Fatchiyah Fatchiyah, Achmad Hanif Naufal, Cicin Vinolia Alvionita, Eko Suyanto
Various grape cultivars are genetically diverse with challenging genetic variations. However, traditional markers such as SSR and SNP in identifying genetic polymor-phism between cultivars are less sensitive for detecting variability between grape plant cultivars. This study aimed to determine the DFR mRNA phylogenetic, pro-tein heatmap, mRNA SNPs, and haplotype network of Vitis vinifera grape cultivars by in silico analysis. DFR mRNA and protein databases of grape cultivars Vitis vi-nifera and Vitis bellula as outgroups were collected from the NCBI database nuccore. The DFR nucleotide sequences were aligned using the ClustalW method in MEGA-X with default parameters. Heatmaps and SNPs were analyzed by calculating p distances to all taxa aligned on MEGA-X and aligned sequences of Vitis vinifera DFR were analysed with DNASP6 to identify haplotype distribution among culti-vars. Based on full-length DFR mRNA sequences, Lambrusco f.f. from Italy fol-lowed by three cultivars from France as the initial lineage of the DFR is the most likely ancestor of grapevines, besides Sylvestris as a known grapevine wild-type. The DFR mRNA heat map of sixteen Vitis cultivars shows genetic variants of Lam-brusco f.f. from Italy and V. bellula from China which are differences in their respec-tive SNPs. The haplotypes of these two cultivars have adaptive properties that af-fect trait variation and organism fitness as genetic markers of the genetic diversity of Vitis species. This finding highlighted that Vitis vinifera DFR mRNA and protein sequence variability is highly influenced by gene recombinants, mutations, and en-vironmental factors across plant breeding sites and geographic regions. © 2025, J. Tropical Biodiversity Biotechnology (CC BY-SA 4.0)
Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Jl. Veteran, Malang, 65145, Indonesia; Research Centre of Smart Molecule of Natural Genetics Resources, Universitas Brawijaya, Malang, 65145, Indonesia
