Evaluation of Salt Tolerance at the Seedling Stage and Genetic Diversity in USDA Tomato (Solanum lycopersicum) Germplasm, and Genomic Insights into Leafminer Resistance and Tallness in Spinach (Spinacia oleracea) through Genome-Wide Association Studies (GWAS) and Genomic Prediction Approaches

Abstract

Genetic diversity and stress tolerance mechanisms in tomato (Solanum lycopersicum) and spinach (Spinacia oleracea) were explored through advanced genomic tools, focusing on salt tolerance in tomato and leafminer resistance and plant height in spinach. Using genome-wide association studies (GWAS) and genomic prediction (GP), this research uncovers key insights into the genetic architecture of these traits, paving the way for improving crop resilience. In tomato, the evaluation of 71 and 280 USDA accessions under saline stress identified genotypes with significant salt tolerance. Population structure analysis revealed three genetic groups, emphasizing the influence of domestication on diversity. These findings provide a strong foundation for breeding salt-tolerant tomato varieties tailored to regions affected by salinity. For spinach, GWAS identified significant single nucleotide polymorphism (SNP) markers associated with leafminer resistance and tallness. Candidate genes related to pest resistance and height were identified, offering valuable targets for breeding programs. Genomic prediction models showed high accuracy in selecting resistant and optimized genotypes, supporting the acceleration of spinach breeding efforts. The integration of genomic technologies with traditional breeding approaches enhances the ability to develop more resilient and productive crop varieties. These findings offer critical contributions to sustainable agriculture, particularly in addressing challenges posed by salinity stress and pest infestations.