This study addresses the underutilization of quinoa, a resilient and nutritionally rich crop, by integrating advanced plant breeding and biotechnological tools. We explored alternative plant screening methods, employing root restriction for efficient phenotype analysis. A genome-wide association study (GWAS) unveiled genetic markers associated with key agronomic traits. Moreover, biotechnological approaches, including Agrobacterium-mediated transient transformation and targeted mutagenesis, were explored to facilitate genetic studies and accelerate crop improvement. These findings contribute to a deeper understanding of quinoa's genetic diversity and offer practical solutions for efficient screening and transformation, ultimately advancing the development of improved quinoa varieties to meet global demand.