Transcriptomic and Proteomic Response to Grain Filling Reveal Potential Grain Size Regulation Mechanisms in Quinoa (<scp><i>Chenopodium quinoa</i></scp> Willd)

ABSTRACT Grain size is an important factor affecting quinoa yield, and studying the molecular mechanism of quinoa grain size formation is of great significance for cultivar selection. In this study, we analysed phenotypic traits, conducted RNA sequencing and proteomic detection during grain filling in different developmental stages. As filling progressed, particularly during the middle to late stages, the fresh and dry weights of large‐grained quinoa were 17.13%–32.57% higher than those of small‐grained quinoa. Combined transcriptomic and proteomic analyses were performed to identify several transcription factors (TFs) during grain maturation, including B3 , zf‐Dof , bZIP_1 , bZIP_2 , AP2 and WRKY . Of these, 42 TFs like AP2 , bZIP and WD40 were specific to large‐grained quinoa, whereas 24, including B3 , were specific to small‐grained quinoa. Subsequently, the core module identified several core genes, such as cytochrome P450 , phytohormone‐related genes and glycosyl hydrolase family‐like genes. The construction of the core network of protein interactions further provided us with potential candidate genes. The data obtained in this study will enhance our understanding of the network of genes regulating quinoa grain size and provide valuable genetic resources for future elite breeding for high yield.