The genus Vitis, known for its economically important fruit—grape—is divided into three geographical groups, American, East Asian, and Eurasian, along with a hybrid group. However, previous studies on grape phylogeny using chloroplast genomes have been hindered by limited sample sizes and inconsistent methodologies, resulting in inaccuracies. In this study, we employed the GetOrganelle software with consistent parameters to assemble the chloroplast genomes of 21 grape cultivars, ensuring comprehensive representation across four distinct groups. A comparative analysis of the 21 grape cultivars revealed structural variation, showing chloroplast genome sizes ranging from 160,813 bp to 161,275 bp. In 21 Vitis cultivars, genome annotation revealed 134 to 136 genes, comprising 89 to 91 protein-coding genes (PCGs), 37 tRNAs, and 8 rRNAs. Our observations have pinpointed specific occurrences of contraction and expansion phenomena at the interfaces between inverted repeat (IR) regions and single-copy (SC) regions, particularly in the vicinity of the rpl2, ycf1, ndhF, and trnN genes. Meanwhile, a total of 193 to 198 SSRs were identified in chloroplast genomes. The diversification pattern of chloroplast genomes exhibited strong concordance with the phylogenetic relationships of the Euvitis subgenera. Phylogenetic analysis based on conserved chloroplast genome strongly clustered the grape varieties according to their geographical origins. In conclusion, these findings enhance our understanding of chloroplast genome variation in Vitis populations and have important implications for cultivar selection, breeding, and conservation efforts.

The grapevine, a globally significant fruit and an essential fruit tree species in China, is vulnerable to the adverse effects of high temperatures. Understanding the roles of microRNA and transcription factors in plant development and stress resistance is crucial for mitigating the impact of high temperature on grape growth and yield. This study investigates the response of miRNA to high-temperature stress in grape leaves. The expression level of Vvi-miR3633a was found to be inhibited under heat treatment in both Thompson seedless and Shen yue varieties, while its potential target genes (Vv-Atg36 and Vv-GA3ox2) were induced. Through transgenic overexpression experiments, it was demonstrated that Vvi-miR3633a plays a role in thermal response by affecting the expression of target genes. Furthermore, under heat stress conditions, overexpression of Vvi-miR3633a in grape callus decreased heat resistance compared to the control group (CK). The study also revealed that the target genes of Vvi-miR3633a regulate the expression of oxidase synthesis genes VvSOD and VvCAT, leading to reduced oxidase synthesis which may compromise the oxidation system. Additionally, the expression level of heat shock proteins in the transgenic lines was changed compared to the control (CK). Overall, this research provides valuable insights into understanding the molecular mechanisms involved in different crossing/breeding programs to produce heat-resistant grape varieties. Such varieties can be appropriate to propagate in warm climate areas with high temperature conditions.

Circular RNAs (circRNAs) are covalently closed RNA molecules that regulate various biological processes in plants. However, the functions of most identified circRNAs remain unclear. Here, we report a nucleoplasmic-localized circRNA, Vv-circRCD1, derived from exons 2 and 3 of the grape VvRCD1 gene. Overexpression of Vv-circRCD1 significantly shortened primary root length and increased root hair number and length, notably, and improved the salt tolerance in Arabidopsis. Transient overexpression also significantly enhanced salt tolerance of grapevines. In silico analyses confirmed direct sequence complementarity between Vv-circRCD1 and the Vvi-miR399 family, and Vv-circRCD1 and Vvi-miR399 target genes (involved in salt stress responses) showed consistent expression patterns under salt stress, indicating a Vv-circRCD1–Vvi-miR399–target gene regulatory module may mediate salt tolerance. These results not only identified Vv-circRCD1 as a novel regulator of grapevine salt tolerance, but also highlighted its potential in improving crop stress resistance, providing a practical reference for crop breeding.

