An interactive genetic fingerprinting database for chestnut genotyping
Creators: name: Fruggiero, Ivan
name: Maisto, Alessandro
name: Passaro, Sara
name: Gentile, Domenico
name: Nunziata, Angelina
name: D'Agostino, Nunzio
Publisher: name: F1000 Research Limited
Year: 2024

description: Background: The European chestnut (Castanea sativa Mill., Fagaceae) holds considerable ecological and economic significance, particularly in countries such as Italy, Greece, Spain and Turkey. This species plays a crucial role in rural economies and ecosystems. <br>
Accurate varietal recognition is essential for managing chestnut groves, influencing everything from planting to marketing. Traditional morpho-physiological methods face limitations, particularly in distinguishing young, dormant, or scion trees, and require extensive expertise, which is hard to transfer and often costly. These challenges can determine investment and impact varietal choices. Recent advancements, such as Single Nucleotide Polymorphisms (SNPs) markers identified through KASP technology, have greatly improved cultivar identification. The availability of KASP-based genotyping data has significantly accelerated the development of a database of genetic fingerprints to assist farmers and researchers in accurately identifying and distinguishing chestnut varieties.<br>
<br>
Methods: To develop the database, we first assessed user needs to determine required data and query functionalities. We then created an Entity-Relationship (ER) diagram for the database structure and implemented it using MySQL. The interactive platform was built with PHP, HTML, CSS, and JavaScript, and integrated bioinformatics tools like BLAST, MAFFT, and BioPython for enhanced data analysis and user experience in genetic fingerprinting and chestnut genotyping.<br>
<br>
Results: The database includes genotypic and phenotypic data for over 150 chestnut genotypes, featuring 38 SNPs with details on primers, sequences, positions, and variations. Users can query the database in three modes:

 Discriminating accessions by SNPs and/or morphological traits: Users can select SNPs and/or phenotypic traits to retrieve accessions that match the criteria, with results highlighting SNPs with the highest PIC values. This mode helps accurately distinguish varieties based on genetic and morphological data.
 Identifying most discriminative SNPs: This tool helps identify the SNPs that are most effective in distinguishing between recorded accessions. By selecting an accession, the platform provides a list of the minimum number of SNPs and associated alleles that are most effective for its discrimination and characterization. This feature is especially valuable for developing specific KASP protocols.
 Searching user-defined genotype strings: Users can input genotype strings (concatenated SNP loci ordered by chromosome and position) to calculate the genetic distance between new and previously genotyped accessions. This function aids in the classification of new varieties by comparing their genetic profiles with existing data.

<br>
<br>
Conclusions: This platform is the first interactive chestnut database for cultivar discrimination using KASP genotyping data, providing tailored feedback and a dynamic tool for cultivar identification and differentiation.