Gene copy number variations in Capsella rubella(a target control approach)

ABSTRACT Structural variations, particularly gene copy number variations (gCNVs), play an important role in shaping genome architecture and evolutionary potential. Despite their biological significance, gCNVs remain understudied in many plant species, including Capsella rubella, a self-fertilizing member of the Brassicaceae family. In this thesis, I investigated genome-wide gCNVs in C. rubella by integrating multiple approaches to improve detection reliability. Using whole-genome resequencing data, I used the rCNV package to identify CNV candidates based on deviations in allele ratios and excess of heterozygosity. To complement this, I used ArDu, a read depth –based method, to estimate copy number across the genome. The combined application of these two tools allowed for a more robust and comprehensive identification of gene CNV. Five genes showing strong CNV signatures in both rCNV and ArDu analyses were selected for experimental validation using quantitative PCR (qPCR). While qPCR results confirmed the presence of CNVs in several genes, discrepancies between computational and experimental results highlighted important limitations, such as potential biases in read depth normalization and primer efficiency. Nonetheless, the general consistency observed in specific genes demonstrated the potential for combining bioinformatic and molecular approaches in CNV research. This study contributes valuable insight into the structural variation landscape of C. rubella and underscores the need for integrated CNV detection strategies. The results lay a foundation for future work investigating the inheritance and evolutionary impact of gCNVs, including ongoing experiments that explore segregation patterns of gene duplications across generations. Keywords: Capsella rubella, gene copy number variation, qPCR, structural variation, genome analysis