Yuhuan Miao

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.

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.

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.