Virtual Tracing of DFR mRNA and Protein Variabilities Trace the Ancestral Origin of Vitis vinifera Grapevine Cultivars Across Geographic Regions

Fatchiyah Fatchiyah; Achmad Hanif  Naufal; Cicin Vinolia  Alvionita; Eko  Suyanto

doi:10.22146/jtbb.16398

Fatchiyah Fatchiyah 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 https://orcid.org/0000-0001-6241-9665
Achmad Hanif Naufal 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 https://orcid.org/0000-0001-7237-7593
Cicin Vinolia Alvionita 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
Eko Suyanto 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 https://orcid.org/0000-0002-0748-4242

DOI: https://doi.org/10.22146/jtbb.16398

Keywords: DFR mRNA, Grapevines, Haplotypes, SNPs, Vitis vinifera

Abstract

Various grape cultivars are genetically diverse with challenging genetic variations. However, traditional markers such as SSR and SNP in identifying genetic polymorphism between cultivars are less sensitive for detecting variability between grape plant cultivars. This study aimed to determine the DFR mRNA phylogenetic, protein heatmap, mRNA SNPs, and haplotype network of Vitis vinifera grape cultivars by in silico analysis. DFR mRNA and protein databases of grape cultivars Vitis vinifera 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 cultivars. Based on full-length DFR mRNA sequences, Lambrusco f.f. from Italy followed 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 Lambrusco f.f. from Italy and V. bellula from China which are differences in their respective SNPs. The haplotypes of these two cultivars have adaptive properties that affect 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 environmental factors across plant breeding sites and geographic regions.

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