1149 个与细胞壁修饰、应激反应和细胞杀伤相关的 DEGs，可能是导致表型变异的原因。结果，进一步研究了“贺莫尔无核”和“津早乌核”之间的 42 个含有遗传变异的 DEGs，包括果胶酯酶、纤维素酶 A、细胞色素 P450（CYP）、UDP-糖基转移酶（UGT）、锌指蛋白、生长素响应因子（ARF）、NAC 转录因子（TF）、蛋白激酶等。这些候选基因为更好地理解葡萄浆果增大的发育调控提供了重要线索。