Investigating the Genetic Diversity and the Genetic Factors influencing Nut Quality in Hazelnut (Corylus avellana L.)

Hazelnut (Corylus avellana L.) is a valuable nut crop with extensive applications in the food industry. Nevertheless, limited information exists regarding its genetic diversity and the specific genomic regions influencing nut morphological traits and the volatile organic compounds (VOCs) responsible for nut aroma. Among these VOCs, that can only be quantified after the trees produce their first nuts, filbertone is considered the most significant for hazelnut aroma. Therefore, this thesis aims to characterise the agrobiodiversity of a global germplasm collection of C. avellana, identify candidate genes associated with nut morphology and aroma, and develop a predictive tool for filbertone levels. We collected leaf samples from 316 C. avellana trees and employed a genotyping-by-sequencing (GBS) approach to sequence their genomic DNA. After quality control measures, including removal of samples with poor quality, the complete dataset consisted of 282 accessions and 44,757 single nucleotide polymorphisms (SNPs). A reduced dataset, used for the genetic diversity analysis, was obtained by both removing 141 clones and markers in linkage via linkage-disequilibrium (LD) pruning, resulting in 141 accessions and 16,378 SNPs retained. Using the reduced dataset, analysis showed that accessions from Eurasia (Azerbaijan, Georgia, and Turkey) exhibited significant genetic differentiation, whereas populations from Europe and the United States demonstrated higher levels of admixture. We used the same number of SNPs from the complete dataset for all genome-wide association studies (GWAS), but different subsets of phenotyped samples depending on the trait. First, we measured nut area, minimum calibre, maximum calibre, and perimeter in 151 genotyped accessions and performed a GWAS on nut morphology, identifying ten SNPs associated with four traits. Second, we quantified 19 volatile organic compounds (VOCs) using gas chromatography–ion mobility spectrometry (GC-IMS) in 104 genotyped accessions and conducted a GWAS, uncovering 18 SNPs associated with six VOCs. Finally, primers were designed for the SNP associated to filbertone dimer on chromosome 5 at position 9,612,761 bp, leading to the development of a portable tool using the tetra primer amplification refractory mutation system polymerase chain reaction (T-ARMS-PCR) technique. This tool can predict a plant's filbertone levels without awaiting the nut harvest. Collectively, these findings enhance our understanding of C. avellana genetics and establish a basis for genomics-assisted breeding. We not only revealed the genetic factors influencing important nut traits but also provided a tool to select varieties better suited for industrial applications, thereby supporting more efficient breeding efforts.