Heat stress negatively affects betalain biosynthesis in Amaranthus tricolor through down-regulation of CYP76AD1 and 5GT

Orphan crops are considered essential climatic-resilient genetic resources due to their native adaptability to various ecological environments. Amaranthus tricolor is one of a few common vegetables widely cultivated in tropical and subtropical regions. Strong vigor, abiotic-stress adaptability, and nutrition richness make it an ideal vegetable to provide food and nutrient security for smallholders. However, the breeding efforts depend on the field yield trials because little genomic information or genetic resources can be accessed. To fill this gap, we first used the Illumina and Pacbio sequencing systems to assemble a novel reference genome of A. tricolor using a Japanese variety Bayam. Together with a core collection developed in our previous study, we investigated the genetic mechanism of betalain biosynthesis under optimal and heat-stress conditions. Betalain is an antioxidant phytonutrient commonly appearing in beets and amaranths. As a result, ATR1.0CH03_5131103 which associate with ATR1.0ch03g000565 was identified in the optimal condition. Meanwhile, according to the transcriptomic profiles in this study, ATR1.0ch03g000565 also show significantly differential expressions under control and heat stress conditions, suggesting this candidate gene regulates the optimal performance of CYP76AD1. Meanwhile, among the homologous genes involving in the betalain biosynthesis, CYP76AD1 and 5GT were down-regulated under heat stress conditions; cDOPA was up-regulated. This result suggested heat stress reduces betacyanin biosynthesis through the downregulation of CYP76AD1 and 5GT; despite that the upregulation of cDOPA cannot rescue the decrease of betalain. More molecular experiments are required to address the regulation of these three enzymes.