Identification, expression analysis of quinoa betalain biosynthesis genes and their role in seed germination and cold stress

Betalains provide <i>Chenopodium quinoa</i> bright color, and the key enzyme genes for betalain biosynthesis include <i>CYP76AD</i>, <i>DODA</i>, and <i>GTs</i>. In this study, 59 <i>CqCYP76AD</i>, <i>CqDODA</i> and <i>CqGTs</i> genes in quinoa were identified and characterized by gene structural characteristics, phylogenetic relationships and gene expression patterns. The <i>CqCYP76AD</i> genes were divided into ɑ, β and γ types, <i>CqDODA</i> into ɑ and β types, and <i>CqGTs</i> into <i>CqcDOPA5GT</i>, <i>CqB5GT</i> and <i>CqB6GT</i> types according to phylogenetic relationships. The analysis of co-linearity identified eight pairs of duplicated genes which were subjected to purifying selection during evolution. <i>CqCYP76AD</i> and <i>CqDODA</i>, as well as <i>CqcDOPA5GT</i> and <i>CqB5GT</i> may have been evolutionarily linked in genetic inheritance, based on gene location and gene structure study. The tissue expression specificity of <i>CqCYP76AD</i>, <i>CqDODA</i>, and <i>CqGTs</i> genes in response to seed germination and cold stress was studied by RNA-Seq data. The genes <i>CqCYP76AD</i>, <i>CqDODA</i>, and <i>CqGTs</i> were involved in betalain biosynthesis and cold stress. <i>CqCYP76AD</i>, <i>CqDODA</i>, <i>CqcDOPA5GT</i> and <i>CqB5GT</i> gene sequences were consistent in the eight quinoa samples and showed significant variations in expression. In contrast, the inconsistency between changes in gene expression and betalain accumulation indicates that other factors may influence betalain biosynthesis in quinoa. This study offers the theoretical basis for the roles of the <i>CqCYP76AD</i>, <i>CqDODA</i>, and <i>CqGTs</i> genes in betalain biosynthesis and cold stress in quinoa, as well as a guide for the full utilization of betalains in quinoa plants.