Investigating the bHLH transcription factor TSARL1 as marker and regulator of saponin biosynthesis in Chenopodium quinoa.

Background: Quinoa (Chenopodium quinoa) is valued for its nutritional benefits and resilience to abiotic stresses. However, its commercial use is limited by bitter-tasting saponins on the seeds, necessitating resource-intensive removal processes.

Results: This study demonstrates a single nucleotide polymorphism (SNP), G2078C, in the Triterpene Saponin Biosynthesis Activating Regulator Like 1 (TSARL1) gene, which encodes a basic helix-loop-helix (bHLH) transcription factor, as significantly associated with the non-bitter phenotype in quinoa. We have developed a PCR assay to demonstrate the pivotal role of this SNP in distinguishing non-bitter from bitter quinoa varieties, thereby providing a practical tool for breeding and quality control. Our findings confirm the SNP's critical function in downregulating the saponin biosynthesis pathway, through quantitative PCR analyses of TSARL1, TSARL2, BAS1, CYP716A78 and CYP716A79. Furthermore, protein modelling of TSARL1 validates its responsibility for the bitter phenotype. Investigating early plant development revealed delayed seedling emergence of bitter quinoa and phylogenetic analysis confirmed the bitter allele as the ancestral trait of quinoa.

Conclusion: Demonstrating a strong correlation between the non-bitter phenotype and the G2078C SNP, our study not only validates the SNP's significance but also introduces an efficient method for its detection. This advancement promises to streamline the breeding of non-bitter quinoa varieties, enhancing the crop's palatability and reducing the need for postharvest processing. Our approach offers significant implications for the agricultural production and nutritional exploitation of quinoa, aligning with efforts to meet global food security and nutritional needs. © 2025 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.