Impact and interpretation of different measures of genetic diversity in inbred lines applied to crop breeding

The application of molecular genetics in crop breeding has grown significantly, largely due to the success of molecular breeding, which utilizes genotype-based approaches to achieve substantial genetic improvements with favorable cost-effectiveness. A successful molecular breeding strategy involves thorough genotyping, enabling detailed genetic characterization of target germplasm, including genetic diversity analysis, relationships, and population structure. Genotype-based methods, favored for their stability and independence from environmental factors, are preferred over phenotype-based approaches. Genetic diversity is assessed by comparing individual genotypes within and across populations, using statistical methods to calculate genetic distances or similarities. This study focuses on establishing a unified framework to compare and evaluate common similarity measures and their relation to distance metrics, specifically in diploid inbred lines genotyped with biallelic SNPs, for use in genetic improvement efforts.