Grapes (Vitis spp.) are a globally significant fruit crop with a long history of cultivation and substantial cultivar diversity. Their high genetic differentiation and complex evolutionary history make them a valuable system for studying plant evolution. The chloroplast genome, known for its structural conservation and uniparental inheritance, offers a reliable molecular marker for phylogenetic reconstruction. In this study, we sequenced and assembled the complete chloroplast genomes of nine representative grape cultivars, analyzed their phylogenetic relationships, and compared structural variations. All chloroplast genomes displayed a typical quadripartite structure, with high conservation in genomic architecture, gene order and content, codon usage, and simple sequence repeats (SSRs). However, additional sequence comparisons revealed seven regions with high variation, including the genes rbcL and ndhF, and the intergenic regions rps16-trnQ, ndhC-trnV, accD-psaI, ndhF-rpl32, and trnL-ccsA. At the same time, seven natural variation sites were identified in the amino acid sequences of rbcL and ndhF. Additionally, the study’s maximum likelihood (ML) phylogenetic trees and photosynthetic index measurements suggest that developmental characteristics of grape photosynthesis may be related to the evolutionary origins of different populations. This phylogenetic classification not only elucidates the evolutionary origins of these germplasm resources but also provides a foundation for molecular-assisted breeding by identifying distinct genetic groups.

Grape (Vitis vinifera spp.) accessions exhibit rich diversity, and understanding their genetic variation and evolutionary relationships is crucial for cultivar selection and utilization. A highly representative SNP marker set was developed in this study based on re-sequencing data analysis, to clarify the phylogenetic relationships among 96 grape accessions and to evaluate the genetic resolution of core markers. Using PN40024 as the reference genome, high-quality SNP loci were screened from resequencing data of the 96 accessions. A phylogenetic tree was constructed, and genetic diversity was analyzed using PCA and population structure analysis. The results showed that the 96 accessions were mainly divided into four groups: European (‘Merlot’, ‘Chardonnay’), American (‘Beta’, ‘Concord’), Euro-American hybrids (‘Vidal’, ‘Miguang’), and wild populations along with their hybrid progeny (‘Zuoyouhong’, ‘Huajia 8’). PCA and ADMIXTURE validated population differentiation, revealing clear separation between wild and cultivated accessions. Through screening of core SNP markers, 384,304 candidate SNPs suitable for probe design were identified. Further refinement yielded 2000 and 10,000 SNP markers. Detailed analysis of core marker characteristics showed that their minor allele frequency (MAF) was predominantly between 0.1 and 0.3, with the majority distributed in CDS (38.65%), intronic (30.2%), and intergenic regions. The most common mutation types were [A/G] (35%) and [C/T] (34%) transitions. The 2000 core SNPs were associated with 1220 functional genes and were significantly enriched in pathways such as protein binding, RNA transport, and plant–pathogen interaction. These findings provide an efficient tool for grape genetic diversity analysis, cultivar identification, and molecular breeding, laying the groundwork for the precise utilization of grape germplasm resources.

Polyploidization can generate morphological and physiological variation in plants, but the molecular basis underlying leaf trait changes after genome doubling in grapevine remains insufficiently understood. This study aimed to characterize phenotypic, physiological, transcriptomic, and metabolomic differences between diploid and induced autotetraploid plants of ‘Thompson Seedless’ and to identify biological processes potentially associated with the observed leaf trait variation. In this study, autotetraploid plants were induced from axillary buds of ‘Thompson Seedless’ using colchicine treatment, and ploidy levels were confirmed by flow cytometry and chromosome counting. Phenotypic, physiological, transcriptomic, and metabolomic analyses were performed to compare diploid and tetraploid plants. Compared with diploids, tetraploids exhibited enlarged leaves, reduced plant stature, larger but less dense stomata, increased chloroplast number in guard cells, and higher total chlorophyll and carotenoid contents. Fv/Fm remained unchanged, whereas increased Vj and decreased ψEo and φEo suggested differences in electron transport-related characteristics beyond QA. Transcriptomic analysis identified 1564 differentially expressed genes, and metabolomic profiling detected 618 differentially accumulated metabolites. Integrated analyses highlighted coordinated molecular differences associated mainly with cell-wall processes, secondary metabolism, redox-related functions, and carbon-related pathways. These findings identify candidate biological processes for future functional validation and provide a basis for evaluating the potential value of autotetraploid germplasm in grapevine breeding.